Liste des publications issues de travaux ayant bénéficié des ressources du mésocentre
2023
Emily Bourne; Philippe Leleux; Katharina Kormann; Carola Kruse; Virginie Grandgirard; Yaman Guclu; Martin J. Kuhn; Ulrich Rude; Eric Sonnendrucker; Edoardo Zoni
Solver comparison for Poisson-like equations on tokamak geometries Article de journal
Dans: JOURNAL OF COMPUTATIONAL PHYSICS, vol. 488, 2023, ISSN: 0021-9991.
@article{WOS:001014762300001,
title = {Solver comparison for Poisson-like equations on tokamak geometries},
author = {Emily Bourne and Philippe Leleux and Katharina Kormann and Carola Kruse and Virginie Grandgirard and Yaman Guclu and Martin J. Kuhn and Ulrich Rude and Eric Sonnendrucker and Edoardo Zoni},
doi = {10.1016/j.jcp.2023.112249},
issn = {0021-9991},
year = {2023},
date = {2023-09-01},
journal = {JOURNAL OF COMPUTATIONAL PHYSICS},
volume = {488},
publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
abstract = {The solution of Poisson-like equations defined on a complex geometry is
required for gyrokinetic simulations, which are important for the
modelling of plasma turbulence in nuclear fusion devices such as the
ITER tokamak. In this paper, we compare three existing solvers finely
tuned to solve this problem, in terms of the accuracy of the solution,
and their computational efficiency. We also consider practical
implementation aspects, including the parallel efficiency of the code,
potentially enabling an integration of the solvers in a state-of-the-art
first-principle gyrokinetic simulation framework. The first, the Spline
FEM solver, uses C1 polar splines to construct a finite elements method
which solves the equation on curvilinear coordinates. The resulting
linear system is solved using a conjugate gradient method. The second,
the GMGPolar solver, uses a symmetric finite difference method to
discretise the differential equation. The resulting linear system is
solved using a tailored geometric multigrid scheme, with a combination
of zebra circle and radial line smoothers, together with an implicit
extrapolation scheme. The third, the Embedded Boundary solver, uses a
finite volumes method on Cartesian coordinates with an embedded boundary
scheme. The resulting linear system is solved using a multigrid scheme.
The Spline FEM solver is shown to be the most accurate. The GMGPolar
solver is shown to use the least memory. The Embedded Boundary solver is
shown to be the fastest in most cases. All three solvers are shown to be
capable of solving the equation on a realistic non-analytical geometry.
The Embedded Boundary solver is additionally used to attempt to solve an
X-point geometry.(C) 2023 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
required for gyrokinetic simulations, which are important for the
modelling of plasma turbulence in nuclear fusion devices such as the
ITER tokamak. In this paper, we compare three existing solvers finely
tuned to solve this problem, in terms of the accuracy of the solution,
and their computational efficiency. We also consider practical
implementation aspects, including the parallel efficiency of the code,
potentially enabling an integration of the solvers in a state-of-the-art
first-principle gyrokinetic simulation framework. The first, the Spline
FEM solver, uses C1 polar splines to construct a finite elements method
which solves the equation on curvilinear coordinates. The resulting
linear system is solved using a conjugate gradient method. The second,
the GMGPolar solver, uses a symmetric finite difference method to
discretise the differential equation. The resulting linear system is
solved using a tailored geometric multigrid scheme, with a combination
of zebra circle and radial line smoothers, together with an implicit
extrapolation scheme. The third, the Embedded Boundary solver, uses a
finite volumes method on Cartesian coordinates with an embedded boundary
scheme. The resulting linear system is solved using a multigrid scheme.
The Spline FEM solver is shown to be the most accurate. The GMGPolar
solver is shown to use the least memory. The Embedded Boundary solver is
shown to be the fastest in most cases. All three solvers are shown to be
capable of solving the equation on a realistic non-analytical geometry.
The Embedded Boundary solver is additionally used to attempt to solve an
X-point geometry.(C) 2023 Elsevier Inc. All rights reserved.
Emily Bourne; Yann Munschy; Virginie Grandgirard; Michel Mehrenberger; Philippe Ghendrih
Non-uniform splines for semi-Lagrangian kinetic simulations of the plasma sheath Article de journal
Dans: JOURNAL OF COMPUTATIONAL PHYSICS, vol. 488, 2023, ISSN: 0021-9991.
@article{WOS:001013577700001,
title = {Non-uniform splines for semi-Lagrangian kinetic simulations of the
plasma sheath},
author = {Emily Bourne and Yann Munschy and Virginie Grandgirard and Michel Mehrenberger and Philippe Ghendrih},
doi = {10.1016/j.jcp.2023.112229},
issn = {0021-9991},
year = {2023},
date = {2023-09-01},
journal = {JOURNAL OF COMPUTATIONAL PHYSICS},
volume = {488},
abstract = {Numerical methods based on non-uniform splines of varying degrees are
used to run kinetic semi-Lagrangian simulations of the plasma sheath.
The sheath describes a region of plasma in contact with a wall, acting
as a heat, momentum, and particle bath. The latter regulates the current
loss and consequently the electric field. At micro scale it then
influences the development of plasma turbulence and at a larger scale
plasma rotation. However this region is particularly difficult to
simulate, due to its kinetic nature and the presence of steep gradients
requiring fine numerical resolution. In this work, a new well
-conditioned method for determining the coefficients for Schoenberg's
``best'' quadrature is presented, providing improved precision
compared to a naive approach based on b-spline derivatives (4 extra
significant figures of precision are obtained for coefficients of the
fifth order scheme). The construction of a simulation grid from Greville
abcissae of judiciously chosen non-uniform knots is shown to reduce the
memory requirements by 89% for the simulation presented. Cubic splines
are found to provide a good compromise between fast convergence and
controlled oscillations preserving positivity. Despite the reduction in
performance associated with using non-uniform spline schemes, effective
parallelisation through the use of GPUs leads to non-uniform simulations
running 5.5 times faster than uniform simulations providing equivalent
results. & COPY; 2023 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
used to run kinetic semi-Lagrangian simulations of the plasma sheath.
The sheath describes a region of plasma in contact with a wall, acting
as a heat, momentum, and particle bath. The latter regulates the current
loss and consequently the electric field. At micro scale it then
influences the development of plasma turbulence and at a larger scale
plasma rotation. However this region is particularly difficult to
simulate, due to its kinetic nature and the presence of steep gradients
requiring fine numerical resolution. In this work, a new well
-conditioned method for determining the coefficients for Schoenberg's
``best'' quadrature is presented, providing improved precision
compared to a naive approach based on b-spline derivatives (4 extra
significant figures of precision are obtained for coefficients of the
fifth order scheme). The construction of a simulation grid from Greville
abcissae of judiciously chosen non-uniform knots is shown to reduce the
memory requirements by 89% for the simulation presented. Cubic splines
are found to provide a good compromise between fast convergence and
controlled oscillations preserving positivity. Despite the reduction in
performance associated with using non-uniform spline schemes, effective
parallelisation through the use of GPUs leads to non-uniform simulations
running 5.5 times faster than uniform simulations providing equivalent
results. & COPY; 2023 Elsevier Inc. All rights reserved.
Song Zhao; Karthik Bhairapurada; Muhammad Tayyab; Renaud Mercier; Pierre Boivin
Lattice-Boltzmann modeling of the quiet and unstable PRECCINSTA burner modes Article de journal
Dans: COMPUTERS & FLUIDS, vol. 260, 2023, ISSN: 0045-7930.
@article{WOS:000993853100001,
title = {Lattice-Boltzmann modeling of the quiet and unstable PRECCINSTA burner
modes},
author = {Song Zhao and Karthik Bhairapurada and Muhammad Tayyab and Renaud Mercier and Pierre Boivin},
doi = {10.1016/j.compfluid.2023.105898},
issn = {0045-7930},
year = {2023},
date = {2023-06-01},
journal = {COMPUTERS & FLUIDS},
volume = {260},
abstract = {Recent studies have shown that Lattice-Boltzmann methods are indeed very
promising in the field of reactive flows. More work is required,
however, to demonstrate its ability to tackle complex reacting cases, as
no study to the authors' knowledge - involves simultaneously high
Reynolds flows (for which the collision kernel needs specific care),
complex geometries (for which models are required at the wall
boundaries), and non-uniform grids (where non-conform meshes need to be
addressed).
The present study intends to fill that gap, by investigating the
well-known PRECCINSTA burner, including (i) characteristic boundary
conditions, (ii) classical turbulent combustion modeling, (iii)
multi-level grid refinements. Combining these elements, numerical
simulations of the PRECCINSTA burner are carried out, both for the quiet (phi = 0.83) and unstable regimes (phi = 0.7). In both regimes, results
are consistent with those obtained with classical (Navier-Stokes)
solvers, but at a much lower cost. In particular, it is the first time
that successful prediction of thermoacoustic instabilities in a complex
burner is shown in the framework of Lattice-Boltzmann methods.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
promising in the field of reactive flows. More work is required,
however, to demonstrate its ability to tackle complex reacting cases, as
no study to the authors' knowledge - involves simultaneously high
Reynolds flows (for which the collision kernel needs specific care),
complex geometries (for which models are required at the wall
boundaries), and non-uniform grids (where non-conform meshes need to be
addressed).
The present study intends to fill that gap, by investigating the
well-known PRECCINSTA burner, including (i) characteristic boundary
conditions, (ii) classical turbulent combustion modeling, (iii)
multi-level grid refinements. Combining these elements, numerical
simulations of the PRECCINSTA burner are carried out, both for the quiet (phi = 0.83) and unstable regimes (phi = 0.7). In both regimes, results
are consistent with those obtained with classical (Navier-Stokes)
solvers, but at a much lower cost. In particular, it is the first time
that successful prediction of thermoacoustic instabilities in a complex
burner is shown in the framework of Lattice-Boltzmann methods.
Shang-Gui Cai; Jerome Jacob; Pierre Sagaut
Immersed boundary based near-wall modeling for large eddy simulation of turbulent wall-bounded flow Article de journal
Dans: COMPUTERS & FLUIDS, vol. 259, 2023, ISSN: 0045-7930.
@article{WOS:000987247600001,
title = {Immersed boundary based near-wall modeling for large eddy simulation of
turbulent wall-bounded flow},
author = {Shang-Gui Cai and Jerome Jacob and Pierre Sagaut},
doi = {10.1016/j.compfluid.2023.105893},
issn = {0045-7930},
year = {2023},
date = {2023-06-01},
journal = {COMPUTERS & FLUIDS},
volume = {259},
abstract = {This paper describes the coupling of the immersed boundary method and
the near-wall modeling of large eddy simulation for high Reynolds number
turbulent flows over complex geometries on Cartesian grids. To overcome
the spurious oscillation problem arising from the imposition of boundary
conditions on the stair-case off-wall boundaries, several key
ingredients have been employed, such as interpolating the friction
velocity instead of the flow velocity from near-wall fluid interior
points, evaluating the gradients by the weighted least square method and
correcting the wall-normal gradient of the tangential velocity with the
law of the wall at the off-wall boundaries. Furthermore, a hybrid
RANS-LES approach has been applied to the near-wall eddy viscosity,
either through an empirical blending function or the Reynolds stress
balance constraint. We systematically discuss the effects of the hybrid
eddy viscosity in a turbulent channel flow and a high lift three
-element airfoil. Enforcing the Reynolds stress balance constraint turns
out to be very robust in the considered cases. For the high lift
three-element airfoil flow, the overall wall pressure and skin friction
are predicted reasonably well and smoothly. The flow details are in a
good agreement with the experimental data as well.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
the near-wall modeling of large eddy simulation for high Reynolds number
turbulent flows over complex geometries on Cartesian grids. To overcome
the spurious oscillation problem arising from the imposition of boundary
conditions on the stair-case off-wall boundaries, several key
ingredients have been employed, such as interpolating the friction
velocity instead of the flow velocity from near-wall fluid interior
points, evaluating the gradients by the weighted least square method and
correcting the wall-normal gradient of the tangential velocity with the
law of the wall at the off-wall boundaries. Furthermore, a hybrid
RANS-LES approach has been applied to the near-wall eddy viscosity,
either through an empirical blending function or the Reynolds stress
balance constraint. We systematically discuss the effects of the hybrid
eddy viscosity in a turbulent channel flow and a high lift three
-element airfoil. Enforcing the Reynolds stress balance constraint turns
out to be very robust in the considered cases. For the high lift
three-element airfoil flow, the overall wall pressure and skin friction
are predicted reasonably well and smoothly. The flow details are in a
good agreement with the experimental data as well.
A. Dufaure; C. Eyraud; L. - I Sorsa; Y. O. Yusuf; S. Pursiainen; J. -M Geffrin
Imaging of the internal structure of an asteroid analogue from quasi-monostatic microwave measurement data I. The frequency domain approach Article de journal
Dans: ASTRONOMY & ASTROPHYSICS, vol. 674, 2023, ISSN: 0004-6361.
@article{WOS:001000513500005,
title = {Imaging of the internal structure of an asteroid analogue from
quasi-monostatic microwave measurement data I. The frequency domain
approach},
author = {A. Dufaure and C. Eyraud and L. - I Sorsa and Y. O. Yusuf and S. Pursiainen and J. -M Geffrin},
doi = {10.1051/0004-6361/202244777},
issn = {0004-6361},
year = {2023},
date = {2023-06-01},
journal = {ASTRONOMY & ASTROPHYSICS},
volume = {674},
abstract = {Context. The internal structure of small Solar System bodies (SSSBs) is
still poorly understood, although it can provide important information
about the formation process of asteroids and comets. Space radars can
provide direct observations of this structure.Aims. In this study, we
investigate the possibility to infer the internal structure with a
simple and fast inversion procedure applied to radar measurements. We
consider a quasi-monostatic configuration with multiple measurements
over a wide frequency band, which is the most common configuration for
space radars. This is the first part (Paper I) of a joint study
considering methods to analyse and invert quasi-monostatic microwave
measurements of an asteroid analogue. This paper focuses on the
frequency domain, while a separate paper focuses on time-domain
methods.Methods. We carried out an experiment in the laboratory
equivalent to the probing of an asteroid using the microwave analogy
(multiplying the wavelength and the target dimension by the same
factor). Two analogues based on the shape of the asteroid 25143 Itokawa
were constructed with different interiors. The electromagnetic
interaction with these analogues was measured in an anechoic chamber
using a multi-frequency radar and a quasi-monostatic configuration. The
electric field was measured on 2372 angular positions (corresponding to
a sampling offering complete information). We then inverted these data
with two classical imaging procedures, allowing us to reach the
structural information of the analogues interior. We also investigated
reducing the number of radar measurements used in the imaging
procedures, that is both the number of transmitter-receiver pairs and
the number of frequencies.Results. The results show that the 3D map of
the analogues can be reconstructed without the need for a reference
target. Internal structural differences are distinguishable between the
analogues. This imaging can be achieved even with a reduced number of
measurements. With only 35 well-selected frequencies over 321 and 1257
transmitter-receiver pairs, the reconstructions are similar to those
obtained with the entire frequency band.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
still poorly understood, although it can provide important information
about the formation process of asteroids and comets. Space radars can
provide direct observations of this structure.Aims. In this study, we
investigate the possibility to infer the internal structure with a
simple and fast inversion procedure applied to radar measurements. We
consider a quasi-monostatic configuration with multiple measurements
over a wide frequency band, which is the most common configuration for
space radars. This is the first part (Paper I) of a joint study
considering methods to analyse and invert quasi-monostatic microwave
measurements of an asteroid analogue. This paper focuses on the
frequency domain, while a separate paper focuses on time-domain
methods.Methods. We carried out an experiment in the laboratory
equivalent to the probing of an asteroid using the microwave analogy
(multiplying the wavelength and the target dimension by the same
factor). Two analogues based on the shape of the asteroid 25143 Itokawa
were constructed with different interiors. The electromagnetic
interaction with these analogues was measured in an anechoic chamber
using a multi-frequency radar and a quasi-monostatic configuration. The
electric field was measured on 2372 angular positions (corresponding to
a sampling offering complete information). We then inverted these data
with two classical imaging procedures, allowing us to reach the
structural information of the analogues interior. We also investigated
reducing the number of radar measurements used in the imaging
procedures, that is both the number of transmitter-receiver pairs and
the number of frequencies.Results. The results show that the 3D map of
the analogues can be reconstructed without the need for a reference
target. Internal structural differences are distinguishable between the
analogues. This imaging can be achieved even with a reduced number of
measurements. With only 35 well-selected frequencies over 321 and 1257
transmitter-receiver pairs, the reconstructions are similar to those
obtained with the entire frequency band.
Liisa-Ida Sorsa; Yusuf Oluwatoki Yusuf; Astrid Dufaure; Jean-Michel Geffrin; Christelle Eyraud; Sampsa Pursiainen
Imaging of the internal structure of an asteroid analogue from quasi-monostatic microwave measurement data II. The time domain approach Article de journal
Dans: ASTRONOMY & ASTROPHYSICS, vol. 674, 2023, ISSN: 0004-6361.
@article{WOS:001000513500001,
title = {Imaging of the internal structure of an asteroid analogue from
quasi-monostatic microwave measurement data II. The time domain approach},
author = {Liisa-Ida Sorsa and Yusuf Oluwatoki Yusuf and Astrid Dufaure and Jean-Michel Geffrin and Christelle Eyraud and Sampsa Pursiainen},
doi = {10.1051/0004-6361/202244778},
issn = {0004-6361},
year = {2023},
date = {2023-06-01},
journal = {ASTRONOMY & ASTROPHYSICS},
volume = {674},
abstract = {Context. The internal structures of small solar system bodies (SSSBs)
are still poorly understood. In this paper, we find an experimental
tomographic reconstruction of coarse high-contrast details inside a
complex-structured target object using multipoint full-wave radar
data.Aims. Our aim is to advance the development of inversion techniques
to be used in potential planetary scientific radar investigations
targeting SSSBs, which have complex shapes and whose internal structure
is largely unknown. Finding out the structure is an important scientific
objective of Solar System research in order to understand its history
and evolution.Methods. This is the second part (Paper II) of a joint
study considering the methods to analyse and invert quasi-monostatic
microwave measurement data of an asteroid analogue. We focused on
incorporating advanced, full-wave, forward simulation in time domain
with experimental data obtained from multiple measurement points. In
particular, this study investigates multiple scattering and multipath
effect suppression (MES) to reduce artefacts in the reconstructions. MES
is necessary since the high-contrast and complex-shaped target and,
especially, its back wall in high curvature regions cause intense
reflections that deteriorate the reconstruction quality if not treated
correctly. We considered the following two approaches to obtain MES: (i)
geometrical optics-based pathlength thresholding and (ii) a peak
detection method to investigate whether a data-driven approach could be
used. At the inversion stage, we investigated marginalisation of random
effects due to modelling by splitting a larger point set into several
sparse sets of measurements.Results. Based on the results, MES is
crucial to localise a void inside the complex analogue target. A
reconstruction can be found when the maximum signal propagation time
approximately matches that of the first back-wall echo for each
measurement point. The marginalisation approach allows us to find a
reconstruction that is comparable in quality to the case of full data,
while reducing the computation effort per subsystem, which is
advantageous when inverting a large data set.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
are still poorly understood. In this paper, we find an experimental
tomographic reconstruction of coarse high-contrast details inside a
complex-structured target object using multipoint full-wave radar
data.Aims. Our aim is to advance the development of inversion techniques
to be used in potential planetary scientific radar investigations
targeting SSSBs, which have complex shapes and whose internal structure
is largely unknown. Finding out the structure is an important scientific
objective of Solar System research in order to understand its history
and evolution.Methods. This is the second part (Paper II) of a joint
study considering the methods to analyse and invert quasi-monostatic
microwave measurement data of an asteroid analogue. We focused on
incorporating advanced, full-wave, forward simulation in time domain
with experimental data obtained from multiple measurement points. In
particular, this study investigates multiple scattering and multipath
effect suppression (MES) to reduce artefacts in the reconstructions. MES
is necessary since the high-contrast and complex-shaped target and,
especially, its back wall in high curvature regions cause intense
reflections that deteriorate the reconstruction quality if not treated
correctly. We considered the following two approaches to obtain MES: (i)
geometrical optics-based pathlength thresholding and (ii) a peak
detection method to investigate whether a data-driven approach could be
used. At the inversion stage, we investigated marginalisation of random
effects due to modelling by splitting a larger point set into several
sparse sets of measurements.Results. Based on the results, MES is
crucial to localise a void inside the complex analogue target. A
reconstruction can be found when the maximum signal propagation time
approximately matches that of the first back-wall echo for each
measurement point. The marginalisation approach allows us to find a
reconstruction that is comparable in quality to the case of full data,
while reducing the computation effort per subsystem, which is
advantageous when inverting a large data set.
T. Jonckheere; J. Rech; B. Gremaud; T. Martin
Anyonic Statistics Revealed by the Hong-Ou-Mandel Dip for Fractional Excitations Article de journal
Dans: PHYSICAL REVIEW LETTERS, vol. 130, no. 18, 2023, ISSN: 0031-9007.
@article{WOS:000992568900005,
title = {Anyonic Statistics Revealed by the Hong-Ou-Mandel Dip for Fractional
Excitations},
author = {T. Jonckheere and J. Rech and B. Gremaud and T. Martin},
doi = {10.1103/PhysRevLett.130.186203},
issn = {0031-9007},
year = {2023},
date = {2023-05-01},
journal = {PHYSICAL REVIEW LETTERS},
volume = {130},
number = {18},
abstract = {The fractional quantum Hall effect (FQHE) is known to host anyons,
quasiparticles whose statistics is intermediate between bosonic and
fermionic. We show here that Hong-Ou-Mandel (HOM) interferences between
excitations created by narrow voltage pulses on the edge states of a
FQHE system at low temperature show a direct signature of anyonic
statistics. The width of the HOM dip is universally fixed by the thermal
time scale, independently of the intrinsic width of the excited
fractional wave packets. This universal width can be related to the
anyonic braiding of the incoming excitations with thermal fluctuations
created at the quantum point contact. We show that this effect could be
realistically observed with periodic trains of narrow voltage pulses
using current experimental techniques.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
quasiparticles whose statistics is intermediate between bosonic and
fermionic. We show here that Hong-Ou-Mandel (HOM) interferences between
excitations created by narrow voltage pulses on the edge states of a
FQHE system at low temperature show a direct signature of anyonic
statistics. The width of the HOM dip is universally fixed by the thermal
time scale, independently of the intrinsic width of the excited
fractional wave packets. This universal width can be related to the
anyonic braiding of the incoming excitations with thermal fluctuations
created at the quantum point contact. We show that this effect could be
realistically observed with periodic trains of narrow voltage pulses
using current experimental techniques.
Qing Li; Jieyi Chen; Pierre Faux; Miguel Eduardo Delgado; Betty Bonfante; Macarena Fuentes-Guajardo; Javier Mendoza-Revilla; J. Camilo Chacon-Duque; Malena Hurtado; Valeria Villegas; Vanessa Granja; Claudia Jaramillo; William Arias; Rodrigo Barquera; Paola Everardo-Martinez; Mirsha Sanchez-Quinto; Jorge Gomez-Valdes; Hugo Villamil-Ramirez; Caio C. Silva de Cerqueira; Tabita Huenemeier; Virginia Ramallo; Sijie Wu; Siyuan Du; Andrea Giardina; Soumya Subhra Paria; Mahfuzur Rahman Khokan; Rolando Gonzalez-Jose; Lavinia Schueler-Faccini; Maria-Catira Bortolini; Victor Acuna-Alonzo; Samuel Canizales-Quinteros; Carla Gallo; Giovanni Poletti; Winston Rojas; Francisco Rothhammer; Nicolas Navarro; Sijia Wang; Kaustubh Adhikari; Andres Ruiz-Linares
Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape Article de journal
Dans: COMMUNICATIONS BIOLOGY, vol. 6, no. 1, 2023.
@article{WOS:000992563300001,
title = {Automatic landmarking identifies new loci associated with face
morphology and implicates Neanderthal introgression in human nasal shape},
author = {Qing Li and Jieyi Chen and Pierre Faux and Miguel Eduardo Delgado and Betty Bonfante and Macarena Fuentes-Guajardo and Javier Mendoza-Revilla and J. Camilo Chacon-Duque and Malena Hurtado and Valeria Villegas and Vanessa Granja and Claudia Jaramillo and William Arias and Rodrigo Barquera and Paola Everardo-Martinez and Mirsha Sanchez-Quinto and Jorge Gomez-Valdes and Hugo Villamil-Ramirez and Caio C. Silva de Cerqueira and Tabita Huenemeier and Virginia Ramallo and Sijie Wu and Siyuan Du and Andrea Giardina and Soumya Subhra Paria and Mahfuzur Rahman Khokan and Rolando Gonzalez-Jose and Lavinia Schueler-Faccini and Maria-Catira Bortolini and Victor Acuna-Alonzo and Samuel Canizales-Quinteros and Carla Gallo and Giovanni Poletti and Winston Rojas and Francisco Rothhammer and Nicolas Navarro and Sijia Wang and Kaustubh Adhikari and Andres Ruiz-Linares},
doi = {10.1038/s42003-023-04838-7},
year = {2023},
date = {2023-05-01},
journal = {COMMUNICATIONS BIOLOGY},
volume = {6},
number = {1},
abstract = {A genome-wide association study and fully automatic landmarking approach
on frontal 2D face photographs of >6000 Latin Americans identifies novel
genomic regions influencing facial features and implicates Neanderthal
introgression in nasal shape.
We report a genome-wide association study of facial features in >6000
Latin Americans based on automatic landmarking of 2D portraits and
testing for association with inter-landmark distances. We detected
significant associations (P-value <5 x 10(-8)) at 42 genome regions,
nine of which have been previously reported. In follow-up analyses, 26
of the 33 novel regions replicate in East Asians, Europeans, or
Africans, and one mouse homologous region influences craniofacial
morphology in mice. The novel region in 1q32.3 shows introgression from
Neanderthals and we find that the introgressed tract increases nasal
height (consistent with the differentiation between Neanderthals and
modern humans). Novel regions include candidate genes and genome
regulatory elements previously implicated in craniofacial development,
and show preferential transcription in cranial neural crest cells. The
automated approach used here should simplify the collection of large
study samples from across the world, facilitating a cosmopolitan
characterization of the genetics of facial features.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
on frontal 2D face photographs of >6000 Latin Americans identifies novel
genomic regions influencing facial features and implicates Neanderthal
introgression in nasal shape.
We report a genome-wide association study of facial features in >6000
Latin Americans based on automatic landmarking of 2D portraits and
testing for association with inter-landmark distances. We detected
significant associations (P-value <5 x 10(-8)) at 42 genome regions,
nine of which have been previously reported. In follow-up analyses, 26
of the 33 novel regions replicate in East Asians, Europeans, or
Africans, and one mouse homologous region influences craniofacial
morphology in mice. The novel region in 1q32.3 shows introgression from
Neanderthals and we find that the introgressed tract increases nasal
height (consistent with the differentiation between Neanderthals and
modern humans). Novel regions include candidate genes and genome
regulatory elements previously implicated in craniofacial development,
and show preferential transcription in cranial neural crest cells. The
automated approach used here should simplify the collection of large
study samples from across the world, facilitating a cosmopolitan
characterization of the genetics of facial features.
Louise Terrien; Benjamin Favier; Edgar Knobloch
Suppression of Wall Modes in Rapidly Rotating Rayleigh-Be ` nard Convection by Narrow Horizontal Fins Article de journal
Dans: PHYSICAL REVIEW LETTERS, vol. 130, no. 17, 2023, ISSN: 0031-9007.
@article{WOS:000992461300003,
title = {Suppression of Wall Modes in Rapidly Rotating Rayleigh-Be ` nard
Convection by Narrow Horizontal Fins},
author = {Louise Terrien and Benjamin Favier and Edgar Knobloch},
doi = {10.1103/PhysRevLett.130.174002},
issn = {0031-9007},
year = {2023},
date = {2023-04-01},
journal = {PHYSICAL REVIEW LETTERS},
volume = {130},
number = {17},
publisher = {AMER PHYSICAL SOC},
address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
abstract = {The heat transport by rapidly rotating Rayleigh-Benard convection is of
fundamental importance to many geophysical flows. Laboratory
measurements are impeded by robust wall modes that develop along
vertical walls, significantly perturbing the heat flux. We show that
narrow horizontal fins along the vertical walls efficiently suppress
wall modes ensuring that their contribution to the global heat flux is
negligible compared with bulk convection in the geostrophic regime,
thereby paving the way for new experimental studies of geophysically
relevant regimes of rotating convection.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
fundamental importance to many geophysical flows. Laboratory
measurements are impeded by robust wall modes that develop along
vertical walls, significantly perturbing the heat flux. We show that
narrow horizontal fins along the vertical walls efficiently suppress
wall modes ensuring that their contribution to the global heat flux is
negligible compared with bulk convection in the geostrophic regime,
thereby paving the way for new experimental studies of geophysically
relevant regimes of rotating convection.
Michael Valente; Nils Collinet; Thien-Phong Vu Manh; Dimitri Popoff; Khalissa Rahmani; Karima Naciri; Gilles Bessou; Rejane Rua; Laurine Gil; Cyrille Mionnet; Pierre Milpied; Elena Tomasello; Marc Dalod
Novel mouse models based on intersectional genetics to identify and characterize plasmacytoid dendritic cells Article de journal
Dans: NATURE IMMUNOLOGY, vol. 24, no. 4, p. 714+, 2023, ISSN: 1529-2908.
@article{WOS:000950499100004,
title = {Novel mouse models based on intersectional genetics to identify and
characterize plasmacytoid dendritic cells},
author = {Michael Valente and Nils Collinet and Thien-Phong Vu Manh and Dimitri Popoff and Khalissa Rahmani and Karima Naciri and Gilles Bessou and Rejane Rua and Laurine Gil and Cyrille Mionnet and Pierre Milpied and Elena Tomasello and Marc Dalod},
doi = {10.1038/s41590-023-01454-9},
issn = {1529-2908},
year = {2023},
date = {2023-04-01},
journal = {NATURE IMMUNOLOGY},
volume = {24},
number = {4},
pages = {714+},
publisher = {NATURE PORTFOLIO},
address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
abstract = {Plasmacytoid dendritic cells (pDCs) are the main source of type I
interferon (IFN-I) during viral infections. Their other functions are
debated, due to a lack of tools to identify and target them in vivo
without affecting pDC-like cells and transitional DCs (tDCs), which
harbor overlapping phenotypes and transcriptomes but a higher efficacy
for T cell activation. In the present report, we present a reporter
mouse, pDC-Tom, designed through intersectional genetics based on unique
Siglech and Pacsin1 coexpression in pDCs. The pDC-Tom mice specifically
tagged pDCs and, on breeding with Zbtb46(GFP) mice, enabled
transcriptomic profiling of all splenic DC types, unraveling diverging
activation of pDC-like cells versus tDCs during a viral infection. The
pDC-Tom mice also revealed initially similar but later divergent
microanatomical relocation of splenic IFN+ versus IFN- pDCs during
infection. The mouse models and specific gene modules we report here
will be useful to delineate the physiological functions of pDCs versus
other DC types.
Dalod and colleagues utilize a combinatorial genetic reporter strategy
to uniquely mark plasmacytoid dendritic cells (pDCs) in mice. They
utilize these mice to identify bona fide pDCs and functionally
characterize before and during viral infection, in comparison to several
other DC types.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
interferon (IFN-I) during viral infections. Their other functions are
debated, due to a lack of tools to identify and target them in vivo
without affecting pDC-like cells and transitional DCs (tDCs), which
harbor overlapping phenotypes and transcriptomes but a higher efficacy
for T cell activation. In the present report, we present a reporter
mouse, pDC-Tom, designed through intersectional genetics based on unique
Siglech and Pacsin1 coexpression in pDCs. The pDC-Tom mice specifically
tagged pDCs and, on breeding with Zbtb46(GFP) mice, enabled
transcriptomic profiling of all splenic DC types, unraveling diverging
activation of pDC-like cells versus tDCs during a viral infection. The
pDC-Tom mice also revealed initially similar but later divergent
microanatomical relocation of splenic IFN+ versus IFN- pDCs during
infection. The mouse models and specific gene modules we report here
will be useful to delineate the physiological functions of pDCs versus
other DC types.
Dalod and colleagues utilize a combinatorial genetic reporter strategy
to uniquely mark plasmacytoid dendritic cells (pDCs) in mice. They
utilize these mice to identify bona fide pDCs and functionally
characterize before and during viral infection, in comparison to several
other DC types.
Mariana T. T. Casal; Josene M. M. Toldo; Mario Barbatti; Felix Plasser
Classification of doubly excited molecular electronic states Article de journal
Dans: CHEMICAL SCIENCE, vol. 14, no. 15, p. 4012-4026, 2023, ISSN: 2041-6520.
@article{WOS:000955149200001,
title = {Classification of doubly excited molecular electronic states},
author = {Mariana T. T. Casal and Josene M. M. Toldo and Mario Barbatti and Felix Plasser},
doi = {10.1039/d2sc06990c},
issn = {2041-6520},
year = {2023},
date = {2023-04-01},
journal = {CHEMICAL SCIENCE},
volume = {14},
number = {15},
pages = {4012-4026},
abstract = {Electronic states with partial or complete doubly excited character play
a crucial role in many areas, such as singlet fission and non-linear
optical spectroscopy. Although doubly excited states have been studied
in polyenes and related systems for many years, the assignment as singly
vs. doubly excited, even in the simplest case of butadiene, has sparked
controversies. So far, no well-defined framework for classifying doubly
excited states has been developed, and even more, there is not even a
well-accepted definition of doubly excited character as such. Here, we
present a solution: a physically motivated definition of doubly excited
character based on operator expectation values and density matrices,
which works independently of the underlying orbital representation,
avoiding ambiguities that have plagued earlier studies. Furthermore, we
propose a classification scheme to differentiate three cases: (i) two
single excitations occurring within two independent pairs of orbitals
leaving four open shells (D-OS), (ii) the promotion of both electrons to
the same orbital, producing a closed-shell determinant (D-CS), and (iii)
a mixture of singly and doubly excited configurations not aligning with
either one of the previous cases (D-mix). We highlight their differences
in underlying energy terms and explain their signatures in practical
computations. The three cases are illustrated through various high-level
computational methods using dimers for D-OS, polyenes for D-mix, and
cyclobutane and tetrazine for D-CS. The conversion between D-OS and D-CS
is investigated using a well-known photochemical reaction, the
photodimerization of ethylene. This work provides a deeper understanding
of doubly excited states and may guide more rigorous discussions toward
improving their computational description while also giving insight into
their fundamental photophysics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
a crucial role in many areas, such as singlet fission and non-linear
optical spectroscopy. Although doubly excited states have been studied
in polyenes and related systems for many years, the assignment as singly
vs. doubly excited, even in the simplest case of butadiene, has sparked
controversies. So far, no well-defined framework for classifying doubly
excited states has been developed, and even more, there is not even a
well-accepted definition of doubly excited character as such. Here, we
present a solution: a physically motivated definition of doubly excited
character based on operator expectation values and density matrices,
which works independently of the underlying orbital representation,
avoiding ambiguities that have plagued earlier studies. Furthermore, we
propose a classification scheme to differentiate three cases: (i) two
single excitations occurring within two independent pairs of orbitals
leaving four open shells (D-OS), (ii) the promotion of both electrons to
the same orbital, producing a closed-shell determinant (D-CS), and (iii)
a mixture of singly and doubly excited configurations not aligning with
either one of the previous cases (D-mix). We highlight their differences
in underlying energy terms and explain their signatures in practical
computations. The three cases are illustrated through various high-level
computational methods using dimers for D-OS, polyenes for D-mix, and
cyclobutane and tetrazine for D-CS. The conversion between D-OS and D-CS
is investigated using a well-known photochemical reaction, the
photodimerization of ethylene. This work provides a deeper understanding
of doubly excited states and may guide more rigorous discussions toward
improving their computational description while also giving insight into
their fundamental photophysics.
Aurore Loisy; Robin A. A. Heinonen
Deep reinforcement learning for the olfactory search POMDP: a quantitative benchmark Article de journal
Dans: EUROPEAN PHYSICAL JOURNAL E, vol. 46, no. 3, 2023, ISSN: 1292-8941.
@article{WOS:000956387200002,
title = {Deep reinforcement learning for the olfactory search POMDP: a
quantitative benchmark},
author = {Aurore Loisy and Robin A. A. Heinonen},
doi = {10.1140/epje/s10189-023-00277-8},
issn = {1292-8941},
year = {2023},
date = {2023-03-01},
journal = {EUROPEAN PHYSICAL JOURNAL E},
volume = {46},
number = {3},
abstract = {The olfactory search POMDP (partially observable Markov decision
process) is a sequential decision-making problem designed to mimic the
task faced by insects searching for a source of odor in turbulence, and
its solutions have applications to sniffer robots. As exact solutions
are out of reach, the challenge consists in finding the best possible
approximate solutions while keeping the computational cost reasonable.
We provide a quantitative benchmarking of a solver based on deep
reinforcement learning against traditional POMDP approximate solvers. We
show that deep reinforcement learning is a competitive alternative to
standard methods, in particular to generate lightweight policies
suitable for robots.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
process) is a sequential decision-making problem designed to mimic the
task faced by insects searching for a source of odor in turbulence, and
its solutions have applications to sniffer robots. As exact solutions
are out of reach, the challenge consists in finding the best possible
approximate solutions while keeping the computational cost reasonable.
We provide a quantitative benchmarking of a solver based on deep
reinforcement learning against traditional POMDP approximate solvers. We
show that deep reinforcement learning is a competitive alternative to
standard methods, in particular to generate lightweight policies
suitable for robots.
Zeyd Benseghier; Li-Hua Luu; Pablo Cuellar; Stephane Bonelli; Pierre Philippe
On the erosion of cohesive granular soils by a submerged jet: a numerical approach Article de journal
Dans: GRANULAR MATTER, vol. 25, no. 1, 2023, ISSN: 1434-5021.
@article{WOS:000896588700001,
title = {On the erosion of cohesive granular soils by a submerged jet: a
numerical approach},
author = {Zeyd Benseghier and Li-Hua Luu and Pablo Cuellar and Stephane Bonelli and Pierre Philippe},
doi = {10.1007/s10035-022-01289-5},
issn = {1434-5021},
year = {2023},
date = {2023-02-01},
journal = {GRANULAR MATTER},
volume = {25},
number = {1},
abstract = {This paper presents an erosion interpretation of cohesive granular
materials stressed by an impinging jet based on the results of a
micromechanical simulation model. The numerical techniques are briefly
described, relying on a two-dimensional Lattice Boltzmann Method coupled
with a Discrete Element Methods including a simple model of solid
intergranular cohesion. These are then used to perform a parametric
study of a planar jet in the laminar regime impinging the surface of
granular samples with different degrees of cohesive strength. The
results show the pertinence of using a generalized form of the Shields
criterion for the quantification of the erosion threshold, which is
valid for cohesionless samples, through empirical calibration, and also
for cohesive ones. Furthermore, the scouring kinetics are analysed here
from the perspective of a self-similar expansion of the eroded crater
leading to the identification of a characteristic erosion time and the
quantification of the classical erosion coefficient. However, the
presented results also challenge the postulate of a local erosion law
including erodibility parameters as intrinsic material properties. The
paper then reviews the main limitations of the simulation and current
interpretation models, and discusses the potential causes for the
observed discrepancies, questioning the pertinence of using
time-averaged macroscopic relations to correctly describe soil erosion.
The paper concludes addressing this question with a complementary study
of the presented simulations re-assessed at the particle-scale. The
resulting local critical shear stress of single grains reveals a very
wide dispersion of the data but nevertheless appears to confirm the
general macroscopic trend derived for the cohesionless samples, while
the introduction of cohesion implies a significant but systematic
quantitative deviation between the microscopic and macroscopic
estimates. Nevertheless, the micro data still shows consistently that
the critical shear stress does actually vary approximately in linear
proportion of the adhesive force.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
materials stressed by an impinging jet based on the results of a
micromechanical simulation model. The numerical techniques are briefly
described, relying on a two-dimensional Lattice Boltzmann Method coupled
with a Discrete Element Methods including a simple model of solid
intergranular cohesion. These are then used to perform a parametric
study of a planar jet in the laminar regime impinging the surface of
granular samples with different degrees of cohesive strength. The
results show the pertinence of using a generalized form of the Shields
criterion for the quantification of the erosion threshold, which is
valid for cohesionless samples, through empirical calibration, and also
for cohesive ones. Furthermore, the scouring kinetics are analysed here
from the perspective of a self-similar expansion of the eroded crater
leading to the identification of a characteristic erosion time and the
quantification of the classical erosion coefficient. However, the
presented results also challenge the postulate of a local erosion law
including erodibility parameters as intrinsic material properties. The
paper then reviews the main limitations of the simulation and current
interpretation models, and discusses the potential causes for the
observed discrepancies, questioning the pertinence of using
time-averaged macroscopic relations to correctly describe soil erosion.
The paper concludes addressing this question with a complementary study
of the presented simulations re-assessed at the particle-scale. The
resulting local critical shear stress of single grains reveals a very
wide dispersion of the data but nevertheless appears to confirm the
general macroscopic trend derived for the cohesionless samples, while
the introduction of cohesion implies a significant but systematic
quantitative deviation between the microscopic and macroscopic
estimates. Nevertheless, the micro data still shows consistently that
the critical shear stress does actually vary approximately in linear
proportion of the adhesive force.
Max Pinheiro Jr; Shuang Zhang; Pavlo O. O. Dral; Mario Barbatti
WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets Article de journal
Dans: SCIENTIFIC DATA, vol. 10, no. 1, 2023.
@article{WOS:000944690700001,
title = {WS22 database, Wigner Sampling and geometry interpolation for
configurationally diverse molecular datasets},
author = {Max Pinheiro Jr and Shuang Zhang and Pavlo O. O. Dral and Mario Barbatti},
doi = {10.1038/s41597-023-01998-3},
year = {2023},
date = {2023-02-01},
journal = {SCIENTIFIC DATA},
volume = {10},
number = {1},
abstract = {Multidimensional surfaces of quantum chemical properties, such as
potential energies and dipole moments, are common targets for machine
learning, requiring the development of robust and diverse databases
extensively exploring molecular configurational spaces. Here we composed
the WS22 database covering several quantum mechanical (QM) properties
(including potential energies, forces, dipole moments, polarizabilities,
HOMO, and LUMO energies) for ten flexible organic molecules of
increasing complexity and with up to 22 atoms. This database consists of
1.18 million equilibrium and non-equilibrium geometries carefully
sampled from Wigner distributions centered at different equilibrium
conformations (either at the ground or excited electronic states) and
further augmented with interpolated structures. The diversity of our
datasets is demonstrated by visualizing the geometries distribution with
dimensionality reduction as well as via comparison of statistical
features of the QM properties with those available in existing datasets.
Our sampling targets broader quantum mechanical distribution of the
configurational space than provided by commonly used sampling through
classical molecular dynamics, upping the challenge for machine learning
models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
potential energies and dipole moments, are common targets for machine
learning, requiring the development of robust and diverse databases
extensively exploring molecular configurational spaces. Here we composed
the WS22 database covering several quantum mechanical (QM) properties
(including potential energies, forces, dipole moments, polarizabilities,
HOMO, and LUMO energies) for ten flexible organic molecules of
increasing complexity and with up to 22 atoms. This database consists of
1.18 million equilibrium and non-equilibrium geometries carefully
sampled from Wigner distributions centered at different equilibrium
conformations (either at the ground or excited electronic states) and
further augmented with interpolated structures. The diversity of our
datasets is demonstrated by visualizing the geometries distribution with
dimensionality reduction as well as via comparison of statistical
features of the QM properties with those available in existing datasets.
Our sampling targets broader quantum mechanical distribution of the
configurational space than provided by commonly used sampling through
classical molecular dynamics, upping the challenge for machine learning
models.
Jinming Lyu; Paul G. Chen; Alexander Farutin; Marc Jaeger; Chaouqi Misbah; Marc Leonetti
Swirling of vesicles: Shapes and dynamics in Poiseuille flow as a model of RBC microcirculation Article de journal
Dans: PHYSICAL REVIEW FLUIDS, vol. 8, no. 2, 2023, ISSN: 2469-990X.
@article{WOS:000932523900003,
title = {Swirling of vesicles: Shapes and dynamics in Poiseuille flow as a model
of RBC microcirculation},
author = {Jinming Lyu and Paul G. Chen and Alexander Farutin and Marc Jaeger and Chaouqi Misbah and Marc Leonetti},
doi = {10.1103/PhysRevFluids.8.L021602},
issn = {2469-990X},
year = {2023},
date = {2023-02-01},
journal = {PHYSICAL REVIEW FLUIDS},
volume = {8},
number = {2},
abstract = {We report on a systematic numerical exploration of the vesicle dynamics
in a channel, which is a model of red blood cells in microcirculation.
We find a spontaneous transition, called swirling, from straight motion
with axisymmetric shape to a motion along a helix with a stationary
deformed shape that rolls on itself and spins around the flow direction.
We also report on a planar oscillatory motion of the mass center, called
three-dimensional snaking, for which the shape deforms periodically.
Both emerge from supercritical pitch-fork bifurcation with the same
threshold. The universality of these oscillatory dynamics emerges from
Hopf bifurcations with two order parameters. These two oscillatory
dy-namics are put in the context of vesicle shape and dynamics in the
parameter space of reduced volume v, capillary number, and confinement. Phase diagrams are established for v = 0.95},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
in a channel, which is a model of red blood cells in microcirculation.
We find a spontaneous transition, called swirling, from straight motion
with axisymmetric shape to a motion along a helix with a stationary
deformed shape that rolls on itself and spins around the flow direction.
We also report on a planar oscillatory motion of the mass center, called
three-dimensional snaking, for which the shape deforms periodically.
Both emerge from supercritical pitch-fork bifurcation with the same
threshold. The universality of these oscillatory dynamics emerges from
Hopf bifurcations with two order parameters. These two oscillatory
dy-namics are put in the context of vesicle shape and dynamics in the
parameter space of reduced volume v, capillary number, and confinement. Phase diagrams are established for v = 0.95
D. Lemasquerier; B. Favier; M. Le Bars
Zonal jets experiments in the gas giants' zonostrophic regime Article de journal
Dans: Icarus, vol. 390, p. 115292, 2023.
@article{Lemasquerier_2023,
title = {Zonal jets experiments in the gas giants' zonostrophic regime},
author = {D. Lemasquerier and B. Favier and M. Le Bars},
url = {https://doi.org/10.1016%2Fj.icarus.2022.115292},
doi = {10.1016/j.icarus.2022.115292},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Icarus},
volume = {390},
pages = {115292},
publisher = {Elsevier BV},
abstract = {Intense east-west winds called zonal jets are observed in the atmospheres of Jupiter and Saturn and extend in their deep interior. We present experimental results from a fully three-dimensional laboratory analog of deep gas giants zonal jets. We use a rapidly rotating deep cylindrical tank, filled with water, and forced by a small-scale hydraulic circulation at the bottom. A topographic β-effect is naturally present because of the curvature of the free surface. Instantaneous turbulent zonal jets spontaneously emerge from the small-scale forcing, equilibrate at large scale, and can contain up to 70% of the total kinetic energy of the flow once in a quasi-steady state. We show that the spectral properties of the experimental flows are consistent with the theoretical predictions in the zonostrophic turbulence regime, argued to be relevant to gas giants. This constitutes the first fully-experimental validation of the zonostrophic theory in a completely three-dimensional framework. Complementary, quasi-geostrophic (QG) simulations show that this result is not sensitive to the forcing scale. Next, we quantify the potential vorticity (PV) mixing. While PV staircasing should emerge in the asymptotic regime of the gas giants, only a moderate PV mixing occurs because of the strong forcing and dissipation, as confirmed by QG simulations at smaller Ekman number. We quantify the local PV mixing by measuring the equivalent of a Thorpe scale, and confirm that it can be used to estimate the upscale energy transfer rate of the flow, which otherwise needs to be estimated from a much more demanding spectral analysis. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Revaz Chachanidze; Kaili Xie; Jinming Lyu; Marc Jaeger; Marc Leonetti
Breakups of Chitosan microcapsules in extensional flow Article de journal
Dans: JOURNAL OF COLLOID AND INTERFACE SCIENCE, vol. 629, no. A, p. 445-454, 2023, ISSN: 0021-9797.
@article{WOS:000860284900009,
title = {Breakups of Chitosan microcapsules in extensional flow},
author = {Revaz Chachanidze and Kaili Xie and Jinming Lyu and Marc Jaeger and Marc Leonetti},
doi = {10.1016/j.jcis.2022.08.169},
issn = {0021-9797},
year = {2023},
date = {2023-01-01},
journal = {JOURNAL OF COLLOID AND INTERFACE SCIENCE},
volume = {629},
number = {A},
pages = {445-454},
abstract = {The controlled rupture of a core-shell capsule and the timely release of
encapsulated materials are essential steps of the efficient design of
such carriers. The mechanical and physico-chemical properties of their
shells (or membranes) mainly govern the evolution of such systems under
stress and notably the link between the dynamics of rupture and the
mechanical properties. This issue is addressed considering weakly
cohesive shells made by the interfacial complexation of Chitosan and
PFacid in a planar extensional flow. Three regimes are observed, thanks
to the two observational planes. Whatever the time of reaction in
membrane assembly, there is no rupture in deformation as long as the
hydrodynamic stress is below a critical value. At low times of
complexation (weak shear elastic modulus), the rupture is reminiscent of
the breakup of dro-plets: a dumbell or a waist. Fluorescent labelling of
the membrane shows that this process is governed by continuous thinning
of the membrane up to the destabilization. It is likely that the
membrane shows a tran-sition from a solid to liquid state. At longer
times of complexation, the rupture has a feature of solid-like breakup
(breakage) with a discontinuity of the membrane. The maximal internal
constraint determined numerically marks the initial location of breakup
as shown. The pattern becomes more complex as the elon-gation rate
increases with several points of rupture. A phase diagram in the space
parameters of the shear elastic modulus and the hydrodynamic stress is
established.(c) 2022 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
encapsulated materials are essential steps of the efficient design of
such carriers. The mechanical and physico-chemical properties of their
shells (or membranes) mainly govern the evolution of such systems under
stress and notably the link between the dynamics of rupture and the
mechanical properties. This issue is addressed considering weakly
cohesive shells made by the interfacial complexation of Chitosan and
PFacid in a planar extensional flow. Three regimes are observed, thanks
to the two observational planes. Whatever the time of reaction in
membrane assembly, there is no rupture in deformation as long as the
hydrodynamic stress is below a critical value. At low times of
complexation (weak shear elastic modulus), the rupture is reminiscent of
the breakup of dro-plets: a dumbell or a waist. Fluorescent labelling of
the membrane shows that this process is governed by continuous thinning
of the membrane up to the destabilization. It is likely that the
membrane shows a tran-sition from a solid to liquid state. At longer
times of complexation, the rupture has a feature of solid-like breakup
(breakage) with a discontinuity of the membrane. The maximal internal
constraint determined numerically marks the initial location of breakup
as shown. The pattern becomes more complex as the elon-gation rate
increases with several points of rupture. A phase diagram in the space
parameters of the shear elastic modulus and the hydrodynamic stress is
established.(c) 2022 Elsevier Inc. All rights reserved.
Ming Xia; Marie-Christine Record; Pascal Boulet
Investigation of PbSnTeSe High-Entropy Thermoelectric Alloy: A DFT Approach Article de journal
Dans: MATERIALS, vol. 16, no. 1, 2023.
@article{WOS:000909958900001,
title = {Investigation of PbSnTeSe High-Entropy Thermoelectric Alloy: A DFT
Approach},
author = {Ming Xia and Marie-Christine Record and Pascal Boulet},
doi = {10.3390/ma16010235},
year = {2023},
date = {2023-01-01},
journal = {MATERIALS},
volume = {16},
number = {1},
abstract = {Thermoelectric materials have attracted extensive attention because they
can directly convert waste heat into electric energy. As a brand-new
method of alloying, high-entropy alloys (HEAs) have attracted much
attention in the fields of materials science and engineering. Recent
researches have found that HEAs could be potentially good thermoelectric
(TE) materials. In this study, special quasi-random structures (SQS) of
PbSnTeSe high-entropy alloys consisting of 64 atoms have been generated.
The thermoelectric transport properties of the highest-entropy
PbSnTeSe-optimized structure were investigated by combining calculations
from first-principles density-functional theory and on-the-fly machine
learning with the semiclassical Boltzmann transport theory and
Green-Kubo theory. The results demonstrate that PbSnTeSe HEA has a very
low lattice thermal conductivity. The electrical conductivity, thermal
electronic conductivity and Seebeck coefficient have been evaluated for
both n-type and p-type doping. N-type PbSnTeSe exhibits better power factor (PF = S-2 sigma) than p-type PbSnTeSe because of larger
electrical conductivity for n-type doping. Despite high electrical
thermal conductivities, the calculated ZT are satisfactory. The maximum
ZT (about 1.1) is found at 500 K for n-type doping. These results
confirm that PbSnTeSe HEA is a promising thermoelectric material.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
can directly convert waste heat into electric energy. As a brand-new
method of alloying, high-entropy alloys (HEAs) have attracted much
attention in the fields of materials science and engineering. Recent
researches have found that HEAs could be potentially good thermoelectric
(TE) materials. In this study, special quasi-random structures (SQS) of
PbSnTeSe high-entropy alloys consisting of 64 atoms have been generated.
The thermoelectric transport properties of the highest-entropy
PbSnTeSe-optimized structure were investigated by combining calculations
from first-principles density-functional theory and on-the-fly machine
learning with the semiclassical Boltzmann transport theory and
Green-Kubo theory. The results demonstrate that PbSnTeSe HEA has a very
low lattice thermal conductivity. The electrical conductivity, thermal
electronic conductivity and Seebeck coefficient have been evaluated for
both n-type and p-type doping. N-type PbSnTeSe exhibits better power factor (PF = S-2 sigma) than p-type PbSnTeSe because of larger
electrical conductivity for n-type doping. Despite high electrical
thermal conductivities, the calculated ZT are satisfactory. The maximum
ZT (about 1.1) is found at 500 K for n-type doping. These results
confirm that PbSnTeSe HEA is a promising thermoelectric material.
Simone Bonfrate; Nicolas Ferre; Miquel Huix-Rotllant
An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators Article de journal
Dans: JOURNAL OF CHEMICAL PHYSICS, vol. 158, no. 2, 2023, ISSN: 0021-9606.
@article{WOS:000911523800003,
title = {An efficient electrostatic embedding QM/MM method using periodic
boundary conditions based on particle-mesh Ewald sums and electrostatic
potential fitted charge operators},
author = {Simone Bonfrate and Nicolas Ferre and Miquel Huix-Rotllant},
doi = {10.1063/5.0133646},
issn = {0021-9606},
year = {2023},
date = {2023-01-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {158},
number = {2},
abstract = {Hybrid quantum mechanics/molecular mechanics (QM/MM) models are
successful at describing the properties and reactivity of biological
macromolecules. Combining ab initio QM/MM methods and periodic boundary
conditions (PBC) is currently the optimal approach for modeling chemical
processes in an infinite environment, but frequently, these models are
too time-consuming for general applicability to biological systems in a
solution. Here, we define a simple and efficient electrostatic embedding
QM/MM model in PBC, combining the benefits of electrostatic potential
fitted atomic charges and particle-mesh Ewald sums, which can
efficiently treat systems of an arbitrary size at a reasonable
computational cost. To illustrate this, we apply our scheme to extract
the lowest singlet excitation energies from a model for Arabidopsis
thaliana cryptochrome 1 containing circa 93 000 atoms, accurately
reproducing the experimental absorption maximum.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
successful at describing the properties and reactivity of biological
macromolecules. Combining ab initio QM/MM methods and periodic boundary
conditions (PBC) is currently the optimal approach for modeling chemical
processes in an infinite environment, but frequently, these models are
too time-consuming for general applicability to biological systems in a
solution. Here, we define a simple and efficient electrostatic embedding
QM/MM model in PBC, combining the benefits of electrostatic potential
fitted atomic charges and particle-mesh Ewald sums, which can
efficiently treat systems of an arbitrary size at a reasonable
computational cost. To illustrate this, we apply our scheme to extract
the lowest singlet excitation energies from a model for Arabidopsis
thaliana cryptochrome 1 containing circa 93 000 atoms, accurately
reproducing the experimental absorption maximum.
Juste A. Goungounga; Nathalie Grafféo; Hadrien Charvat; Roch Giorgi
Correcting for heterogeneity and non-comparability bias in multicenter clinical trials with a rescaled random-effect excess hazard model Article de journal
Dans: Biometrical Journal, vol. 65, no. 4, p. 2100210, 2023.
@article{https://doi.org/10.1002/bimj.202100210,
title = {Correcting for heterogeneity and non-comparability bias in multicenter clinical trials with a rescaled random-effect excess hazard model},
author = {Juste A. Goungounga and Nathalie Grafféo and Hadrien Charvat and Roch Giorgi},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bimj.202100210},
doi = {https://doi.org/10.1002/bimj.202100210},
year = {2023},
date = {2023-01-01},
journal = {Biometrical Journal},
volume = {65},
number = {4},
pages = {2100210},
abstract = {Abstract In the presence of competing causes of event occurrence (e.g., death), the interest might not only be in the overall survival but also in the so-called net survival, that is, the hypothetical survival that would be observed if the disease under study were the only possible cause of death. Net survival estimation is commonly based on the excess hazard approach in which the hazard rate of individuals is assumed to be the sum of a disease-specific and expected hazard rate, supposed to be correctly approximated by the mortality rates obtained from general population life tables. However, this assumption might not be realistic if the study participants are not comparable with the general population. Also, the hierarchical structure of the data can induces a correlation between the outcomes of individuals coming from the same clusters (e.g., hospital, registry). We proposed an excess hazard model that corrects simultaneously for these two sources of bias, instead of dealing with them independently as before. We assessed the performance of this new model and compared it with three similar models, using extensive simulation study, as well as an application to breast cancer data from a multicenter clinical trial. The new model performed better than the others in terms of bias, root mean square error, and empirical coverage rate. The proposed approach might be useful to account simultaneously for the hierarchical structure of the data and the non-comparability bias in studies such as long-term multicenter clinical trials, when there is interest in the estimation of net survival.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sophie Benitez Stulz; Matthieu Gilson; Demian Battaglia
When local alterations meet collective oscillatory dynamics: On the causes of functional connectivity changes Article de journal
Dans: JOURNAL OF COMPUTATIONAL NEUROSCIENCE, vol. 51, no. 1, p. S24, 2023, ISSN: 0929-5313.
@article{WOS:001043129200034,
title = {When local alterations meet collective oscillatory dynamics: On the
causes of functional connectivity changes},
author = {Sophie Benitez Stulz and Matthieu Gilson and Demian Battaglia},
issn = {0929-5313},
year = {2023},
date = {2023-01-01},
journal = {JOURNAL OF COMPUTATIONAL NEUROSCIENCE},
volume = {51},
number = {1},
pages = {S24},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2022
Gregoire David; Nicolas Ferre; Boris Le Guennic
Consistent Evaluation of Magnetic Exchange Couplings in Multicenter Compounds in KS-DFT: The Recomposition Method Article de journal
Dans: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, ISSN: 1549-9618.
@article{WOS:000893459000001,
title = {Consistent Evaluation of Magnetic Exchange Couplings in Multicenter Compounds in KS-DFT: The Recomposition Method},
author = {Gregoire David and Nicolas Ferre and Boris Le Guennic},
doi = {10.1021/acs.jctc.2c01022},
issn = {1549-9618},
year = {2022},
date = {2022-12-31},
journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
abstract = {The use of broken-symmetry calculations in Kohn- Sham density functional
theory has offered an affordable route to study magnetic exchange
couplings in transition-metal-based compounds. However, computing this
property in compounds exhibiting several couplings is still challenging
and especially due to the difficulties to overcome the well-known
problem of spin contamination. Here, we present a new and general method
to compute magnetic exchange couplings in systems featuring several spin
sites. To provide a consistent spin decontamination of J values, our
strategy exploits the decomposition method of the magnetic exchange
coupling proposed by Coulaud et al. and generalizes our previous work on
diradical compounds where the overall magnetic exchange coupling is
defined as the sum of its three main and properly extracted physical
contributions (direct exchange, kinetic exchange, and spin
polarization). In this aim, the generalized extraction of all
contributions is presented to systems with multiple spin sites bearing
one unpaired electron. This is done by proposing a new paradigm to treat
the kinetic exchange contribution, which proceeds through
monorelaxations of the magnetic orbitals. This method, so-called the
recomposition method, is applied to a compound featuring three Cu(II)
ions with a linear arrangement and to a recently synthesized complex
containing a Cu4O4 cubane unit presenting an unusual magnetic behavior.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
theory has offered an affordable route to study magnetic exchange
couplings in transition-metal-based compounds. However, computing this
property in compounds exhibiting several couplings is still challenging
and especially due to the difficulties to overcome the well-known
problem of spin contamination. Here, we present a new and general method
to compute magnetic exchange couplings in systems featuring several spin
sites. To provide a consistent spin decontamination of J values, our
strategy exploits the decomposition method of the magnetic exchange
coupling proposed by Coulaud et al. and generalizes our previous work on
diradical compounds where the overall magnetic exchange coupling is
defined as the sum of its three main and properly extracted physical
contributions (direct exchange, kinetic exchange, and spin
polarization). In this aim, the generalized extraction of all
contributions is presented to systems with multiple spin sites bearing
one unpaired electron. This is done by proposing a new paradigm to treat
the kinetic exchange contribution, which proceeds through
monorelaxations of the magnetic orbitals. This method, so-called the
recomposition method, is applied to a compound featuring three Cu(II)
ions with a linear arrangement and to a recently synthesized complex
containing a Cu4O4 cubane unit presenting an unusual magnetic behavior.
Miquel Huix-Rotllant; Karno Schwinn; Vladimir Pomogaev; Maryam Farmani; Nicolas Ferre; Seunghoon Lee; Cheol Ho Choi
Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT Article de journal
Dans: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, ISSN: 1549-9618.
@article{WOS:000906466000001,
title = {Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT},
author = {Miquel Huix-Rotllant and Karno Schwinn and Vladimir Pomogaev and Maryam Farmani and Nicolas Ferre and Seunghoon Lee and Cheol Ho Choi},
doi = {10.1021/acs.jctc.2c01010},
issn = {1549-9618},
year = {2022},
date = {2022-12-31},
journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
abstract = {The photochemistry of nucleobases, important for their role as building
blocks of DNA, is largely affected by the electrostatic environment in
which they are soaked. For example, despite the numerous studies of
thymine in solution and DNA, there is still a debate on the
photochemical deactivation pathways after UV absorption. Many
theoretical models are oversimplified due to the lack of computationally
accurate and efficient electronic structure methodologies that capture
excited state electron correlation effects when nucleobases are embedded
in large electrostatic media. Here, we combine mixed-reference spin-flip
time-dependent density functional theory (MRSF-TDDFT) with electrostatic
embedding QM/MM using electrostatic potential fittingfitted (ESPF)
atomic charges, as a strategy to accurately and efficiently describe the
electronic structure of chromophores polarized by an electrostatic
medium. In particular, we develop analytic expressions for the energy
and gradient of MRSF/MM based on the ESPF coupling using atom-centered
grids and total charge conservation. We apply this methodology to the
study of solvation effects on thymine photochemistry in water and
thymine dimers in DNA. In the former, the combination of trajectory
surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with
MRSF/MM remarkably revealed accelerated deactivation decay pathways,
which is consistent with the experimental decay time of similar to 400
fs. The enhanced hopping rate can be explained by the preferential
stabilization of corresponding conical interactions due to their
increased dipole moments. Structurally, it is a consequence of
characteristic methyl puckered geometries near the conical intersection
region. For the thymine dimer in B-DNA, we found new photochemical
pathways through conical intersections that could explain the formation
of cyclobutadiene dimers and 6-4 photoproducts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
blocks of DNA, is largely affected by the electrostatic environment in
which they are soaked. For example, despite the numerous studies of
thymine in solution and DNA, there is still a debate on the
photochemical deactivation pathways after UV absorption. Many
theoretical models are oversimplified due to the lack of computationally
accurate and efficient electronic structure methodologies that capture
excited state electron correlation effects when nucleobases are embedded
in large electrostatic media. Here, we combine mixed-reference spin-flip
time-dependent density functional theory (MRSF-TDDFT) with electrostatic
embedding QM/MM using electrostatic potential fittingfitted (ESPF)
atomic charges, as a strategy to accurately and efficiently describe the
electronic structure of chromophores polarized by an electrostatic
medium. In particular, we develop analytic expressions for the energy
and gradient of MRSF/MM based on the ESPF coupling using atom-centered
grids and total charge conservation. We apply this methodology to the
study of solvation effects on thymine photochemistry in water and
thymine dimers in DNA. In the former, the combination of trajectory
surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with
MRSF/MM remarkably revealed accelerated deactivation decay pathways,
which is consistent with the experimental decay time of similar to 400
fs. The enhanced hopping rate can be explained by the preferential
stabilization of corresponding conical interactions due to their
increased dipole moments. Structurally, it is a consequence of
characteristic methyl puckered geometries near the conical intersection
region. For the thymine dimer in B-DNA, we found new photochemical
pathways through conical intersections that could explain the formation
of cyclobutadiene dimers and 6-4 photoproducts.
Adrian Kan; Benjamin Favier; Keith Julien; Edgar Knobloch
Spontaneous suppression of inverse energy cascade in instability-driven 2-D turbulence Article de journal
Dans: JOURNAL OF FLUID MECHANICS, vol. 952, 2022, ISSN: 0022-1120.
@article{WOS:000892955400001,
title = {Spontaneous suppression of inverse energy cascade in instability-driven
2-D turbulence},
author = {Adrian Kan and Benjamin Favier and Keith Julien and Edgar Knobloch},
doi = {10.1017/jfm.2022.935},
issn = {0022-1120},
year = {2022},
date = {2022-12-01},
journal = {JOURNAL OF FLUID MECHANICS},
volume = {952},
abstract = {Instabilities of fluid flows often generate turbulence. Using extensive
direct numerical simulations, we study two-dimensional turbulence driven
by a wavenumber-localised instability superposed on stochastic forcing,
in contrast to previous studies of state-independent forcing. As the
contribution of the instability forcing, measured by a parameter gamma ,
increases, the system undergoes two transitions. For gamma below a first
threshold, a regular large-scale vortex condensate forms. Above this
threshold, shielded vortices (SVs) emerge within the condensate. At a
second, larger value of gamma , the condensate breaks down, and a gas of
weakly interacting vortices with broken symmetry spontaneously emerges,
characterised by preponderance of vortices of one sign only and
suppressed inverse energy cascade. The latter transition is shown to
depend on the damping mechanism. The number density of SVs in the broken
symmetry state slowly increases via a random nucleation process.
Bistability is observed between the condensate and mixed SV-condensate
states. Our findings provide new evidence for a strong dependence of
two-dimensional turbulence phenomenology on the forcing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
direct numerical simulations, we study two-dimensional turbulence driven
by a wavenumber-localised instability superposed on stochastic forcing,
in contrast to previous studies of state-independent forcing. As the
contribution of the instability forcing, measured by a parameter gamma ,
increases, the system undergoes two transitions. For gamma below a first
threshold, a regular large-scale vortex condensate forms. Above this
threshold, shielded vortices (SVs) emerge within the condensate. At a
second, larger value of gamma , the condensate breaks down, and a gas of
weakly interacting vortices with broken symmetry spontaneously emerges,
characterised by preponderance of vortices of one sign only and
suppressed inverse energy cascade. The latter transition is shown to
depend on the damping mechanism. The number density of SVs in the broken
symmetry state slowly increases via a random nucleation process.
Bistability is observed between the condensate and mixed SV-condensate
states. Our findings provide new evidence for a strong dependence of
two-dimensional turbulence phenomenology on the forcing.
Daniele Villa; Nicolas Dubuit; Olivier Agullo; Alexandre Poye; Xavier Garbet; Andrei Smolyakov
Localized compressional self-heating in magnetic islands Article de journal
Dans: JOURNAL OF PLASMA PHYSICS, vol. 88, no. 6, 2022, ISSN: 0022-3778.
@article{WOS:000897848100001,
title = {Localized compressional self-heating in magnetic islands},
author = {Daniele Villa and Nicolas Dubuit and Olivier Agullo and Alexandre Poye and Xavier Garbet and Andrei Smolyakov},
doi = {10.1017/S0022377822001234},
issn = {0022-3778},
year = {2022},
date = {2022-12-01},
journal = {JOURNAL OF PLASMA PHYSICS},
volume = {88},
number = {6},
abstract = {A spontaneous heating process is found to arise in a system where a
magnetic island is present due to a linearly unstable tearing mode. The
parity, the relative phases and the structure of the fields determined
linearly by the tearing mode cause the compression of the plasma in the
direction parallel to the magnetic field to heat the plasma in the
vicinity of the separatrix in the nonlinear phase. Using a six-field
electromagnetic fluid model, the process is found to be present in both
two-dimensional single-helicity and three-dimensional multi-helicity
simulations with both symmetric and asymmetric magnetic equilibrium
profiles. A noteworthy feature of the model is that the higher-order
compression terms responsible for the heating process are retained in
the equations. The process is believed to be linked to experimental
observations of localized hot-spots on externally induced magnetic
islands.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
magnetic island is present due to a linearly unstable tearing mode. The
parity, the relative phases and the structure of the fields determined
linearly by the tearing mode cause the compression of the plasma in the
direction parallel to the magnetic field to heat the plasma in the
vicinity of the separatrix in the nonlinear phase. Using a six-field
electromagnetic fluid model, the process is found to be present in both
two-dimensional single-helicity and three-dimensional multi-helicity
simulations with both symmetric and asymmetric magnetic equilibrium
profiles. A noteworthy feature of the model is that the higher-order
compression terms responsible for the heating process are retained in
the equations. The process is believed to be linked to experimental
observations of localized hot-spots on externally induced magnetic
islands.
Miquel Huix-Rotllan Karno Schwinn Vladimir Pomogaev Maryam Farmani Nicolas Ferre Seunghoon Lee Cheol Ho Choi
Photochemistry of thymine in solution and DNA revealed by an electrostatic embedding QM/MM combined with mixed-reference spin-flip TDDFT Article de journal
Dans: Theoretical and Computational Chemistry, 2022.
@article{Huix-Rotllan2023,
title = {Photochemistry of thymine in solution and DNA revealed by an electrostatic embedding QM/MM combined with mixed-reference spin-flip TDDFT},
author = {Miquel Huix-Rotllan Karno Schwinn Vladimir Pomogaev Maryam Farmani Nicolas Ferre Seunghoon Lee Cheol Ho Choi },
url = {https://chemrxiv.org/engage/chemrxiv/article-details/63885f6debc1c741aed9bf03},
doi = {10.26434/chemrxiv-2022-g2jf3},
year = {2022},
date = {2022-12-01},
journal = {Theoretical and Computational Chemistry},
abstract = {The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density-functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fitting (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) non-adiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed the accelerated deactivation decay pathways, which is consistent with the experimental decay time of ~ 400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Liangzhao Huang; Paul Eymeoud; Philippe Maugis
Atomistic investigation on the impact of substitutional Al and Si atoms on the carbon kinetics in ferrite Article de journal
Dans: JOURNAL OF ALLOYS AND COMPOUNDS, vol. 921, 2022, ISSN: 0925-8388.
@article{WOS:000828406700001,
title = {Atomistic investigation on the impact of substitutional Al and Si atoms
on the carbon kinetics in ferrite},
author = {Liangzhao Huang and Paul Eymeoud and Philippe Maugis},
doi = {10.1016/j.jallcom.2022.166031},
issn = {0925-8388},
year = {2022},
date = {2022-11-01},
journal = {JOURNAL OF ALLOYS AND COMPOUNDS},
volume = {921},
abstract = {The pairwise interactions of substitutional solute atom X = Al, Si with
interstitial carbon at stable (octa-hedral) and saddle-point
(tetrahedral) positions in body-centered-cubic iron (alpha-Fe) are
computed using density-functional theory. These pairwise interactions
are used in atomistic kinetic Monte Carlo approach to simulate carbon
internal friction and tracer diffusion measurements in Fe-Si, Fe-Al, and
Fe-Al-Si ferritic alloys without any adjusting parameters. The good
agreement between the simulated and experimental Snoek relaxation
profiles validates the pair interaction model for kinetic simulations.
The predicted effect of Al on slowing down carbon diffusion is
consistent with previous studies. We highlight a super-cell size effect
on the Si-carbon interactions obtained from first principles. Using a
carefully tested database, it is shown that the introduction of Si into
ferrite only decreases the carbon diffusivity below a critical
tem-perature.(c) 2022 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
interstitial carbon at stable (octa-hedral) and saddle-point
(tetrahedral) positions in body-centered-cubic iron (alpha-Fe) are
computed using density-functional theory. These pairwise interactions
are used in atomistic kinetic Monte Carlo approach to simulate carbon
internal friction and tracer diffusion measurements in Fe-Si, Fe-Al, and
Fe-Al-Si ferritic alloys without any adjusting parameters. The good
agreement between the simulated and experimental Snoek relaxation
profiles validates the pair interaction model for kinetic simulations.
The predicted effect of Al on slowing down carbon diffusion is
consistent with previous studies. We highlight a super-cell size effect
on the Si-carbon interactions obtained from first principles. Using a
carefully tested database, it is shown that the introduction of Si into
ferrite only decreases the carbon diffusivity below a critical
tem-perature.(c) 2022 Elsevier B.V. All rights reserved.
Said Taileb; Alejandro Millan-Merino; Song Zhao; Pierre Boivin
Lattice-Boltzmann modeling of lifted hydrogen jet flames: A new model for hazardous ignition prediction Article de journal
Dans: COMBUSTION AND FLAME, vol. 245, 2022, ISSN: 0010-2180.
@article{WOS:000861453100010,
title = {Lattice-Boltzmann modeling of lifted hydrogen jet flames: A new model
for hazardous ignition prediction},
author = {Said Taileb and Alejandro Millan-Merino and Song Zhao and Pierre Boivin},
doi = {10.1016/j.combustflame.2022.112317},
issn = {0010-2180},
year = {2022},
date = {2022-11-01},
journal = {COMBUSTION AND FLAME},
volume = {245},
abstract = {This numerical study deals with the hazardous ignition of a jet flame in
a vitiated co-flow. A novel formulation, based on a passive scalar
variable, will be presented to predict hydrogen auto-ignition events.
The model, derived from the theoretical analysis of the Jacobian,
correctly describes the appearance and absence of auto-ignition in
complex configurations based on initial thermodynamic and mixture
conditions. No chemical reaction and species equations are required to
perform the simulations. Results of Lattice Boltzmann Methods (LBM)
simulations of a 3D H-2/N-2 Cabra flame will be presented using a
detailed H-2-Air mechanism. Validation against experimental and
numerical results will be provided for the lift-off (distance to
auto-ignition). The passive scalar predictions are successfully compared
with the reactive simulations. The results show a potential extension of
this model to an extensive spectrum of hydrogen safety and large-scale
turbulent combustion applications. (C) 2022 The Combustion Institute.
Published by Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
a vitiated co-flow. A novel formulation, based on a passive scalar
variable, will be presented to predict hydrogen auto-ignition events.
The model, derived from the theoretical analysis of the Jacobian,
correctly describes the appearance and absence of auto-ignition in
complex configurations based on initial thermodynamic and mixture
conditions. No chemical reaction and species equations are required to
perform the simulations. Results of Lattice Boltzmann Methods (LBM)
simulations of a 3D H-2/N-2 Cabra flame will be presented using a
detailed H-2-Air mechanism. Validation against experimental and
numerical results will be provided for the lift-off (distance to
auto-ignition). The passive scalar predictions are successfully compared
with the reactive simulations. The results show a potential extension of
this model to an extensive spectrum of hydrogen safety and large-scale
turbulent combustion applications. (C) 2022 The Combustion Institute.
Published by Elsevier Inc. All rights reserved.
Sanjeev Kumar; Marc Medale; David Brutin
Numerical model for sessile drop evaporation on heated substrate under microgravity Article de journal
Dans: INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER, vol. 195, 2022, ISSN: 0017-9310.
@article{WOS:000829352300004,
title = {Numerical model for sessile drop evaporation on heated substrate under
microgravity},
author = {Sanjeev Kumar and Marc Medale and David Brutin},
doi = {10.1016/j.ijheatmasstransfer.2022.123150},
issn = {0017-9310},
year = {2022},
date = {2022-10-01},
journal = {INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER},
volume = {195},
abstract = {Although sessile drops have simple geometries, the physics involved in
their evaporation process is com-plex owing to their numerous intricate
interactions and their fluid nature. An accurate quantitative model of
the evaporation process will enable increased understanding and control
over the process. In this study, a numerical model is developed for
sessile drop evaporation on a heated substrate under microgravity based
on the results of rocket and parabolic experiments to understand the
`internal dynamics of a ses-sile drop. The model is quantitatively
validated through experiments. Subsequently, a correlation between
substrate temperature and evaporation rate is suggested for an ethanol
sessile drop. The flow motion is analyzed by conducting
three-dimensional resolved computations of an evaporating sessile drop.
This provides insights into the Marangoni effect in the dynamics of the
evaporation process and the occur-rence of secondary instabilities. For
the first time, the fine effects of secondary instabilities on the
evap-oration rate are captured. Our numerical model is valid in the
absence of convection in the vapor phase, producing an interface of an
evaporating drop in a fully saturated vapor, which typically exists
under microgravity conditions. (c) 2022 Elsevier Ltd. All rights
reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
their evaporation process is com-plex owing to their numerous intricate
interactions and their fluid nature. An accurate quantitative model of
the evaporation process will enable increased understanding and control
over the process. In this study, a numerical model is developed for
sessile drop evaporation on a heated substrate under microgravity based
on the results of rocket and parabolic experiments to understand the
`internal dynamics of a ses-sile drop. The model is quantitatively
validated through experiments. Subsequently, a correlation between
substrate temperature and evaporation rate is suggested for an ethanol
sessile drop. The flow motion is analyzed by conducting
three-dimensional resolved computations of an evaporating sessile drop.
This provides insights into the Marangoni effect in the dynamics of the
evaporation process and the occur-rence of secondary instabilities. For
the first time, the fine effects of secondary instabilities on the
evap-oration rate are captured. Our numerical model is valid in the
absence of convection in the vapor phase, producing an interface of an
evaporating drop in a fully saturated vapor, which typically exists
under microgravity conditions. (c) 2022 Elsevier Ltd. All rights
reserved.
Gabriel Braun; Itamar Borges Jr; Adelia J. A. Aquino; Hans Lischka; Felix Plasser; Silmar A. Monte; Elizete Ventura; Saikat Mukherjee; Mario Barbatti
Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states Article de journal
Dans: JOURNAL OF CHEMICAL PHYSICS, vol. 157, no. 15, 2022, ISSN: 0021-9606.
@article{WOS:000885378200003,
title = {Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium
between excited states},
author = {Gabriel Braun and Itamar Borges Jr and Adelia J. A. Aquino and Hans Lischka and Felix Plasser and Silmar A. Monte and Elizete Ventura and Saikat Mukherjee and Mario Barbatti},
doi = {10.1063/5.0113908},
issn = {0021-9606},
year = {2022},
date = {2022-10-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {157},
number = {15},
abstract = {Pyrene fluorescence after a high-energy electronic excitation exhibits a
prominent band shoulder not present after excitation at low energies.
The standard assignment of this shoulder as a non-Kasha emission from
the second-excited state (S-2) has been recently questioned. To
elucidate this issue, we simulated the fluorescence of pyrene using two
different theoretical approaches based on vertical convolution and
nonadiabatic dynamics with nuclear ensembles. To conduct the necessary
nonadiabatic dynamics simulations with high-lying electronic states and
deal with fluorescence timescales of about 100 ns of this large
molecule, we developed new computational protocols. The results from
both approaches confirm that the band shoulder is, in fact, due to S-2
emission. We show that the non-Kasha behavior is a dynamic-equilibrium
effect not caused by a metastable S-2 minimum. However, it requires
considerable vibrational energy, which can only be achieved in
collisionless regimes after transitions into highly excited states. This
strict condition explains why the S-2 emission was not observed in some
experiments. (C) 2022 Author(s).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
prominent band shoulder not present after excitation at low energies.
The standard assignment of this shoulder as a non-Kasha emission from
the second-excited state (S-2) has been recently questioned. To
elucidate this issue, we simulated the fluorescence of pyrene using two
different theoretical approaches based on vertical convolution and
nonadiabatic dynamics with nuclear ensembles. To conduct the necessary
nonadiabatic dynamics simulations with high-lying electronic states and
deal with fluorescence timescales of about 100 ns of this large
molecule, we developed new computational protocols. The results from
both approaches confirm that the band shoulder is, in fact, due to S-2
emission. We show that the non-Kasha behavior is a dynamic-equilibrium
effect not caused by a metastable S-2 minimum. However, it requires
considerable vibrational energy, which can only be achieved in
collisionless regimes after transitions into highly excited states. This
strict condition explains why the S-2 emission was not observed in some
experiments. (C) 2022 Author(s).
S. Rendon Restrepo; P. Barge
Morphology and dynamical stability of self-gravitating vortices Numerical simulations Article de journal
Dans: ASTRONOMY & ASTROPHYSICS, vol. 666, 2022, ISSN: 0004-6361.
@article{WOS:000867091700011,
title = {Morphology and dynamical stability of self-gravitating vortices
Numerical simulations},
author = {S. Rendon Restrepo and P. Barge},
doi = {10.1051/0004-6361/202243518},
issn = {0004-6361},
year = {2022},
date = {2022-10-01},
journal = {ASTRONOMY & ASTROPHYSICS},
volume = {666},
abstract = {Context. Theoretical and numerical studies have shown that large-scale
vortices in protoplanetary discs can result from various hydro-dynamical
instabilities. Once produced, such vortices can survive nearly unchanged
over a large number of rotation periods, slowly migrating towards the
star. Lopsided asymmetries recently observed at sub-millimetre and
millimetre wavelengths in a number of transition discs could be
explained by the emission of the solid particles trapped by vortices in
the outer disc. However, at such a distance from the star, disc
self-gravity (SG) may affect the vortex evolution and must be included
in models.
Aims. Our first goal is to identify how vortex morphology is affected by
its own gravity. Next, we look for conditions that a self-gravitating
disc must satisfy in order to permit vortex survival at long timescales.
Finally, we characterise as well as possible the persistent
self-gravitating vortices we have found in isothermal and non-isothermal
discs.
Methods. We performed 2D hydrodynamic simulations using the RoSSBi 3.0
code. The outline of our computations was limited to Euler's equations
assuming a non-homentropic and non-adiabatic flow for an ideal gas. A
series of 45 runs were carried out starting from a Gaussian
vortex-model; the evolution of vortices was followed during 300 orbits
for various values of the vortex parameters and the Toomre parameter.
Two simulations, with the highest resolution thus far for studies of
vortices, were also run to better characterise the internal structure of
the vortices and for the purpose of comparison with an isothermal case.
Results. We find that SG tends to destabilise the injected vortices, but
compact small-scale vortices seem to be more robust than large-scale
oblong vortices. Vortex survival critically depends on the value of the
disc's Toomre parameter, but may also depend on the disc temperature at
equilibrium. Disc SG must be small enough to avoid destruction in
successive splitting and an approximate `stability' criterion is deduced
for vortices. The self-gravitating vortices that we found persist during
hundreds of rotation periods and look like the quasi-steady vortices
obtained in the non-self-gravitating case. A number of these
self-gravitating vortices are eventually accompanied by a secondary
vortex with a horseshoe motion. These vortices reach a new rotational
equilibrium in their core, tend to contract in the radial direction, and
spin faster.
Conclusions. We propose an approximate `robustness criterion', which
states that, for a given morphology, a vortex appears stable provided
that the disc's Toomre parameter overcomes a fixed threshold. Global
simulations with a high enough numerical resolution are required to
avoid inappropriate decay and to follow the evolution of
self-gravitating vortices in protoplanetary discs. Vortices reach a
nearly steady-state more easily in non-isothermal discs than in
isothermal discs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
vortices in protoplanetary discs can result from various hydro-dynamical
instabilities. Once produced, such vortices can survive nearly unchanged
over a large number of rotation periods, slowly migrating towards the
star. Lopsided asymmetries recently observed at sub-millimetre and
millimetre wavelengths in a number of transition discs could be
explained by the emission of the solid particles trapped by vortices in
the outer disc. However, at such a distance from the star, disc
self-gravity (SG) may affect the vortex evolution and must be included
in models.
Aims. Our first goal is to identify how vortex morphology is affected by
its own gravity. Next, we look for conditions that a self-gravitating
disc must satisfy in order to permit vortex survival at long timescales.
Finally, we characterise as well as possible the persistent
self-gravitating vortices we have found in isothermal and non-isothermal
discs.
Methods. We performed 2D hydrodynamic simulations using the RoSSBi 3.0
code. The outline of our computations was limited to Euler's equations
assuming a non-homentropic and non-adiabatic flow for an ideal gas. A
series of 45 runs were carried out starting from a Gaussian
vortex-model; the evolution of vortices was followed during 300 orbits
for various values of the vortex parameters and the Toomre parameter.
Two simulations, with the highest resolution thus far for studies of
vortices, were also run to better characterise the internal structure of
the vortices and for the purpose of comparison with an isothermal case.
Results. We find that SG tends to destabilise the injected vortices, but
compact small-scale vortices seem to be more robust than large-scale
oblong vortices. Vortex survival critically depends on the value of the
disc's Toomre parameter, but may also depend on the disc temperature at
equilibrium. Disc SG must be small enough to avoid destruction in
successive splitting and an approximate `stability' criterion is deduced
for vortices. The self-gravitating vortices that we found persist during
hundreds of rotation periods and look like the quasi-steady vortices
obtained in the non-self-gravitating case. A number of these
self-gravitating vortices are eventually accompanied by a secondary
vortex with a horseshoe motion. These vortices reach a new rotational
equilibrium in their core, tend to contract in the radial direction, and
spin faster.
Conclusions. We propose an approximate `robustness criterion', which
states that, for a given morphology, a vortex appears stable provided
that the disc's Toomre parameter overcomes a fixed threshold. Global
simulations with a high enough numerical resolution are required to
avoid inappropriate decay and to follow the evolution of
self-gravitating vortices in protoplanetary discs. Vortices reach a
nearly steady-state more easily in non-isothermal discs than in
isothermal discs.
Temitope T. Abiola; Josene M. Toldo; Mariana T. Casal; Amandine L. Flourat; Benjamin Rioux; Jack M. Woolley; Daniel Murdock; Florent Allais; Mario Barbatti; Vasilios G. Stavros
Direct structural observation of ultrafast photoisomerization dynamics in sinapate esters Article de journal
Dans: COMMUNICATIONS CHEMISTRY, vol. 5, no. 1, 2022, ISSN: 2399-3669.
@article{WOS:000876981400001,
title = {Direct structural observation of ultrafast photoisomerization dynamics
in sinapate esters},
author = {Temitope T. Abiola and Josene M. Toldo and Mariana T. Casal and Amandine L. Flourat and Benjamin Rioux and Jack M. Woolley and Daniel Murdock and Florent Allais and Mario Barbatti and Vasilios G. Stavros},
doi = {10.1038/s42004-022-00757-6},
issn = {2399-3669},
year = {2022},
date = {2022-10-01},
journal = {COMMUNICATIONS CHEMISTRY},
volume = {5},
number = {1},
abstract = {Sinapate esters have been extensively studied for their potential
application in `nature-inspired' photoprotection. There is general
consensus that the relaxation mechanism of sinapate esters following
photoexcitation with ultraviolet radiation is mediated by geometric
isomerization. This has been largely inferred through indirect studies
involving transient electronic absorption spectroscopy in conjunction
with steady-state spectroscopies. However, to-date, there is no direct
experimental evidence tracking the formation of the photoisomer in
real-time. Using transient vibrational absorption spectroscopy, we
report on the direct structural changes that occur upon photoexcitation,
resulting in the photoisomer formation. Our mechanistic analysis
predicts that, from the photoprepared pi pi* state, internal
conversion takes place through a conical intersection (CI) near the
geometry of the initial isomer. Our calculations suggest that different
CI topographies at relevant points on the seam of intersection may
influence the isomerization yield. Altogether, we provide compelling
evidence suggesting that a sinapate ester's geometric isomerization can
be a more complex dynamical process than originally thought.
Photoinduced isomerization reactions can be used to efficiently
dissipate absorbed energy in photosystems such as molecular motors, but
the ultrafast processes are challenging to characterize. Here, the
authors track the formation of the E and Z isomers of ethyl sinapate in
real time via transient vibrational absorption spectroscopy and find
that photoinduced internal conversion occurs at multiple points along
the potential energy surface.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
application in `nature-inspired' photoprotection. There is general
consensus that the relaxation mechanism of sinapate esters following
photoexcitation with ultraviolet radiation is mediated by geometric
isomerization. This has been largely inferred through indirect studies
involving transient electronic absorption spectroscopy in conjunction
with steady-state spectroscopies. However, to-date, there is no direct
experimental evidence tracking the formation of the photoisomer in
real-time. Using transient vibrational absorption spectroscopy, we
report on the direct structural changes that occur upon photoexcitation,
resulting in the photoisomer formation. Our mechanistic analysis
predicts that, from the photoprepared pi pi* state, internal
conversion takes place through a conical intersection (CI) near the
geometry of the initial isomer. Our calculations suggest that different
CI topographies at relevant points on the seam of intersection may
influence the isomerization yield. Altogether, we provide compelling
evidence suggesting that a sinapate ester's geometric isomerization can
be a more complex dynamical process than originally thought.
Photoinduced isomerization reactions can be used to efficiently
dissipate absorbed energy in photosystems such as molecular motors, but
the ultrafast processes are challenging to characterize. Here, the
authors track the formation of the E and Z isomers of ethyl sinapate in
real time via transient vibrational absorption spectroscopy and find
that photoinduced internal conversion occurs at multiple points along
the potential energy surface.
Benjamin Kadoch; Diego del-Castillo-Negrete; Wouter J. T. Bos; Kai Schneider
Lagrangian conditional statistics and flow topology in edge plasma turbulence Article de journal
Dans: PHYSICS OF PLASMAS, vol. 29, no. 10, 2022, ISSN: 1070-664X.
@article{WOS:000868782300001,
title = {Lagrangian conditional statistics and flow topology in edge plasma
turbulence},
author = {Benjamin Kadoch and Diego del-Castillo-Negrete and Wouter J. T. Bos and Kai Schneider},
doi = {10.1063/5.0098501},
issn = {1070-664X},
year = {2022},
date = {2022-10-01},
journal = {PHYSICS OF PLASMAS},
volume = {29},
number = {10},
abstract = {Lagrangian statistics and particle transport in edge plasma turbulence
are investigated using the Hasegawa-Wakatani model and its modified
version. The latter shows the emergence of pronounced zonal flows.
Different values of the adiabaticity parameter are considered. The main
goal is to characterize the role of coherent structures, i.e., vortices
and zonal flows, and their impact on the Lagrangian statistics of
particles. Computationally intensive long time simulations following
ensembles of test particles over hundreds of eddy turnover times are
considered in statistically stationary turbulent flows. The flow
topology is characterized using the Lagrangian Okubo-Weiss criterion in
order to split the flow into topologically different domains. In
elliptic and hyperbolic regions, the probability density functions
(PDFs) of the residence time have self-similar algebraic decaying tails.
However, in the intermediate regions, the PDFs exhibit exponentially
decaying tails. Topologically conditioned PDFs of the Lagrangian
velocity, and acceleration and density fluctuations are likewise
computed. The differences between the classical Hasegawa-Wakatani system
and its modified version are assessed, and the role of zonal flows is
highlighted. The density flux spectrum, which characterizes the
contributions of different length scales, is studied, and its inertial
scaling is found to be in agreement with predictions based on
dimensional arguments. Analyzing the angular change of particle tracers
at different time scales, corresponding to coarse grained curvature,
completes the study, and these multiscale geometric statistics quantify
the directional properties of the particle motion in different flow
regimes. Published under an exclusive license by AIP Publishing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
are investigated using the Hasegawa-Wakatani model and its modified
version. The latter shows the emergence of pronounced zonal flows.
Different values of the adiabaticity parameter are considered. The main
goal is to characterize the role of coherent structures, i.e., vortices
and zonal flows, and their impact on the Lagrangian statistics of
particles. Computationally intensive long time simulations following
ensembles of test particles over hundreds of eddy turnover times are
considered in statistically stationary turbulent flows. The flow
topology is characterized using the Lagrangian Okubo-Weiss criterion in
order to split the flow into topologically different domains. In
elliptic and hyperbolic regions, the probability density functions
(PDFs) of the residence time have self-similar algebraic decaying tails.
However, in the intermediate regions, the PDFs exhibit exponentially
decaying tails. Topologically conditioned PDFs of the Lagrangian
velocity, and acceleration and density fluctuations are likewise
computed. The differences between the classical Hasegawa-Wakatani system
and its modified version are assessed, and the role of zonal flows is
highlighted. The density flux spectrum, which characterizes the
contributions of different length scales, is studied, and its inertial
scaling is found to be in agreement with predictions based on
dimensional arguments. Analyzing the angular change of particle tracers
at different time scales, corresponding to coarse grained curvature,
completes the study, and these multiscale geometric statistics quantify
the directional properties of the particle motion in different flow
regimes. Published under an exclusive license by AIP Publishing.
Mariana T. Casal; Josene M. Toldo; Felix Plasser; Mario Barbatti
Using diketopyrrolopyrroles to stabilize double excitation and control internal conversion Article de journal
Dans: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 38, p. 23279-23288, 2022, ISSN: 1463-9076.
@article{WOS:000859790500001,
title = {Using diketopyrrolopyrroles to stabilize double excitation and control
internal conversion},
author = {Mariana T. Casal and Josene M. Toldo and Felix Plasser and Mario Barbatti},
doi = {10.1039/d2cp03533b},
issn = {1463-9076},
year = {2022},
date = {2022-10-01},
journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
volume = {24},
number = {38},
pages = {23279-23288},
abstract = {Diketopyrrolopyrrole (DPP) is a pivotal functional group to tune the
physicochemical properties of novel organic photoelectronic materials.
Among multiple uses, DPP-thiophene derivatives forming a dimer through a
vinyl linker were recently shown to quench the fluorescence observed in
their isolated monomers. Here, we explain this fluorescence quenching
using computational chemistry. The DPP-thiophene dimer has a low-lying
doubly excited state that is not energetically accessible for the
monomer. This state delays the fluorescence allowing internal conversion
to occur first. We characterize the doubly excited state wavefunction by
systematically changing the derivatives to tune the pi-scaffold size and
the acceptor and donor characters. The origin of this state's
stabilization is related to the increase in the pi-system and not to the
charge-transfer features. This analysis delivers core conceptual
information on the electronic properties of organic chromophores
arranged symmetrically around a vinyl linker, opening new ways to
control the balance between luminescence and internal conversion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
physicochemical properties of novel organic photoelectronic materials.
Among multiple uses, DPP-thiophene derivatives forming a dimer through a
vinyl linker were recently shown to quench the fluorescence observed in
their isolated monomers. Here, we explain this fluorescence quenching
using computational chemistry. The DPP-thiophene dimer has a low-lying
doubly excited state that is not energetically accessible for the
monomer. This state delays the fluorescence allowing internal conversion
to occur first. We characterize the doubly excited state wavefunction by
systematically changing the derivatives to tune the pi-scaffold size and
the acceptor and donor characters. The origin of this state's
stabilization is related to the increase in the pi-system and not to the
charge-transfer features. This analysis delivers core conceptual
information on the electronic properties of organic chromophores
arranged symmetrically around a vinyl linker, opening new ways to
control the balance between luminescence and internal conversion.
Etienne Combrisson; Michele Allegra; Ruggero Basanisi; Robin A. A. Ince; Bruno L. Giordano; Julien Bastin; Andrea Brovelli
Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data Article de journal
Dans: NEUROIMAGE, vol. 258, 2022, ISSN: 1053-8119.
@article{WOS:000814754000002,
title = {Group-level inference of information-based measures for the analyses of
cognitive brain networks from neurophysiological data},
author = {Etienne Combrisson and Michele Allegra and Ruggero Basanisi and Robin A. A. Ince and Bruno L. Giordano and Julien Bastin and Andrea Brovelli},
doi = {10.1016/j.neuroimage.2022.119347},
issn = {1053-8119},
year = {2022},
date = {2022-09-01},
journal = {NEUROIMAGE},
volume = {258},
abstract = {The reproducibility crisis in neuroimaging and in particular in the case
of underpowered studies has introduced doubts on our ability to
reproduce, replicate and generalize findings. As a response, we have
seen the emergence of suggested guidelines and principles for
neuroscientists known as Good Scientific Practice for conducting more
reliable research. Still, every study remains almost unique in its
combination of analytical and statistical approaches. While it is
understandable considering the diversity of designs and brain data
recording, it also represents a striking point against reproducibility.
Here, we propose a non-parametric permutation-based statistical
framework, primarily designed for neurophysiological data, in order to
perform group-level inferences on non negative measures of information
encompassing metrics from information-theory, machine-learning or
measures of distances. The framework supports both fixed-and
random-effect models to adapt to inter-individuals and inter-sessions
variability. Using numerical simulations, we compared the accuracy in
ground-truth retrieving of both group models, such as test-and
cluster-wise corrections for multiple comparisons. We then reproduced
and extended existing results using both spatially uniform MEG and
non-uniform intracranial neurophysiological data. We showed how the
framework can be used to extract stereotypical task-and behavior-related
effects across the population covering scales from the local level of
brain regions, inter-areal functional connectivity to measures
summarizing network properties. We also present an open-source Python
toolbox called Frites1 that includes the proposed statistical pipeline
using information-theoretic metrics such as single-trial functional
connectivity estimations for the extraction of cognitive brain networks.
Taken together, we believe that this framework deserves careful
attention as its robustness and flexibility could be the starting point
toward the uniformization of statistical approaches.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
of underpowered studies has introduced doubts on our ability to
reproduce, replicate and generalize findings. As a response, we have
seen the emergence of suggested guidelines and principles for
neuroscientists known as Good Scientific Practice for conducting more
reliable research. Still, every study remains almost unique in its
combination of analytical and statistical approaches. While it is
understandable considering the diversity of designs and brain data
recording, it also represents a striking point against reproducibility.
Here, we propose a non-parametric permutation-based statistical
framework, primarily designed for neurophysiological data, in order to
perform group-level inferences on non negative measures of information
encompassing metrics from information-theory, machine-learning or
measures of distances. The framework supports both fixed-and
random-effect models to adapt to inter-individuals and inter-sessions
variability. Using numerical simulations, we compared the accuracy in
ground-truth retrieving of both group models, such as test-and
cluster-wise corrections for multiple comparisons. We then reproduced
and extended existing results using both spatially uniform MEG and
non-uniform intracranial neurophysiological data. We showed how the
framework can be used to extract stereotypical task-and behavior-related
effects across the population covering scales from the local level of
brain regions, inter-areal functional connectivity to measures
summarizing network properties. We also present an open-source Python
toolbox called Frites1 that includes the proposed statistical pipeline
using information-theoretic metrics such as single-trial functional
connectivity estimations for the extraction of cognitive brain networks.
Taken together, we believe that this framework deserves careful
attention as its robustness and flexibility could be the starting point
toward the uniformization of statistical approaches.
Leo Chaussy; Denis Hagebaum-Reignier; Stephane Humbel; Paola Nava
Accurate computed singlet-triplet energy differences for cobalt systems: implication for two-state reactivity Article de journal
Dans: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 36, p. 21841-21852, 2022, ISSN: 1463-9076.
@article{WOS:000850173400001,
title = {Accurate computed singlet-triplet energy differences for cobalt systems:
implication for two-state reactivity},
author = {Leo Chaussy and Denis Hagebaum-Reignier and Stephane Humbel and Paola Nava},
doi = {10.1039/d2cp03291k},
issn = {1463-9076},
year = {2022},
date = {2022-09-01},
journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
volume = {24},
number = {36},
pages = {21841-21852},
abstract = {Accurate singlet-triplet energy differences for cobalt and rhodium
complexes were calculated by using several wave function methods, such
as MRCISD, CASPT2, CCSD(T) and BCCD(T). Relaxed energy differences were
obtained by considering the singlet and triplet complexes, each at the
minimum of their potential energy surfaces. Active spaces for
multireference calculations were carefully checked to provide accurate
results. The considered systems are built by increasing progressively
the first coordination sphere around the metal. We included in our set two CpCoX complexes (Cp = cyclopentadienyl},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
complexes were calculated by using several wave function methods, such
as MRCISD, CASPT2, CCSD(T) and BCCD(T). Relaxed energy differences were
obtained by considering the singlet and triplet complexes, each at the
minimum of their potential energy surfaces. Active spaces for
multireference calculations were carefully checked to provide accurate
results. The considered systems are built by increasing progressively
the first coordination sphere around the metal. We included in our set two CpCoX complexes (Cp = cyclopentadienyl
Shang-Gui Cai; Sajad Mozaffari; Jerome Jacob; Pierre Sagaut
Application of immersed boundary based turbulence wall modeling to the Ahmed body aerodynamics Article de journal
Dans: PHYSICS OF FLUIDS, vol. 34, no. 9, 2022, ISSN: 1070-6631.
@article{WOS:000874281500001,
title = {Application of immersed boundary based turbulence wall modeling to the
Ahmed body aerodynamics},
author = {Shang-Gui Cai and Sajad Mozaffari and Jerome Jacob and Pierre Sagaut},
doi = {10.1063/5.0098232},
issn = {1070-6631},
year = {2022},
date = {2022-09-01},
journal = {PHYSICS OF FLUIDS},
volume = {34},
number = {9},
abstract = {This paper applies a recently developed immersed boundary-turbulence
wall modeling approach to turbulent flows over a generic car geometry,
known as the Ahmed body, under massive flow separation within a lattice
Boltzmann solver. Although the immersed boundary method combined with
hierarchical Cartesian grid offers high flexibility in automatic grid
generation around complex geometries, the near-wall solution is
significantly deteriorated compared to the body-fitted simulation,
especially when coupled to wall models for turbulent flows at high
Reynolds number. Enhanced wall treatments have been proposed in the
literature and validated for attached flow configurations. In this work,
the Ahmed body with a slant surface of angle 35 degrees is considered
where the flow separates massively over the slant surface and the
vertical base. The large eddy simulation is performed with a Reynolds
stress constraint near-wall. The eddy viscosity is computed dynamically
by taking into account the actually resolved Reynolds stresses. It
approaches the mixing length eddy viscosity in attached boundary layers
and returns to the subgrid eddy viscosity in detached boundary layers.
An explicit equilibrium wall model has also been proposed to accelerate
the calculation. Comparison with the no-slip boundary condition on the
separated surfaces shows that the near-wall treatments with the
equilibrium wall model operate reasonably well on both attached and
detached boundary layers. Published under an exclusive license by AIP
Publishing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
wall modeling approach to turbulent flows over a generic car geometry,
known as the Ahmed body, under massive flow separation within a lattice
Boltzmann solver. Although the immersed boundary method combined with
hierarchical Cartesian grid offers high flexibility in automatic grid
generation around complex geometries, the near-wall solution is
significantly deteriorated compared to the body-fitted simulation,
especially when coupled to wall models for turbulent flows at high
Reynolds number. Enhanced wall treatments have been proposed in the
literature and validated for attached flow configurations. In this work,
the Ahmed body with a slant surface of angle 35 degrees is considered
where the flow separates massively over the slant surface and the
vertical base. The large eddy simulation is performed with a Reynolds
stress constraint near-wall. The eddy viscosity is computed dynamically
by taking into account the actually resolved Reynolds stresses. It
approaches the mixing length eddy viscosity in attached boundary layers
and returns to the subgrid eddy viscosity in detached boundary layers.
An explicit equilibrium wall model has also been proposed to accelerate
the calculation. Comparison with the no-slip boundary condition on the
separated surfaces shows that the near-wall treatments with the
equilibrium wall model operate reasonably well on both attached and
detached boundary layers. Published under an exclusive license by AIP
Publishing.
Louis-Alexandre Couston; Joseph Nandaha; Benjamin Favier
Competition between Rayleigh-Benard and horizontal convection Article de journal
Dans: JOURNAL OF FLUID MECHANICS, vol. 947, 2022, ISSN: 0022-1120.
@article{WOS:000842506600001,
title = {Competition between Rayleigh-Benard and horizontal convection},
author = {Louis-Alexandre Couston and Joseph Nandaha and Benjamin Favier},
doi = {10.1017/jfm.2022.613},
issn = {0022-1120},
year = {2022},
date = {2022-08-01},
journal = {JOURNAL OF FLUID MECHANICS},
volume = {947},
abstract = {We investigate the dynamics of a fluid layer subject to a bottom heat
flux and a top monotonically increasing temperature profile driving
horizontal convection (HC). We use direct numerical simulations and consider a large range of flux-based Rayleigh numbers 10(6) <= Ra-F <=
10(9) and imposed top horizontal to bottom vertical heat flux ratios 0 <= Lambda <= 1. The fluid domain is a closed two-dimensional box with aspect ratio 4 <= Gamma <= 16 and we consider no-slip boundaries and
adiabatic side walls. We demonstrate a regime transition from
Rayleigh-Bdnard (RB) convection to HC at Lambda approximate to 10(-2),
which is independent of Ra-F and Gamma. At small Lambda, the flow is
organised in multiple overturning cells with approximately unit aspect
ratio, whereas at large Lambda a single cell is obtained. The
RB-relevant Nusselt number scaling with Ra-F and the HC-relevant Nusselt number scaling with the horizontal Rayleigh number Ra-L = Ra-F Lambda
Gamma(4) are in good agreement with previous results from classical RB
convection and HC studies in the limit Lambda << 10(-2) and Lambda >>
10(-2), respectively. We demonstrate that the system is multi-stable
near the transition Lambda approximate to 10(-2), i.e. the exact number
of cells not only depends on Lambda but also on the system's history.
Our results suggest that subglacial lakes, which motivated this study,
are likely to be dominated by RB convection, unless the slope of the
ice-water interface, which controls the horizontal temperature gradient
via the pressure-dependence of the freezing point, is greater than
unity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
flux and a top monotonically increasing temperature profile driving
horizontal convection (HC). We use direct numerical simulations and consider a large range of flux-based Rayleigh numbers 10(6) <= Ra-F <=
10(9) and imposed top horizontal to bottom vertical heat flux ratios 0 <= Lambda <= 1. The fluid domain is a closed two-dimensional box with aspect ratio 4 <= Gamma <= 16 and we consider no-slip boundaries and
adiabatic side walls. We demonstrate a regime transition from
Rayleigh-Bdnard (RB) convection to HC at Lambda approximate to 10(-2),
which is independent of Ra-F and Gamma. At small Lambda, the flow is
organised in multiple overturning cells with approximately unit aspect
ratio, whereas at large Lambda a single cell is obtained. The
RB-relevant Nusselt number scaling with Ra-F and the HC-relevant Nusselt number scaling with the horizontal Rayleigh number Ra-L = Ra-F Lambda
Gamma(4) are in good agreement with previous results from classical RB
convection and HC studies in the limit Lambda << 10(-2) and Lambda >>
10(-2), respectively. We demonstrate that the system is multi-stable
near the transition Lambda approximate to 10(-2), i.e. the exact number
of cells not only depends on Lambda but also on the system's history.
Our results suggest that subglacial lakes, which motivated this study,
are likely to be dominated by RB convection, unless the slope of the
ice-water interface, which controls the horizontal temperature gradient
via the pressure-dependence of the freezing point, is greater than
unity.
Daniel W. Polak; Mariana T. Casal; Josene M. Toldo; Xiantao Hu; Giordano Amoruso; Olivia Pomeranc; Martin Heeney; Mario Barbatti; Michael N. R. Ashfold; Thomas A. A. Oliver
Probing the electronic structure and photophysics of thiophene-diketopyrrolopyrrole derivatives in solution Article de journal
Dans: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 34, p. 20138-20151, 2022, ISSN: 1463-9076.
@article{WOS:000842613300001,
title = {Probing the electronic structure and photophysics of
thiophene-diketopyrrolopyrrole derivatives in solution},
author = {Daniel W. Polak and Mariana T. Casal and Josene M. Toldo and Xiantao Hu and Giordano Amoruso and Olivia Pomeranc and Martin Heeney and Mario Barbatti and Michael N. R. Ashfold and Thomas A. A. Oliver},
doi = {10.1039/d2cp03238d},
issn = {1463-9076},
year = {2022},
date = {2022-08-01},
journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
volume = {24},
number = {34},
pages = {20138-20151},
abstract = {Diketopyrrolopyrroles are a popular class of electron-withdrawing unit
in optoelectronic materials. When combined with electron donating
side-chain functional groups such as thiophenes, they form a very broad
class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles
(TDPPs). Despite their widescale use in biosensors and photovoltaic
materials, studies have yet to establish the important link between the
electronic structure of the specific TDPP and the critical optical
properties. To bridge this gap, ultrafast transient absorption with 22
fs time resolution has been used to explore the photophysics of three
prototypical TDPP molecules: a monomer, dimer and polymer in solution.
Interpretation of experimental data was assisted by a recent high-level
theoretical study, and additional density functional theory
calculations. These studies show that the photophysics of these
molecular prototypes under visible photoexcitation are determined by
just two excited electronic states, having very different electronic
characters (one is optically bright, the other dark), their relative
energetic ordering and the timescales for internal conversion from one
to the other and/or to the ground state. The underlying difference in
electronic structure alters the branching between these excited states
and their associated dynamics. In turn, these factors dictate the
fluorescence quantum yields, which are shown to vary by similar to 1-2
orders of magnitude across the TDPP prototypes investigated here. The
fast non-radiative transfer of molecules from the bright to dark states
is mediated by conical intersections. Remarkably, wavepacket signals in
the measured transient absorption data carry signatures of the nuclear
motions that enable mixing of the electronic-nuclear wavefunction and
facilitate non-adiabatic coupling between the bright and dark states.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
in optoelectronic materials. When combined with electron donating
side-chain functional groups such as thiophenes, they form a very broad
class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles
(TDPPs). Despite their widescale use in biosensors and photovoltaic
materials, studies have yet to establish the important link between the
electronic structure of the specific TDPP and the critical optical
properties. To bridge this gap, ultrafast transient absorption with 22
fs time resolution has been used to explore the photophysics of three
prototypical TDPP molecules: a monomer, dimer and polymer in solution.
Interpretation of experimental data was assisted by a recent high-level
theoretical study, and additional density functional theory
calculations. These studies show that the photophysics of these
molecular prototypes under visible photoexcitation are determined by
just two excited electronic states, having very different electronic
characters (one is optically bright, the other dark), their relative
energetic ordering and the timescales for internal conversion from one
to the other and/or to the ground state. The underlying difference in
electronic structure alters the branching between these excited states
and their associated dynamics. In turn, these factors dictate the
fluorescence quantum yields, which are shown to vary by similar to 1-2
orders of magnitude across the TDPP prototypes investigated here. The
fast non-radiative transfer of molecules from the bright to dark states
is mediated by conical intersections. Remarkably, wavepacket signals in
the measured transient absorption data carry signatures of the nuclear
motions that enable mixing of the electronic-nuclear wavefunction and
facilitate non-adiabatic coupling between the bright and dark states.
Daniel W. Polak; Mariana T. Casal; Josene M. Toldo; Xiantao Hu; Giordano Amoruso; Olivia Pomeranc; Martin Heeney; Mario Barbatti; Michael N. R. Ashfold; Thomas A. A. Oliver
Probing the electronic structure and photophysics of thiophene-diketopyrrolopyrrole derivatives in solution Article de journal
Dans: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 34, p. 20138-20151, 2022, ISSN: 1463-9076.
@article{WOS:000842613300001b,
title = {Probing the electronic structure and photophysics of
thiophene-diketopyrrolopyrrole derivatives in solution},
author = {Daniel W. Polak and Mariana T. Casal and Josene M. Toldo and Xiantao Hu and Giordano Amoruso and Olivia Pomeranc and Martin Heeney and Mario Barbatti and Michael N. R. Ashfold and Thomas A. A. Oliver},
doi = {10.1039/d2cp03238d},
issn = {1463-9076},
year = {2022},
date = {2022-08-01},
journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
volume = {24},
number = {34},
pages = {20138-20151},
abstract = {Diketopyrrolopyrroles are a popular class of electron-withdrawing unit
in optoelectronic materials. When combined with electron donating
side-chain functional groups such as thiophenes, they form a very broad
class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles
(TDPPs). Despite their widescale use in biosensors and photovoltaic
materials, studies have yet to establish the important link between the
electronic structure of the specific TDPP and the critical optical
properties. To bridge this gap, ultrafast transient absorption with 22
fs time resolution has been used to explore the photophysics of three
prototypical TDPP molecules: a monomer, dimer and polymer in solution.
Interpretation of experimental data was assisted by a recent high-level
theoretical study, and additional density functional theory
calculations. These studies show that the photophysics of these
molecular prototypes under visible photoexcitation are determined by
just two excited electronic states, having very different electronic
characters (one is optically bright, the other dark), their relative
energetic ordering and the timescales for internal conversion from one
to the other and/or to the ground state. The underlying difference in
electronic structure alters the branching between these excited states
and their associated dynamics. In turn, these factors dictate the
fluorescence quantum yields, which are shown to vary by similar to 1-2
orders of magnitude across the TDPP prototypes investigated here. The
fast non-radiative transfer of molecules from the bright to dark states
is mediated by conical intersections. Remarkably, wavepacket signals in
the measured transient absorption data carry signatures of the nuclear
motions that enable mixing of the electronic-nuclear wavefunction and
facilitate non-adiabatic coupling between the bright and dark states.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
in optoelectronic materials. When combined with electron donating
side-chain functional groups such as thiophenes, they form a very broad
class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles
(TDPPs). Despite their widescale use in biosensors and photovoltaic
materials, studies have yet to establish the important link between the
electronic structure of the specific TDPP and the critical optical
properties. To bridge this gap, ultrafast transient absorption with 22
fs time resolution has been used to explore the photophysics of three
prototypical TDPP molecules: a monomer, dimer and polymer in solution.
Interpretation of experimental data was assisted by a recent high-level
theoretical study, and additional density functional theory
calculations. These studies show that the photophysics of these
molecular prototypes under visible photoexcitation are determined by
just two excited electronic states, having very different electronic
characters (one is optically bright, the other dark), their relative
energetic ordering and the timescales for internal conversion from one
to the other and/or to the ground state. The underlying difference in
electronic structure alters the branching between these excited states
and their associated dynamics. In turn, these factors dictate the
fluorescence quantum yields, which are shown to vary by similar to 1-2
orders of magnitude across the TDPP prototypes investigated here. The
fast non-radiative transfer of molecules from the bright to dark states
is mediated by conical intersections. Remarkably, wavepacket signals in
the measured transient absorption data carry signatures of the nuclear
motions that enable mixing of the electronic-nuclear wavefunction and
facilitate non-adiabatic coupling between the bright and dark states.
Saikat Mukherjee; Mario Barbatti
A Hessian-Free Method to Prevent Zero-Point Energy Leakage in Classical Trajectories Article de journal
Dans: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, ISSN: 1549-9618.
@article{WOS:000819454900001,
title = {A Hessian-Free Method to Prevent Zero-Point Energy Leakage in Classical Trajectories},
author = {Saikat Mukherjee and Mario Barbatti},
doi = {10.1021/acs.jctc.2c00216},
issn = {1549-9618},
year = {2022},
date = {2022-07-08},
journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
abstract = {The problem associated with the zero-point energy (ZPE) leak in
classical trajectory calculations is well known. Since ZPE is a
manifestation of the quantum uncertainty principle, there are no
restrictions on energy during the classical propagation of nuclei. This
phenomenon can lead to unphysical results, such as forming products
without the ZPE in the internal vibrational degrees of freedom (DOFs).
The ZPE leakage also permits reactions below the quantum threshold for
the reaction. We have developed a new Hessian-free method, inspired by
the LoweAndersen thermostat model, to prevent energy dipping below a
threshold in the localpair (LP) vibrational DOFs. The idea is to pump
the leaked energy to the corresponding local vibrational mode taken from
the other vibrational DOFs. We have applied the new correction protocol
on the ab-initio ground-state molecular dynamics simulation of the water
dimer (H2O)2, which dissociates due to unphysical ZPE spilling from
high-frequency OH modes. The LP-ZPE method has been able to prevent the
ZPE spilling of the OH stretching modes by pumping back the leaked
energy into the corresponding modes, while this energy is taken from the
other modes of the dimer itself, keeping the system as a microcanonical
ensemble.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
classical trajectory calculations is well known. Since ZPE is a
manifestation of the quantum uncertainty principle, there are no
restrictions on energy during the classical propagation of nuclei. This
phenomenon can lead to unphysical results, such as forming products
without the ZPE in the internal vibrational degrees of freedom (DOFs).
The ZPE leakage also permits reactions below the quantum threshold for
the reaction. We have developed a new Hessian-free method, inspired by
the LoweAndersen thermostat model, to prevent energy dipping below a
threshold in the localpair (LP) vibrational DOFs. The idea is to pump
the leaked energy to the corresponding local vibrational mode taken from
the other vibrational DOFs. We have applied the new correction protocol
on the ab-initio ground-state molecular dynamics simulation of the water
dimer (H2O)2, which dissociates due to unphysical ZPE spilling from
high-frequency OH modes. The LP-ZPE method has been able to prevent the
ZPE spilling of the OH stretching modes by pumping back the leaked
energy into the corresponding modes, while this energy is taken from the
other modes of the dimer itself, keeping the system as a microcanonical
ensemble.
Claude Gregoire; Lionel Spinelli; Sergio Villazala-Merino; Laurine Gil; Maria Pia Holgado; Myriam Moussa; Chuang Dong; Ana Zarubica; Mathieu Fallet; Jean-Marc Navarro; Bernard Malissen; Pierre Milpied; Mauro Gaya
Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism Article de journal
Dans: IMMUNITY, vol. 55, no. 7, p. 1216+, 2022, ISSN: 1074-7613.
@article{WOS:000831554100012,
title = {Viral infection engenders bona fide and bystander subsets of
lung-resident memory B cells through a permissive mechanism},
author = {Claude Gregoire and Lionel Spinelli and Sergio Villazala-Merino and Laurine Gil and Maria Pia Holgado and Myriam Moussa and Chuang Dong and Ana Zarubica and Mathieu Fallet and Jean-Marc Navarro and Bernard Malissen and Pierre Milpied and Mauro Gaya},
doi = {10.1016/j.immuni.2022.06.002},
issn = {1074-7613},
year = {2022},
date = {2022-07-01},
journal = {IMMUNITY},
volume = {55},
number = {7},
pages = {1216+},
abstract = {Lung-resident memory B cells (MBCs) provide localized protection against
reinfection in respiratory airways. Currently, the biology of these
cells remains largely unexplored. Here, we combined influenza and
SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs
regardless of antigen specificity. We found that two main
transcriptionally distinct subsets of MBCs colonized the lung
peribronchial niche after infec-tion. These subsets arose from different
progenitors and were both class switched, somatically mutated, and
intrinsically biased in their differentiation fate toward plasma cells.
Combined analysis of antigen spec-ificity and B cell receptor repertoire
segregated these subsets into ???bona fide???virus-specific MBCs and
???bystander???MBCs with no apparent specificity for eliciting viruses
generated through an alternative permis-sive process. Thus, diverse
transcriptional programs in MBCs are not linked to specific effector
fates but rather to divergent strategies of the immune system to
simultaneously provide rapid protection from reinfec-tion while
diversifying the initial B cell repertoire.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
reinfection in respiratory airways. Currently, the biology of these
cells remains largely unexplored. Here, we combined influenza and
SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs
regardless of antigen specificity. We found that two main
transcriptionally distinct subsets of MBCs colonized the lung
peribronchial niche after infec-tion. These subsets arose from different
progenitors and were both class switched, somatically mutated, and
intrinsically biased in their differentiation fate toward plasma cells.
Combined analysis of antigen spec-ificity and B cell receptor repertoire
segregated these subsets into ???bona fide???virus-specific MBCs and
???bystander???MBCs with no apparent specificity for eliciting viruses
generated through an alternative permis-sive process. Thus, diverse
transcriptional programs in MBCs are not linked to specific effector
fates but rather to divergent strategies of the immune system to
simultaneously provide rapid protection from reinfec-tion while
diversifying the initial B cell repertoire.
Dmytro Kandaskalov; Liangzhao Huang; Johnathan Emo; Philippe Maugis
Carbon diffusion in bcc- and bct-Fe: Influence of short-range C-C pair interactions studied from first-principles calculations Article de journal
Dans: MATERIALS CHEMISTRY AND PHYSICS, vol. 286, 2022, ISSN: 0254-0584.
@article{WOS:000806828200002,
title = {Carbon diffusion in bcc- and bct-Fe: Influence of short-range C-C pair
interactions studied from first-principles calculations},
author = {Dmytro Kandaskalov and Liangzhao Huang and Johnathan Emo and Philippe Maugis},
doi = {10.1016/j.matchemphys.2022.126159},
issn = {0254-0584},
year = {2022},
date = {2022-07-01},
journal = {MATERIALS CHEMISTRY AND PHYSICS},
volume = {286},
abstract = {Identifying the mechanisms of interstitial diffusion in iron is
important to understanding the low-temperature ageing of Fe-C ferritic
and martensitic alloys. In spite of the low solubility of carbon in
ferrite at equilibrium, carbon-rich areas are often found at segregated
grain boundaries and in Cottrell atmospheres around dislo-cations.
Carbon-rich areas also form by spinodal decomposition in martensite. In
those cases, carbon atoms experience short-range interactions,
susceptible to modify their migration behaviour. We performed
first-principles calculations to study the influence of these C-C
interactions on the migration of interstitial carbon in body -centered
iron. The ab initio energy database was introduced in kinetic Monte
Carlo simulations to compute the thermodynamic and kinetic parameters.
We found that the migration energies of carbon are largely affected by
the presence of a neighbouring carbon atom. We explain the evolution of
these energies by the relative stability of the C-C configurations
corresponding to stable and transition-state positions. The C-C pair
interactions slightly modify the ferrite/martensite transition
conditions and significantly change the carbon atomic migration path.
The latter leads to an increase of the diffusivity up to 10 times and an
important kinetic correlation at low temperature (< 300 K) and high
carbon contents (> 1 at.%).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
important to understanding the low-temperature ageing of Fe-C ferritic
and martensitic alloys. In spite of the low solubility of carbon in
ferrite at equilibrium, carbon-rich areas are often found at segregated
grain boundaries and in Cottrell atmospheres around dislo-cations.
Carbon-rich areas also form by spinodal decomposition in martensite. In
those cases, carbon atoms experience short-range interactions,
susceptible to modify their migration behaviour. We performed
first-principles calculations to study the influence of these C-C
interactions on the migration of interstitial carbon in body -centered
iron. The ab initio energy database was introduced in kinetic Monte
Carlo simulations to compute the thermodynamic and kinetic parameters.
We found that the migration energies of carbon are largely affected by
the presence of a neighbouring carbon atom. We explain the evolution of
these energies by the relative stability of the C-C configurations
corresponding to stable and transition-state positions. The C-C pair
interactions slightly modify the ferrite/martensite transition
conditions and significantly change the carbon atomic migration path.
The latter leads to an increase of the diffusivity up to 10 times and an
important kinetic correlation at low temperature (< 300 K) and high
carbon contents (> 1 at.%).
Karthik Bhairapurada; Bruno Denet; Pierre Boivin
A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities Article de journal
Dans: COMBUSTION AND FLAME, vol. 240, 2022, ISSN: 0010-2180.
@article{WOS:000770897700001,
title = {A Lattice-Boltzmann study of premixed flames thermo-acoustic
instabilities},
author = {Karthik Bhairapurada and Bruno Denet and Pierre Boivin},
doi = {10.1016/j.combustflame.2022.112049},
issn = {0010-2180},
year = {2022},
date = {2022-06-01},
journal = {COMBUSTION AND FLAME},
volume = {240},
abstract = {We present possibly for the first time Lattice-Boltzmann numerical
simulations of thermo-acoustic instabilities of premixed flames. We
study flames interacting with an imposed acoustic field where flames
submitted to a parametric instability can be observed, as well as plane
flames re-stabilized by the acoustic forcing. Self-induced
thermo-acoustic oscillations of flames propagating in narrow channels
are also studied, indicating an unexpected dependency with the channel
width. For both excited and self-excited flames, results confirm that
Lattice-Boltzmann method can capture the complex coupling between flame
dynamics and acoustics.(c) 2022 The Combustion Institute. Published by
Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
simulations of thermo-acoustic instabilities of premixed flames. We
study flames interacting with an imposed acoustic field where flames
submitted to a parametric instability can be observed, as well as plane
flames re-stabilized by the acoustic forcing. Self-induced
thermo-acoustic oscillations of flames propagating in narrow channels
are also studied, indicating an unexpected dependency with the channel
width. For both excited and self-excited flames, results confirm that
Lattice-Boltzmann method can capture the complex coupling between flame
dynamics and acoustics.(c) 2022 The Combustion Institute. Published by
Elsevier Inc. All rights reserved.
M. Taha; S. Zhao; A. Lamorlette; J. L. Consalvi; P. Boivin
Lattice-Boltzmann modeling of buoyancy-driven turbulent flows Article de journal
Dans: PHYSICS OF FLUIDS, vol. 34, no. 5, 2022, ISSN: 1070-6631.
@article{WOS:000804941300001,
title = {Lattice-Boltzmann modeling of buoyancy-driven turbulent flows},
author = {M. Taha and S. Zhao and A. Lamorlette and J. L. Consalvi and P. Boivin},
doi = {10.1063/5.0088409},
issn = {1070-6631},
year = {2022},
date = {2022-05-01},
journal = {PHYSICS OF FLUIDS},
volume = {34},
number = {5},
abstract = {The pressure-based hybrid lattice-Boltzmann method presented by Farag et
al. [ ``A pressure-based regularized lattice-Boltzmann method for the
simulation of compressible flows, `` Phys. Fluids 32, 066106 (2020)] is
assessed for the simulation of buoyancy driven flows. The model is first
validated on Rayleigh-Benard and Rayleigh-Taylor two-dimensional cases.
A large-eddy simulation of a turbulent forced plume is then carried out,
and results are validated against experiments. Good overall agreement is
obtained, both for mean and fluctuation quantities, as well as global
entrainment. The self-similarity characteristic of the plume in the
far-field is also recovered.Published under an exclusive license by AIP
Publishing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
al. [ ``A pressure-based regularized lattice-Boltzmann method for the
simulation of compressible flows, `` Phys. Fluids 32, 066106 (2020)] is
assessed for the simulation of buoyancy driven flows. The model is first
validated on Rayleigh-Benard and Rayleigh-Taylor two-dimensional cases.
A large-eddy simulation of a turbulent forced plume is then carried out,
and results are validated against experiments. Good overall agreement is
obtained, both for mean and fluctuation quantities, as well as global
entrainment. The self-similarity characteristic of the plume in the
far-field is also recovered.Published under an exclusive license by AIP
Publishing.
Jianhua Fan; Li-Hua Luu; Pierre Philippe; Gildas Noury
Discharge rate characterization for submerged grains flowing through a hopper using DEM-LBM simulations Article de journal
Dans: POWDER TECHNOLOGY, vol. 404, 2022, ISSN: 0032-5910.
@article{WOS:000798221900004,
title = {Discharge rate characterization for submerged grains flowing through a
hopper using DEM-LBM simulations},
author = {Jianhua Fan and Li-Hua Luu and Pierre Philippe and Gildas Noury},
doi = {10.1016/j.powtec.2022.117421},
issn = {0032-5910},
year = {2022},
date = {2022-05-01},
journal = {POWDER TECHNOLOGY},
volume = {404},
abstract = {Submerged granular flows through an orifice were investigated
numerically in the context of sinkhole occur-rences during a flood due
to the presence of underground conduits. To account for fluid-solid
interaction at the pore-scale, we use a numerical modelling that
combines the Discrete Element Method (DEM) for the solid par-ticles with
the Lattice Boltzmann Method (LBM) for the fluid dynamics. The numerical
setup studied is a sub-merged granular discharge from a hopper, which is
shown to be particularly sensitive to hydraulic boundary conditions.
With a given choice of configuration, we performed a parametric study by
varying particle diameters, fluid viscosity and hopper orifice size,
enabling the exploration of the Archimedes number over five orders of
magnitude. The solid discharge rates are shown to have self-similar
temporal evolutions and the grains at the or-ifice display self-similar
velocity profiles, normalized by the maximum velocity reached at the
center of the ori-fice. In this paper, we finally propose an extension
of the classical Beverloo law that takes into account the effect of
fluid entrainment by the downward granular flow.(c) 2022 Elsevier B.V.
All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
numerically in the context of sinkhole occur-rences during a flood due
to the presence of underground conduits. To account for fluid-solid
interaction at the pore-scale, we use a numerical modelling that
combines the Discrete Element Method (DEM) for the solid par-ticles with
the Lattice Boltzmann Method (LBM) for the fluid dynamics. The numerical
setup studied is a sub-merged granular discharge from a hopper, which is
shown to be particularly sensitive to hydraulic boundary conditions.
With a given choice of configuration, we performed a parametric study by
varying particle diameters, fluid viscosity and hopper orifice size,
enabling the exploration of the Archimedes number over five orders of
magnitude. The solid discharge rates are shown to have self-similar
temporal evolutions and the grains at the or-ifice display self-similar
velocity profiles, normalized by the maximum velocity reached at the
center of the ori-fice. In this paper, we finally propose an extension
of the classical Beverloo law that takes into account the effect of
fluid entrainment by the downward granular flow.(c) 2022 Elsevier B.V.
All rights reserved.
G. Bonnet; E. Nezri; K. Kraljic; C. Schimd
Morphology of dark matter haloes beyond triaxiality Article de journal
Dans: MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, vol. 513, no. 4, p. 4929-4944, 2022, ISSN: 0035-8711.
@article{WOS:000798925200010,
title = {Morphology of dark matter haloes beyond triaxiality},
author = {G. Bonnet and E. Nezri and K. Kraljic and C. Schimd},
doi = {10.1093/mnras/stac1222},
issn = {0035-8711},
year = {2022},
date = {2022-05-01},
journal = {MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY},
volume = {513},
number = {4},
pages = {4929-4944},
abstract = {The morphology of haloes inform about both cosmological and galaxy
formation models. We use the Minkowski Functionals (MFs) to characterize
the actual morphology of haloes, only partially captured by smooth
density profile, going beyond the spherical or ellipsoidal symmetry. We
employ semi-analytical haloes with NFW and alpha beta gamma-profile and
spherical or ellipsoidal shape to obtain a clear interpretation of MFs
as function of inner and outer slope, concentration and sphericity
parameters. We use the same models to mimic the density profile of
N-body haloes, showing that their MFs clearly differ as sensitive to
internal substructures. This highlights the benefit of MFs at the halo
scales as promising statistics to improve the spatial modelling of dark
matter, crucial for future lensing, Sunyaev-Zel'dovich, and X-ray mass
maps as well as dark matter detection based on high-accuracy data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
formation models. We use the Minkowski Functionals (MFs) to characterize
the actual morphology of haloes, only partially captured by smooth
density profile, going beyond the spherical or ellipsoidal symmetry. We
employ semi-analytical haloes with NFW and alpha beta gamma-profile and
spherical or ellipsoidal shape to obtain a clear interpretation of MFs
as function of inner and outer slope, concentration and sphericity
parameters. We use the same models to mimic the density profile of
N-body haloes, showing that their MFs clearly differ as sensitive to
internal substructures. This highlights the benefit of MFs at the halo
scales as promising statistics to improve the spatial modelling of dark
matter, crucial for future lensing, Sunyaev-Zel'dovich, and X-ray mass
maps as well as dark matter detection based on high-accuracy data.
Ritam Mansour; Saikat Mukherjee; Max Jr. Pinheiro; Jennifer A. Noble; Christophe Jouvet; Mario Barbatti
Pre-Dewar structure modulates protonated azaindole photodynamics Article de journal
Dans: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 20, p. 12346-12353, 2022, ISSN: 1463-9076.
@article{WOS:000793891300001,
title = {Pre-Dewar structure modulates protonated azaindole photodynamics},
author = {Ritam Mansour and Saikat Mukherjee and Max Jr. Pinheiro and Jennifer A. Noble and Christophe Jouvet and Mario Barbatti},
doi = {10.1039/d2cp01056a},
issn = {1463-9076},
year = {2022},
date = {2022-05-01},
journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
volume = {24},
number = {20},
pages = {12346-12353},
abstract = {Recent experimental work revealed that the lifetime of the S-3 state of
protonated 7-azaindole is about ten times longer than that of protonated
6-azaindole. We simulated the nonradiative decay pathways of these
molecules using trajectory surface hopping dynamics after
photoexcitation into S-3 to elucidate the reason for this difference.
Both isomers mainly follow a common pi pi* relaxation pathway
involving multiple state crossings while coming down from S-3 to S-1 in
the subpicosecond time scale. However, the simulations reveal that the
excited-state topographies are such that while the 6-isomer can easily
access the region of nonadiabatic transitions, the internal conversion
of the 7-isomer is delayed by a pre-Dewar bond formation with a boat
conformation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
protonated 7-azaindole is about ten times longer than that of protonated
6-azaindole. We simulated the nonradiative decay pathways of these
molecules using trajectory surface hopping dynamics after
photoexcitation into S-3 to elucidate the reason for this difference.
Both isomers mainly follow a common pi pi* relaxation pathway
involving multiple state crossings while coming down from S-3 to S-1 in
the subpicosecond time scale. However, the simulations reveal that the
excited-state topographies are such that while the 6-isomer can easily
access the region of nonadiabatic transitions, the internal conversion
of the 7-isomer is delayed by a pre-Dewar bond formation with a boat
conformation.
Antoine Galko; Simon Gsell; Umberto D'Ortona; Laurent Morin; Julien Favier
Pulsated Herschel-Bulkley flows in two-dimensional channels: A model for mucus clearance devices Article de journal
Dans: PHYSICAL REVIEW FLUIDS, vol. 7, no. 5, 2022, ISSN: 2469-990X.
@article{WOS:000883226100001,
title = {Pulsated Herschel-Bulkley flows in two-dimensional channels: A model for
mucus clearance devices},
author = {Antoine Galko and Simon Gsell and Umberto D'Ortona and Laurent Morin and Julien Favier},
doi = {10.1103/PhysRevFluids.7.053301},
issn = {2469-990X},
year = {2022},
date = {2022-05-01},
journal = {PHYSICAL REVIEW FLUIDS},
volume = {7},
number = {5},
abstract = {Pressure oscillations applied to human airways can help patients to
evacuate bronchial mucus, a highly non-Newtonian gel. To explore the
fluid mechanics aspects of these therapies, we perform numerical
simulations of pulsated non-Newtonian fluids in two-dimensional
channels. The fluid rheology is modeled with the Herschel-Bulkley law,
reproducing two essential nonlinear mechanical properties of the mucus,
namely, the yield-stress and shear-thinning/thickening properties. The
flow dynamics is simulated using the lattice-Boltzmann method over large
ranges of the three main nondimensional parameters, i.e., the pulsation
rate or Womersley number a, the flow index n quantifying the
shear-thinning/thickening effect, and the Bingham number controlling the
yield stress. The ratio between the fluctuating and average parts of the
oscillatory forcing is examined through three typical cases: a purely
oscillating flow, a weakly oscillating flow, and a strongly oscillating
flow. For each configuration, specific sets of parameters are found to
have a drastic effect on the dynamics of mucus plugs, which suggests new
therapeutic strategies for patients suffering from bronchial
obstructions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
evacuate bronchial mucus, a highly non-Newtonian gel. To explore the
fluid mechanics aspects of these therapies, we perform numerical
simulations of pulsated non-Newtonian fluids in two-dimensional
channels. The fluid rheology is modeled with the Herschel-Bulkley law,
reproducing two essential nonlinear mechanical properties of the mucus,
namely, the yield-stress and shear-thinning/thickening properties. The
flow dynamics is simulated using the lattice-Boltzmann method over large
ranges of the three main nondimensional parameters, i.e., the pulsation
rate or Womersley number a, the flow index n quantifying the
shear-thinning/thickening effect, and the Bingham number controlling the
yield stress. The ratio between the fluctuating and average parts of the
oscillatory forcing is examined through three typical cases: a purely
oscillating flow, a weakly oscillating flow, and a strongly oscillating
flow. For each configuration, specific sets of parameters are found to
have a drastic effect on the dynamics of mucus plugs, which suggests new
therapeutic strategies for patients suffering from bronchial
obstructions.
G. Wissocq; T. Coratger; G. Farag; S. Zhao; P. Boivin; P. Sagaut
Restoring the conservativity of characteristic-based segregated models: Application to the hybrid lattice Boltzmann method Article de journal
Dans: PHYSICS OF FLUIDS, vol. 34, no. 4, 2022, ISSN: 1070-6631.
@article{WOS:000832204400011,
title = {Restoring the conservativity of characteristic-based segregated models:
Application to the hybrid lattice Boltzmann method},
author = {G. Wissocq and T. Coratger and G. Farag and S. Zhao and P. Boivin and P. Sagaut},
doi = {10.1063/5.0083377},
issn = {1070-6631},
year = {2022},
date = {2022-04-01},
journal = {PHYSICS OF FLUIDS},
volume = {34},
number = {4},
abstract = {A general methodology is introduced to build conservative numerical
models for fluid simulations based on segregated schemes, where mass,
momentum, and energy equations are solved by different methods. It is
especially designed here for developing new numerical discretizations of
the total energy equation and adapted to a thermal coupling with the
lattice Boltzmann method (LBM). The proposed methodology is based on a
linear equivalence with standard discretizations of the entropy
equation, which, as a characteristic variable of the Euler system,
allows efficiently decoupling the energy equation with the LBM. To this
extent, any LBM scheme is equivalently written under a finite-volume
formulation involving fluxes, which are further included in the total
energy equation as numerical corrections. The viscous heat production is
implicitly considered thanks to the knowledge of the LBM momentum flux.
Three models are subsequently derived: a first-order upwind, a
Lax-Wendroff, and a third-order Godunov-type schemes. They are assessed
on standard academic test cases: a Couette flow, entropy spot and vortex
convections, a Sod shock tube, several two-dimensional Riemann problems,
and a shock-vortex interaction. Three key features are then exhibited:
(1) the models are conservative by construction, recovering correct jump
relations across shock waves; (2) the stability and accuracy of entropy
modes can be explicitly controlled; and (3) the low dissipation of the
LBM for isentropic phenomena is preserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
models for fluid simulations based on segregated schemes, where mass,
momentum, and energy equations are solved by different methods. It is
especially designed here for developing new numerical discretizations of
the total energy equation and adapted to a thermal coupling with the
lattice Boltzmann method (LBM). The proposed methodology is based on a
linear equivalence with standard discretizations of the entropy
equation, which, as a characteristic variable of the Euler system,
allows efficiently decoupling the energy equation with the LBM. To this
extent, any LBM scheme is equivalently written under a finite-volume
formulation involving fluxes, which are further included in the total
energy equation as numerical corrections. The viscous heat production is
implicitly considered thanks to the knowledge of the LBM momentum flux.
Three models are subsequently derived: a first-order upwind, a
Lax-Wendroff, and a third-order Godunov-type schemes. They are assessed
on standard academic test cases: a Couette flow, entropy spot and vortex
convections, a Sod shock tube, several two-dimensional Riemann problems,
and a shock-vortex interaction. Three key features are then exhibited:
(1) the models are conservative by construction, recovering correct jump
relations across shock waves; (2) the stability and accuracy of entropy
modes can be explicitly controlled; and (3) the low dissipation of the
LBM for isentropic phenomena is preserved.
Hung Truong; Thomas Engels; Henja Wehmann; Dmitry Kolomenskiy; Fritz-Olaf Lehmann; Kai Schneider
An experimental data-driven mass-spring model of flexible Calliphora wings Article de journal
Dans: BIOINSPIRATION & BIOMIMETICS, vol. 17, no. 2, 2022, ISSN: 1748-3182.
@article{WOS:000746697400001,
title = {An experimental data-driven mass-spring model of flexible Calliphora
wings},
author = {Hung Truong and Thomas Engels and Henja Wehmann and Dmitry Kolomenskiy and Fritz-Olaf Lehmann and Kai Schneider},
doi = {10.1088/1748-3190/ac2f56},
issn = {1748-3182},
year = {2022},
date = {2022-03-01},
journal = {BIOINSPIRATION & BIOMIMETICS},
volume = {17},
number = {2},
publisher = {IOP Publishing Ltd},
address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},
abstract = {Insect wings can undergo significant deformation during flapping motion
owing to inertial, elastic and aerodynamic forces. Changes in shape then
alter aerodynamic forces, resulting in a fully coupled fluid-structure
interaction (FSI) problem. Here, we present detailed three-dimensional
FSI simulations of deformable blowfly (Calliphora vomitoria) wings in
flapping flight. A wing model is proposed using a multi-parameter
mass-spring approach, chosen for its implementation simplicity and
computational efficiency. We train the model to reproduce static
elasticity measurements by optimizing its parameters using a genetic
algorithm with covariance matrix adaptation (CMA-ES). Wing models
trained with experimental data are then coupled to a high-performance
flow solver run on massively parallel supercomputers. Different features
of the modeling approach and the intra-species variability of elastic
properties are discussed. We found that individuals with different wing
stiffness exhibit similar aerodynamic properties characterized by
dimensionless forces and power at the same Reynolds number. We further
study the influence of wing flexibility by comparing between the
flexible wings and their rigid counterparts. Under equal prescribed
kinematic conditions for rigid and flexible wings, wing flexibility
improves lift-to-drag ratio as well as lift-to-power ratio and reduces
peak force observed during wing rotation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
owing to inertial, elastic and aerodynamic forces. Changes in shape then
alter aerodynamic forces, resulting in a fully coupled fluid-structure
interaction (FSI) problem. Here, we present detailed three-dimensional
FSI simulations of deformable blowfly (Calliphora vomitoria) wings in
flapping flight. A wing model is proposed using a multi-parameter
mass-spring approach, chosen for its implementation simplicity and
computational efficiency. We train the model to reproduce static
elasticity measurements by optimizing its parameters using a genetic
algorithm with covariance matrix adaptation (CMA-ES). Wing models
trained with experimental data are then coupled to a high-performance
flow solver run on massively parallel supercomputers. Different features
of the modeling approach and the intra-species variability of elastic
properties are discussed. We found that individuals with different wing
stiffness exhibit similar aerodynamic properties characterized by
dimensionless forces and power at the same Reynolds number. We further
study the influence of wing flexibility by comparing between the
flexible wings and their rigid counterparts. Under equal prescribed
kinematic conditions for rigid and flexible wings, wing flexibility
improves lift-to-drag ratio as well as lift-to-power ratio and reduces
peak force observed during wing rotation.
H Bufferand; J Balbin; S Baschetti; J Bucalossi; G Ciraolo; Ph Ghendrih; R Mao; N Rivals; P Tamain; H Yang; G Giorgiani; F Schwander; M Scotto d'Abusco; E Serre; J Denis; Y Marandet; M Raghunathan; P Innocente; D Galassi
Implementation of multi-component Zhdanov closure in SOLEDGE3X Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 64, no. 5, p. 055001, 2022.
@article{Bufferand_2022,
title = {Implementation of multi-component Zhdanov closure in SOLEDGE3X},
author = {H Bufferand and J Balbin and S Baschetti and J Bucalossi and G Ciraolo and Ph Ghendrih and R Mao and N Rivals and P Tamain and H Yang and G Giorgiani and F Schwander and M Scotto d'Abusco and E Serre and J Denis and Y Marandet and M Raghunathan and P Innocente and D Galassi},
url = {https://doi.org/10.1088/1361-6587/ac4fac},
doi = {10.1088/1361-6587/ac4fac},
year = {2022},
date = {2022-03-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {64},
number = {5},
pages = {055001},
publisher = {IOP Publishing},
abstract = {The multi-component fluid closure derived by Zhdanov (2002 Transport Processes in Multicomponent Plasma (London: Taylor and Francis)) is implemented in the fluid code SOLEDGE3X-EIRENE to deal with arbitrary edge plasma composition. The closure assumes no distinction between species such as light versus heavy species separation. The work of Zhdanov is rewritten in a matricial form in order to clearly link friction forces and heat fluxes to the different species velocities and temperature gradients.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sara Scaramuzzino; Delphine Potier; Robin Ordioni; Pierre Grenot; Dominique Payet-Bornet; Herve Luche; Bernard Malissen
Single-cell transcriptomics uncovers an instructive T-cell receptor role in adult gamma delta T-cell lineage commitment Article de journal
Dans: EMBO JOURNAL, 2022, ISSN: 0261-4189.
@article{WOS:000751809800001c,
title = {Single-cell transcriptomics uncovers an instructive T-cell receptor role in adult gamma delta T-cell lineage commitment},
author = {Sara Scaramuzzino and Delphine Potier and Robin Ordioni and Pierre Grenot and Dominique Payet-Bornet and Herve Luche and Bernard Malissen},
doi = {10.15252/embj.2021110023},
issn = {0261-4189},
year = {2022},
date = {2022-02-17},
journal = {EMBO JOURNAL},
abstract = {After entering the adult thymus, bipotent T-cell progenitors give rise
to alpha beta or gamma delta T cells. To determine whether the gamma
delta T-cell receptor (TCR) has an instructive role in gamma delta
T-cell lineage commitment or only ``confirms'' a pre-established gamma
delta T-cell lineage state, we exploited mice lacking expression of LAT,
an adaptor required for gamma delta TCR signaling. Although these mice
showed a T-cell development block at the CD4(-)CD8(-) double-negative
third (DN3) stage, 0.3% of their DN3 cells expressed intermediate
levels of gamma delta TCR (further referred to as gamma delta(int)) at
their surface. Single-cell transcriptomics of LAT-deficient DN3 gamma
delta(int) cells demonstrated no sign of commitment to the gamma delta
T-cell lineage, apart from gamma delta TCR expression. Although the lack
of LAT is thought to tightly block DN3 cell development, we unexpectedly
found that 25% of LAT-deficient DN3 gamma delta(int) cells were
actively proliferating and progressed up to the DN4 stage. However, even
those cells failed to turn on the transcriptional program associated
with the gamma delta T-cell lineage. Therefore, the gamma delta TCR-LAT
signaling axis builds upon a yi5 T-cell uncommitted lineage state to
fully instruct adult gamma delta T-cell lineage specification.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
to alpha beta or gamma delta T cells. To determine whether the gamma
delta T-cell receptor (TCR) has an instructive role in gamma delta
T-cell lineage commitment or only ``confirms'' a pre-established gamma
delta T-cell lineage state, we exploited mice lacking expression of LAT,
an adaptor required for gamma delta TCR signaling. Although these mice
showed a T-cell development block at the CD4(-)CD8(-) double-negative
third (DN3) stage, 0.3% of their DN3 cells expressed intermediate
levels of gamma delta TCR (further referred to as gamma delta(int)) at
their surface. Single-cell transcriptomics of LAT-deficient DN3 gamma
delta(int) cells demonstrated no sign of commitment to the gamma delta
T-cell lineage, apart from gamma delta TCR expression. Although the lack
of LAT is thought to tightly block DN3 cell development, we unexpectedly
found that 25% of LAT-deficient DN3 gamma delta(int) cells were
actively proliferating and progressed up to the DN4 stage. However, even
those cells failed to turn on the transcriptional program associated
with the gamma delta T-cell lineage. Therefore, the gamma delta TCR-LAT
signaling axis builds upon a yi5 T-cell uncommitted lineage state to
fully instruct adult gamma delta T-cell lineage specification.
Umberto D'Ortona; Nathalie Thomas; Richard M. Lueptow
Mechanisms for recirculation cells in granular flows in rotating cylindrical rough tumblers Article de journal
Dans: Physical Review E, vol. 105, no. 1, 2022, ISSN: 2470-0053.
@article{2022,
title = {Mechanisms for recirculation cells in granular flows in rotating cylindrical rough tumblers},
author = {Umberto D'Ortona and Nathalie Thomas and Richard M. Lueptow},
url = {http://dx.doi.org/10.1103/PhysRevE.105.014901},
doi = {10.1103/physreve.105.014901},
issn = {2470-0053},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Physical Review E},
volume = {105},
number = {1},
publisher = {American Physical Society (APS)},
abstract = {Friction at the endwalls of partially-filled horizontal rotating tumblers induces curvature and axial drift of particle trajectories in the surface flowing layer. Here we describe the results of a detailed discrete element method study of the dry granular flow of monodisperse particles in threedimensional cylindrical tumblers with endwalls and cylindrical wall that can be either smooth or rough. Endwall roughness induces more curved particle trajectories, while a smooth cylindrical wall enhances drift near the endwall. This drift induces recirculation cells near the endwall. The use of mixed roughness (cylindrical wall and endwalls having different roughness) shows the influence of each wall on the drift and curvature of particle trajectories as well as the modification of the free surface topography. The effects act in opposite directions and have variable magnitude along the length of the tumbler such that their sum determines both direction of net drift and the recirculation cells. Near the endwalls, the dominant effect is always the endwall effect, and the axial drift for surface particles is toward the endwalls. For long enough tumblers, a counter-rotating cell occurs adjacent to each of the endwall cells having a surface drift toward the center because the cylindrical wall effect is dominant there. These cells are not dynamically coupled with the two endwall cells. The competition between the drifts induced by the endwalls and the cylindrical wall determines the width and drift amplitude for both types of cells. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Elena Alekseenko; Bernard Roux; Konstantin Kuznetsov
Wind-Induced Resuspension and Transport of Contaminated Sediment from the Rove Canal into the Etang De Berre, France Article de journal
Dans: Water, vol. 14, no. 1, 2022, ISSN: 2073-4441.
@article{w14010062,
title = {Wind-Induced Resuspension and Transport of Contaminated Sediment from the Rove Canal into the Etang De Berre, France},
author = {Elena Alekseenko and Bernard Roux and Konstantin Kuznetsov},
url = {https://www.mdpi.com/2073-4441/14/1/62},
doi = {10.3390/w14010062},
issn = {2073-4441},
year = {2022},
date = {2022-01-01},
journal = {Water},
volume = {14},
number = {1},
abstract = {The present study concerns the erosion and transport of severely contaminated sediments in a Canal. It begins in the context of an engineering project aimed to re-introduce a forced convection at the entrance of this Canal by pumping marine water. The local wind is often strong enough to overpass the resuspension threshold; thus, there is a serious risk of downstream contamination of a Mediterranean lagoon. So, the goal is to evaluate this risk as a function of the pumping rate; this contamination is transported by the fine suspended particles. Different scenarios are investigated to determine the downstream transport of suspensions in terms of runoff. These scenarios (of 24 h) contains a succession of 3 periods: constant wind speed, wind slowdown and calm, for two opposite wind directions. Special attention is devoted to the modeling of complex mechanisms of erosion and resuspension during wind periods, deposition during windless periods and sediment consolidation. The main results concern the total flux of the suspended particles through the exit of the Canal at the confluence with the lagoon. It is shown that even for moderate runoff (<6 m3/s) this total flux is large enough, not only during the wind period, but also after several hours of calm.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M. Bouffard; B. Favier; D. Lecoanet; M. Le Bars
Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell Article de journal
Dans: GEOPHYSICAL JOURNAL INTERNATIONAL, vol. 228, no. 1, p. 337-354, 2022, ISSN: 0956-540X.
@article{WOS:000697391500020,
title = {Internal gravity waves in a stratified layer atop a convecting liquid
core in a non-rotating spherical shell},
author = {M. Bouffard and B. Favier and D. Lecoanet and M. Le Bars},
doi = {10.1093/gji/ggab343},
issn = {0956-540X},
year = {2022},
date = {2022-01-01},
journal = {GEOPHYSICAL JOURNAL INTERNATIONAL},
volume = {228},
number = {1},
pages = {337-354},
abstract = {Seismic and magnetic observations have suggested the presence of a
stably stratified layer atop Earth's core. Such a layer could affect the
morphology of the geomagnetic field and the evolution of the core, but
the precise impact of this layer depends largely on its internal
dynamics. Among other physical phenomena, stratified layers host
internal gravity waves (IGW), which can be excited by adjacent
convective motions. Internal waves are known to play an important role
on the large-scale dynamics of the Earth's climate and on the long-term
evolution of stars. Yet, they have received relatively little attention
in the Earth's outer core so far and deserve detailed investigations in
this context. Here, we make a first step in that direction by running
numerical simulations of IGW in a non-rotating spherical shell in which
a stratified layer lies on top of a convective region. We use a
nonlinear equation of state to produce self-consistently such a
two-layer system. Both propagating waves and global modes coexist in the
stratified layer. We characterize the spectral properties of these waves
and find that energy is distributed across a wide range of frequencies
and length scales, that depends on the Prandtl number. For the control
parameters considered and in the absence of rotational and magnetic
effects, the mean kinetic energy in the layer is about 0.1 percent that
of the convective region. IGW produce perturbations in the gravity field
that may fall within the sensitivity limit of present-day instruments
and could potentially be detected in available data. We finally provide
a road map for future, more geophysically realistic, studies towards a
more thorough understanding of the dynamics and impact of internal waves
in a stratified layer atop Earth's core.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
stably stratified layer atop Earth's core. Such a layer could affect the
morphology of the geomagnetic field and the evolution of the core, but
the precise impact of this layer depends largely on its internal
dynamics. Among other physical phenomena, stratified layers host
internal gravity waves (IGW), which can be excited by adjacent
convective motions. Internal waves are known to play an important role
on the large-scale dynamics of the Earth's climate and on the long-term
evolution of stars. Yet, they have received relatively little attention
in the Earth's outer core so far and deserve detailed investigations in
this context. Here, we make a first step in that direction by running
numerical simulations of IGW in a non-rotating spherical shell in which
a stratified layer lies on top of a convective region. We use a
nonlinear equation of state to produce self-consistently such a
two-layer system. Both propagating waves and global modes coexist in the
stratified layer. We characterize the spectral properties of these waves
and find that energy is distributed across a wide range of frequencies
and length scales, that depends on the Prandtl number. For the control
parameters considered and in the absence of rotational and magnetic
effects, the mean kinetic energy in the layer is about 0.1 percent that
of the convective region. IGW produce perturbations in the gravity field
that may fall within the sensitivity limit of present-day instruments
and could potentially be detected in available data. We finally provide
a road map for future, more geophysically realistic, studies towards a
more thorough understanding of the dynamics and impact of internal waves
in a stratified layer atop Earth's core.
Karthik Bhairapurada; Bruno Denet; Pierre Boivin
A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities Article de journal
Dans: Combustion and Flame, vol. 240, p. 112049, 2022, ISSN: 0010-2180.
@article{BHAIRAPURADA2022112049,
title = {A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities},
author = {Karthik Bhairapurada and Bruno Denet and Pierre Boivin},
url = {https://www.sciencedirect.com/science/article/pii/S0010218022000682},
doi = {https://doi.org/10.1016/j.combustflame.2022.112049},
issn = {0010-2180},
year = {2022},
date = {2022-01-01},
journal = {Combustion and Flame},
volume = {240},
pages = {112049},
abstract = {We present possibly for the first time Lattice-Boltzmann numerical simulations of thermo-acoustic instabilities of premixed flames. We study flames interacting with an imposed acoustic field where flames submitted to a parametric instability can be observed, as well as plane flames re-stabilized by the acoustic forcing. Self-induced thermo-acoustic oscillations of flames propagating in narrow channels are also studied, indicating an unexpected dependency with the channel width. For both excited and self-excited flames, results confirm that Lattice-Boltzmann method can capture the complex coupling between flame dynamics and acoustics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Paul Eymeoud; Liangzhao Huang; Philippe Maugis
Impact of Ni alloying on Fe-C martensite ageing: an atomistic investigation Article de journal
Dans: Scripta materialia, vol. 205, 2021, ISSN: 1359-6462.
@article{WOS:000692550000006,
title = {Impact of Ni alloying on Fe-C martensite ageing: an atomistic investigation},
author = {Paul Eymeoud and Liangzhao Huang and Philippe Maugis},
doi = {10.1016/j.scriptamat.2021.114182},
issn = {1359-6462},
year = {2021},
date = {2021-12-01},
journal = {Scripta materialia},
volume = {205},
abstract = {We propose a computational investigation of Ni-alloying impact on Fe-C
martensite ageing, at the atomic scale. Using the Climbing Image Nudged
Elastic Band technique, we showed the repulsive nature of NiC pairwise
interactions in alpha-iron, and demonstrated that Ni alloying lowers the
migration energies and force dipole tensor components associated to an
interstitial carbon in alpha-iron. Computed values of pair wise
interactions, migration energies and dipole components were used to
implement a Kinetic Monte Carlo approach. We found that Ni alloying: (i)
has negligible impact on martensite thermodynamical stability, (ii)
accelerates ageing kinetics, by increasing carbon diffusivity. (C) 2021
Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
martensite ageing, at the atomic scale. Using the Climbing Image Nudged
Elastic Band technique, we showed the repulsive nature of NiC pairwise
interactions in alpha-iron, and demonstrated that Ni alloying lowers the
migration energies and force dipole tensor components associated to an
interstitial carbon in alpha-iron. Computed values of pair wise
interactions, migration energies and dipole components were used to
implement a Kinetic Monte Carlo approach. We found that Ni alloying: (i)
has negligible impact on martensite thermodynamical stability, (ii)
accelerates ageing kinetics, by increasing carbon diffusivity. (C) 2021
Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
T. Coratger; G. Farag; S. Zhao; Pierre Boivin; P. Sagaut
Large-eddy lattice-Boltzmann modeling of transonic flows Article de journal
Dans: Physics of Fluids, vol. 33, no. 11, p. 115112, 2021.
@article{coratger:hal-03424286,
title = {Large-eddy lattice-Boltzmann modeling of transonic flows},
author = {T. Coratger and G. Farag and S. Zhao and Pierre Boivin and P. Sagaut},
url = {https://hal.archives-ouvertes.fr/hal-03424286},
doi = {10.1063/5.0064944},
year = {2021},
date = {2021-11-01},
urldate = {2021-11-01},
journal = {Physics of Fluids},
volume = {33},
number = {11},
pages = {115112},
publisher = {American Institute of Physics},
abstract = {A D3Q19 hybrid recursive regularized pressure based lattice-Boltzmann method (HRR-P LBM) is assessed for the simulation of complex transonic flows. Mass and momentum conservation equations are resolved through a classical LBM solver coupled with a finite volume resolution of entropy equation for a complete compressible solver preserving stability, accuracy, and computational costs. An efficient treatment for wall and open boundaries is coupled with a grid refinement technique and extended to the HRR-P LBM in the scope of compressible aerodynamics. A Vreman subgrid turbulence model and an improved coupling of immersed boundary method with turbulence wall model on Cartesian grid accounts for unresolved scales by large-eddy simulation. The validity of the present method for transonic applications is investigated through various test cases with increasing complexity starting from an inviscid flow over a 10% bump and ending with a turbulent flow over a ONERA M6 three-dimensional wing.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Guanxiong Wang; Lincheng Xu; Eric Serre; Pierre Sagaut
Large temperature difference heat dominated flow simulations using a pressure-based lattice Boltzmann method with mass correction Article de journal
Dans: Physics of Fluids, vol. 33, no. 11, p. 116107, 2021.
@article{wang:hal-03438869,
title = {Large temperature difference heat dominated flow simulations using a pressure-based lattice Boltzmann method with mass correction},
author = {Guanxiong Wang and Lincheng Xu and Eric Serre and Pierre Sagaut},
url = {https://hal.archives-ouvertes.fr/hal-03438869},
doi = {10.1063/5.0073178},
year = {2021},
date = {2021-11-01},
urldate = {2021-11-01},
journal = {Physics of Fluids},
volume = {33},
number = {11},
pages = {116107},
publisher = {American Institute of Physics},
abstract = {This paper addresses simulation of heat dominated compressible flows in a closed cavity using a pressure-based lattice Boltzmann (LB) method, in which thermal effects are modeled by applying a pressure-featured zero-order moment of distribution functions. A focus is made on the conservation of mass at boundary nodes, which is a challenging issue that significantly complicated by the density-decoupled zero-order moment here. The mass leakage at boundary nodes is mathematically quantified, which enables an efficient local mass correction scheme. The performance of this solver is assessed by simulating buoyancy-driven flows in a closed deferentially heated cavity with large temperature differences (non-Boussinesq) at Rayleigh numbers ranging from 10³ to 10⁷. Simulations show that mass leakage at solid walls in such configurations is a critical issue to obtain reliable solutions, and it eventually leads to simulations overflow when the cavity is inclined. The proposed mass correction scheme is, however, shown to be effective to control the mass leakage and get accurate solutions. Thus, associated with the proposed mass conservation scheme, the pressure-based LB method becomes reliable to study natural convection dominated flows at large temperature differences in closed geometries with mesh aligned boundaries or not.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
E A Hodille; R Delaporte-Mathurin; J Denis; M Pecovnik; E Bernard; Y Ferro; R Sakamoto; Y Charles; J Mougenot; De A Backer; C S Becquart; S Markelj; C Grisolia
Modelling of hydrogen isotopes trapping, diffusion and permeation in divertor monoblocks under ITER-like conditions Article de journal
Dans: vol. 61, no. 12, p. 126003, 2021.
@article{2021j,
title = {Modelling of hydrogen isotopes trapping, diffusion and permeation in divertor monoblocks under ITER-like conditions},
author = {E A Hodille and R Delaporte-Mathurin and J Denis and M Pecovnik and E Bernard and Y Ferro and R Sakamoto and Y Charles and J Mougenot and De A Backer and C S Becquart and S Markelj and C Grisolia},
url = {https://doi.org/10.1088/1741-4326/ac2abc},
doi = {10.1088/1741-4326/ac2abc},
year = {2021},
date = {2021-10-01},
volume = {61},
number = {12},
pages = {126003},
publisher = {IOP Publishing},
abstract = {In this work, the deuterium (D) retention in plasma facing components of the divertor of ITER is estimated. Three scenarios are simulated with 3 different surface temperatures, 1456 K, 870 K and 435 K. They represent the exposure of different parts of the divertor during an attached plasma. Our 1D rate equation code MHIMS (migration of hydrogen in materials) is used to model the retention in the super-saturated layer formed in the first 10 nm: the D retention integrated in this 10 nm-layer is ≈1019 D m−2 for the coldest scenarios. It is also used to differentiate the evolution of deuterium retention during pulsed and continuous plasma exposures which shows that: (i) there is a retention during the ramp-down in the first 10 μm which is released during the ramp up and (ii) the bulk retention is not affected by the cycling of plasma exposure. The concentration of mobile deuterium in the implantation zone is used as an input of our finite element code FESTIM (finite element simulation of tritium in materials) which is used to assess the deuterium retention and migration in the 2D complex geometry of the actively cooled plasma facing components. In the end, this work enable to determine the three following macroscopic quantities: the total deuterium retention, the permeation flux to the cooling pipe and the desorption flux from the toroidal edges of the components. It is shown that (i) the coldest scenario leads to the highest retention despite the lowest exposure flux which has already been observed in past retention studies, (ii) the permeation to the cooling pipes happens after few thousands of seconds only for the hottest scenario, (iii) the release of deuterium from the toroidal edges is a small fuel recycling source.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hung Truong; Thomas Engels; Henja Wehmann; Dmitry Kolomenskiy; Fritz-Olaf Lehmann; Kai Schneider
An experimental data-driven mass-spring model of flexible Calliphora wings Article de journal
Dans: Bioinspiration & Biomimetics, 2021.
@article{Truong_2021,
title = {An experimental data-driven mass-spring model of flexible Calliphora wings},
author = {Hung Truong and Thomas Engels and Henja Wehmann and Dmitry Kolomenskiy and Fritz-Olaf Lehmann and Kai Schneider},
url = {https://doi.org/10.1088/1748-3190/ac2f56},
doi = {10.1088/1748-3190/ac2f56},
year = {2021},
date = {2021-10-01},
urldate = {2021-10-01},
journal = {Bioinspiration & Biomimetics},
publisher = {IOP Publishing},
abstract = {Insect wings can undergo significant deformation during flapping motion owing to inertial, elastic and aerodynamic forces. Changes in shape then alter aerodynamic forces, resulting in a fully coupled fluid–structure interaction (FSI) problem. Here, we present detailed three-dimensional FSI simulations of deformable blowfly (Calliphora vomitoria) wings in flapping flight. A wing model is proposed using a multi-parameter mass-spring approach, chosen for its implementation simplicity and computational efficiency. We train the model to reproduce static elasticity measurements by optimizing its parameters using a genetic algorithm with covariance matrix adaptation (CMA-ES). Wing models trained with experimental data are then coupled to a high-performance flow solver run on massively parallel supercomputers. Different features of the modeling approach and the intra-species variability of elastic properties are discussed. We found that individuals with different wing stiffness exhibit similar aerodynamic properties characterized by dimensionless forces and power at the same Reynolds number. We further study the influence of wing flexibility by comparing between the flexible wings and their rigid counterparts. Under equal prescribed kinematic conditions for rigid and flexible wings, wing flexibility improves lift-to-drag ratio as well as lift-to-power ratio and reduces peak force observed during wing rotation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
J V Gomes; M C de Sousa; R L Viana; I L Caldas; Y Elskens
Low-dimensional chaos in the single wave model for self-consistent wave particle Hamiltonian Article de journal
Dans: Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 31, no. 8, p. 083104, 2021, ISSN: 1089-7682.
@article{Gomes_2021,
title = {Low-dimensional chaos in the single wave model for self-consistent wave particle Hamiltonian},
author = {J V Gomes and M C de Sousa and R L Viana and I L Caldas and Y Elskens},
url = {http://dx.doi.org/10.1063/5.0040939},
doi = {10.1063/5.0040939},
issn = {1089-7682},
year = {2021},
date = {2021-08-01},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
volume = {31},
number = {8},
pages = {083104},
publisher = {AIP Publishing},
abstract = {We analyze nonlinear aspects of the self-consistent wave-particle interaction using Hamiltonian dynamics in the single wave model, where the wave is modified due to the particle dynamics. This interaction plays an important role in the emergence of plasma instabilities and turbulence. The simplest case, where one particle (N = 1) is coupled with one wave (M = 1), is completely integrable, and the nonlinear effects reduce to the wave potential pulsating while the particle either remains trapped or circulates forever. On increasing the number of particles (N = 2, M = 1), integrability is lost and chaos develops. Our analyses identify the two standard ways for chaos to appear and grow (the homoclinic tangle born from a separatrix, and the resonance overlap near an elliptic fixed point). Moreover, a strong form of chaos occurs when the energy is high enough for the wave amplitude to vanish occasionally. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sudip Das; Marc Jaeger; Marc Leonetti; Rochish M Thaokar; Paul G Chen
Effect of pulse width on the dynamics of a deflated vesicle in unipolar and bipolar pulsed electric fields Article de journal
Dans: Physics of Fluids, vol. 33, no. 8, p. 081905, 2021, ISSN: 1089-7666.
@article{Das_2021,
title = {Effect of pulse width on the dynamics of a deflated vesicle in unipolar and bipolar pulsed electric fields},
author = {Sudip Das and Marc Jaeger and Marc Leonetti and Rochish M Thaokar and Paul G Chen},
url = {http://dx.doi.org/10.1063/5.0057168},
doi = {10.1063/5.0057168},
issn = {1089-7666},
year = {2021},
date = {2021-08-01},
journal = {Physics of Fluids},
volume = {33},
number = {8},
pages = {081905},
publisher = {AIP Publishing},
abstract = {Giant unilamellar vesicles subjected to pulsed direct-current (pulsed-DC) fields are promising biomimetic systems to investigate the electroporation of cells. In strong electric fields, vesicles undergo significant deformation, which strongly alters the transmembrane potential, consequently the electroporation. Previous theoretical studies investigated the electrodeformation of vesicles in DC fields (which are not pulsed). In this work, we computationally investigate the deformation of a deflated vesicle under unipolar, bipolar, and two-step unipolar pulses and show sensitive dependence of intermediate shapes on type of pulse and the pulse width. Starting with the stress-free initial shape of a deflated vesicle, which is similar to a prolate spheroid, the analysis is presented for the cases with higher and lower conductivities of the inner fluid medium relative to the outer fluid medium. For the ratio of inner to outer fluid conductivity, σr = 10, the shape always remains prolate, including when the field is turned off. For σr=0.1, several complex dynamics are observed, such as the prolate-to-oblate (PO), prolate-to-oblate-to-prolate (POP) shape transitions in time depending upon the strength of the field and the pulse properties. In this case, on turning off the field, a metastable oblate equilibrium shape is seen, that seems to be a characteristics of a deflated vesicle leading to POPO transitions. When a two-step unipolar pulse (a combination of a strong and a weak subpulse) is applied, a vesicle can reach an oblate or a prolate final shape depending upon the relative durations of the two subpulses. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Elisa Buffa; Jerome Jacob; Pierre Sagaut
Lattice-Boltzmann-based large-eddy simulation of high-rise building aerodynamics with inlet turbulence reconstruction Article de journal
Dans: Journal of wind engineering and industrial aerodynamics, vol. 212, 2021, ISSN: 0167-6105.
@article{WOS:000692557000001,
title = {Lattice-Boltzmann-based large-eddy simulation of high-rise building aerodynamics with inlet turbulence reconstruction},
author = {Elisa Buffa and Jerome Jacob and Pierre Sagaut},
doi = {10.1016/j.jweia.2021.104560},
issn = {0167-6105},
year = {2021},
date = {2021-05-01},
journal = {Journal of wind engineering and industrial aerodynamics},
volume = {212},
abstract = {A Lattice-Boltzmann-based Large-Eddy Simulation approach for wind load
prediction on high-rise building is proposed and validated. An extension
of the original incompressible Synthetic Eddy Method to reconstruct
inlet turbulence is proposed within the Lattice-Boltzmann framework,
including a low-noise frozen density variant. Extensive successful
comparisons with experimental data are carried out, for both quantities
defined on the building surface and in its wake. A detailed sensitivity
analysis of the results with respect to inlet turbulence reconstruction,
boundary conditions at the building surface and grid resolution is also
provided. An almost unique set of comparisons with experimental data is
presented, including mean and rms values, spectra, but also peak values
of pressure at the building surface.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
prediction on high-rise building is proposed and validated. An extension
of the original incompressible Synthetic Eddy Method to reconstruct
inlet turbulence is proposed within the Lattice-Boltzmann framework,
including a low-noise frozen density variant. Extensive successful
comparisons with experimental data are carried out, for both quantities
defined on the building surface and in its wake. A detailed sensitivity
analysis of the results with respect to inlet turbulence reconstruction,
boundary conditions at the building surface and grid resolution is also
provided. An almost unique set of comparisons with experimental data is
presented, including mean and rms values, spectra, but also peak values
of pressure at the building surface.
Katherine M Xiang; David M Nataf; E Athanassoula; Nadia L Zakamska; Kate Rowlands; Karen Masters; Amelia Fraser-McKelvie; Niv Drory; Katarina Kraljic
Buckling Bars in Nearly Face-on Galaxies Observed with MaNGA Article de journal
Dans: The Astrophysical Journal, vol. 909, no. 2, p. 125, 2021, ISSN: 1538-4357.
@article{Xiang_2021,
title = {Buckling Bars in Nearly Face-on Galaxies Observed with MaNGA},
author = {Katherine M Xiang and David M Nataf and E Athanassoula and Nadia L Zakamska and Kate Rowlands and Karen Masters and Amelia Fraser-McKelvie and Niv Drory and Katarina Kraljic},
url = {http://dx.doi.org/10.3847/1538-4357/abdab5},
doi = {10.3847/1538-4357/abdab5},
issn = {1538-4357},
year = {2021},
date = {2021-03-01},
journal = {The Astrophysical Journal},
volume = {909},
number = {2},
pages = {125},
publisher = {American Astronomical Society},
abstract = {Over half of disk galaxies are barred, yet the mechanisms for bar formation and the life-time of bar buckling remain poorly understood. In simulations, a thin bar undergoes a rapid (<1 Gyr) event called "buckling," during which the inner part of the bar is asymmetrically bent out of the galaxy plane and eventually thickens, developing a peanut/X-shaped profile when viewed side-on. Through analyzing stellar kinematics of N-body model snapshots of a galaxy before, during, and after the buckling phase, we confirm a distinct quadrupolar pattern of out-of-plane stellar velocities in nearly face-on galaxies. This kinematic signature of buckling allows us to identify five candidates of currently buckling bars among 434 barred galaxies in the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) Survey, an integral field unit (IFU) spectroscopic survey that measures the composition and kinematic structure of nearby galaxies. The frequency of buckling events detected is consistent with the 0.5-1 Gyr timescale predicted by simulations. The five candidates we present more than double the total number of candidate buckling bars, and are the only ones found using the kinematic signature.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Christophe Brouzet; Raphaël Guiné; Marie-Julie Dalbe; Benjamin Favier; Nicolas Vandenberghe; Emmanuel Villermaux; Gautier Verhille
Laboratory model for plastic fragmentation in the turbulent ocean Article de journal
Dans: Phys. Rev. Fluids, vol. 6, p. 024601, 2021.
@article{PhysRevFluids.6.024601,
title = {Laboratory model for plastic fragmentation in the turbulent ocean},
author = {Christophe Brouzet and Raphaël Guiné and Marie-Julie Dalbe and Benjamin Favier and Nicolas Vandenberghe and Emmanuel Villermaux and Gautier Verhille},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.6.024601},
doi = {10.1103/PhysRevFluids.6.024601},
year = {2021},
date = {2021-02-01},
journal = {Phys. Rev. Fluids},
volume = {6},
pages = {024601},
publisher = {American Physical Society},
abstract = {The fragmentation of solid objects in turbulence is of paramount importance in a large number of situations, especially for marine plastic pollution where small plastic debris are formed by the fragmentation of plastic litter under hydrodynamic forces. Up to now, investigations have focused on the fragmentation of particle aggregates in turbulent flows. Here we study the fragmentation of a single deformable object that behaves elastically up to breakage, in the inertial range of turbulence. Using laboratory experiments with glass fibers as a model system, complemented by numerical simulations and theoretical analyses, we exhibit a comprehensive fragmentation scenario, further modeled by an evolution equation. Our results demonstrate that the fragmentation process is limited at small scales by a physical cutoff length originating from the fluid-structure interactions between the objects and the turbulence, and therefore independent of the brittleness of the fibers. This scenario leads to the accumulation of fragments with a typical length slightly longer than the cutoff scale, as smaller fragments are too short to be deformed and broken by the turbulence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jeroen P J Bruekers; Matthijs A Hellinghuizen; Nicolas Vanthuyne; Paul Tinnemans; Pieter J Gilissen; Wybren Jan Buma; Jean-Valère Naubron; Jeanne Crassous; Johannes A A W Elemans; Roeland J M Nolte
Front Cover: Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages (Eur. J. Org. Chem. 4/2021) Article de journal
Dans: European Journal of Organic Chemistry, vol. 2021, no. 4, p. 512-512, 2021.
@article{https://doi.org/10.1002/ejoc.202001599,
title = {Front Cover: Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages (Eur. J. Org. Chem. 4/2021)},
author = {Jeroen P J Bruekers and Matthijs A Hellinghuizen and Nicolas Vanthuyne and Paul Tinnemans and Pieter J Gilissen and Wybren Jan Buma and Jean-Valère Naubron and Jeanne Crassous and Johannes A A W Elemans and Roeland J M Nolte},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/ejoc.202001599},
doi = {https://doi.org/10.1002/ejoc.202001599},
year = {2021},
date = {2021-01-01},
journal = {European Journal of Organic Chemistry},
volume = {2021},
number = {4},
pages = {512-512},
abstract = {The Front Cover shows a chiral double decker porphyrin cage, which has been resolved into enantiomers (red and blue structures). The compound was characterized by various physical techniques, including X-ray and circular dichroism (spectra in the center). The porphyrin cage compound forms well-defined self-assembled monolayers on HOPG surfaces, which are visible by scanning tunneling microscopy (background). The binding of a guest (viologen) in one of the cages of the compound leads to a contraction of the other cage (indicated by the white wiggles), resulting in a greatly reduced guest binding in the latter cage (negative allosteric effect). More information can be found in the Full Paper by Roeland J.M. Nolte et al.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shang-Gui Cai; Johan Degrigny; Jean-François Boussuge; Pierre Sagaut
Coupling of turbulence wall models and immersed boundaries on Cartesian grids Article de journal
Dans: Journal of Computational Physics, vol. 429, p. 109995, 2021, ISSN: 0021-9991.
@article{CAI2021109995,
title = {Coupling of turbulence wall models and immersed boundaries on Cartesian grids},
author = {Shang-Gui Cai and Johan Degrigny and Jean-François Boussuge and Pierre Sagaut},
url = {https://www.sciencedirect.com/science/article/pii/S0021999120307695},
doi = {https://doi.org/10.1016/j.jcp.2020.109995},
issn = {0021-9991},
year = {2021},
date = {2021-01-01},
journal = {Journal of Computational Physics},
volume = {429},
pages = {109995},
abstract = {An improved coupling of immersed boundary method and turbulence wall models on Cartesian grids is proposed, for producing smooth wall surface pressure and skin friction at high Reynolds numbers. Spurious oscillations are frequently observed on these quantities with most immersed boundary wall modeling methods, especially for the skin friction which is found to be very sensitive to the solid surface's position and orientation against the Cartesian grids. The problem originates from the irregularity of the wall distance on the stair-step grid boundaries where the immersed boundary conditions are applied. To reduce this directional error, several modifications are presented to enhance the near wall solution. First, the commonly used interpolation for the flow velocity is replaced by one for the friction velocity, which has much less variation near wall. The concept of using a fictitious point to retrieve flow fields in the wall normal direction is abandoned and the interpolation is performed in the wall parallel plane with existing fluid points. Secondly, the velocity gradients at the approximated boundary are computed with advanced schemes and the normal gradient of the tangential velocity is reconstructed from the wall laws. To further protect the near wall solution, the normal velocity gradient and the working viscosity from the Spalart-Allmaras turbulence model are enforced by their theoretical solutions in the interior fluid close to the wall. Additionally, various post-processing algorithms for reconstructing wall surface quantities and force integrations are investigated. Other related factors are also discussed for their effects on the results. The validity of present method has been demonstrated through numerical benchmark tests on a flat plate at zero pressure gradient, both aligned and inclined with respect to the grid, as well as aerodynamic cases of NACA 23012 airfoil and NASA trap wing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Philippe Maugis; Damien Connétable; Paul Eyméoud
Stability of Zener order in martensite: an atomistic evidence Article de journal
Dans: Scripta Materialia, vol. 194, p. 113632, 2021, ISSN: 1359-6462.
@article{MAUGIS2021113632,
title = {Stability of Zener order in martensite: an atomistic evidence},
author = {Philippe Maugis and Damien Connétable and Paul Eyméoud},
url = {https://www.sciencedirect.com/science/article/pii/S1359646220307442},
doi = {https://doi.org/10.1016/j.scriptamat.2020.113632},
issn = {1359-6462},
year = {2021},
date = {2021-01-01},
journal = {Scripta Materialia},
volume = {194},
pages = {113632},
abstract = {Martensite is a supersaturated solid solution of carbon in body-centered iron wherein interstitial carbon atoms preferentially occupy a single octahedral sublattice. Despite a century of research, the mechanism of this long-range ordering is still a subject of debate. Recently, Zener’s theory of ordering was challenged both experimentally and theoretically. In an attempt to settle the controversy, we investigated by density functional theory the ground states of Fe-C configurations having various degrees of order. We conclude that the fully Zener-ordered configurations are always the most stable energetically, thus confirming Zener’s theory. Comparison with mean-field elasticity and Ising-type modelling supports the elastic origin of Zener ordering.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M Tayyab; S Zhao; Pierre Boivin
Lattice-Boltzmann modeling of a turbulent bluff-body stabilized flame Article de journal
Dans: Physics of Fluids, vol. 33, no. 3, p. 031701, 2021.
@article{tayyab:hal-03160901,
title = {Lattice-Boltzmann modeling of a turbulent bluff-body stabilized flame},
author = {M Tayyab and S Zhao and Pierre Boivin},
url = {https://hal.archives-ouvertes.fr/hal-03160901},
doi = {10.1063/5.0038089},
year = {2021},
date = {2021-01-01},
journal = {Physics of Fluids},
volume = {33},
number = {3},
pages = {031701},
publisher = {American Institute of Physics},
abstract = {This letter reports the first large eddy simulation of a turbulent flame using a Lattice-Boltzmann model. To that end, simulation of a bluff-body stabilized propane-air flame is carried out, showing an agreement similar to those available in the literature. Computational costs are also reported, indicating that Lattice-Boltzmann modelling of reactive flows is competitive, with around 1000cpuh required to simulate one residence time in the 1,5m burner. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
D Mandal; Y Elskens; X Leoncini; N Lemoine; F Doveil
Sticky islands in stochastic webs and anomalous chaotic cross-field particle transport by E×B electron drift instability Article de journal
Dans: Chaos, Solitons & Fractals, vol. 145, p. 110810, 2021, ISSN: 0960-0779.
@article{MANDAL2021110810,
title = {Sticky islands in stochastic webs and anomalous chaotic cross-field particle transport by E×B electron drift instability},
author = {D Mandal and Y Elskens and X Leoncini and N Lemoine and F Doveil},
url = {https://www.sciencedirect.com/science/article/pii/S0960077921001624},
doi = {https://doi.org/10.1016/j.chaos.2021.110810},
issn = {0960-0779},
year = {2021},
date = {2021-01-01},
journal = {Chaos, Solitons & Fractals},
volume = {145},
pages = {110810},
abstract = {The E×B electron drift instability, present in many plasma devices, is an important agent in cross-field particle transport. In presence of a resulting low frequency electrostatic wave, the motion of a charged particle becomes chaotic and generates a stochastic web in phase space. We define a scaling exponent to characterise transport in phase space and we show that the transport is anomalous, of super-diffusive type. Given the values of the model parameters, the trajectories stick to different kinds of islands in phase space, and their different sticking time power-law statistics generate successive regimes of the super-diffusive transport.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicolas Frangieh; Gilbert Accary; Jean-Louis Rossi; Dominique Morvan; Sofiane Meradji; Thierry Marcelli; François-Joseph Chatelon
Fuelbreak effectiveness against wind-driven and plume-dominated fires: A 3D numerical study Article de journal
Dans: Fire Safety Journal, vol. 124, p. 103383, 2021, ISSN: 0379-7112.
@article{FRANGIEH2021103383,
title = {Fuelbreak effectiveness against wind-driven and plume-dominated fires: A 3D numerical study},
author = {Nicolas Frangieh and Gilbert Accary and Jean-Louis Rossi and Dominique Morvan and Sofiane Meradji and Thierry Marcelli and François-Joseph Chatelon},
url = {https://www.sciencedirect.com/science/article/pii/S0379711221001247},
doi = {https://doi.org/10.1016/j.firesaf.2021.103383},
issn = {0379-7112},
year = {2021},
date = {2021-01-01},
journal = {Fire Safety Journal},
volume = {124},
pages = {103383},
abstract = {The effectiveness of a fuelbreak, created in a homogeneous grassland on a flat terrain, was studied numerically. The analysis relies on 3D numerical simulations that were performed using a detailed physical-fire-model (FIRESTAR3D) based on a multiphase formulation. To avoid border effects, calculations were carried out by imposing periodic boundary conditions along the two lateral sides of the computational domain, reproducing that way a quasi-infinitely long fire front. A total of 72 simulations were carried out for various wind speeds, fuel heights, and fuelbreak widths, which allowed to cover a large spectrum of fire behaviour, ranging from plume-dominated fires to wind-driven fires. The results were classified in three main categories: 1- “Propagation” if fire crossed the fuelbreak with a continuous fire front, 2- “Overshooting” and “Marginal” if fire marginally crosses the fuelbreak with the formation of burning pockets, and 3- “No propagation” if fire does not cross at all the fuelbreak. The ratio of fuelbreak width to fuel height, marking the “Propagation”/“No propagation” transition, was found to be scaled with Byram's convection number Nc as 75.07 × Nc−0.46. The numerical results were also compared to an operational wildfire engineering tool (DIMZAL) dedicated to fuelbreaks dimensioning.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Romain Pinguet; S Kanner; M Benoit; B Molin
Modeling the Dynamics of Freely-Floating Offshore Wind Turbine Subjected to Waves With an Open-Source Overset Mesh Method Manuel technique
2021.
@manual{Pinguet2021ModelingTD,
title = {Modeling the Dynamics of Freely-Floating Offshore Wind Turbine Subjected to Waves With an Open-Source Overset Mesh Method},
author = {Romain Pinguet and S Kanner and M Benoit and B Molin},
url = {https://www.researchgate.net/publication/349379786_Modeling_the_Dynamics_of_Freely-Floating_Offshore_Wind_Turbine_Subjected_to_Waves_With_an_Open-Source_Overset_Mesh_Method},
year = {2021},
date = {2021-01-01},
abstract = {The aim of this study is to develop a viscous numerical wave tank using a coupled solver between the wave generation and absorption toolbox waves2Foam, developed by Jacobsen et al. [1] and the overset method built in the open source CFD software OpenFOAM©. This wave tank can be used to analyze the behavior of Floating Offshore Wind Turbine (FOWT) in nonlinear waves. A mesh convergence analysis is presented on a simple 2D case in order to validate the CFD model. The results are compared to experimental data from the literature and show good agreement. The response of a floater developed for a FOWT is analyzed. The free surface elevation, heave and pitch motions are compared to experimental results from the literature. Comparisons between experimental data and numerical results are discussed.},
keywords = {},
pubstate = {published},
tppubtype = {manual}
}
Pierre Boivin; M Tayyab; S Zhao
Benchmarking a lattice-Boltzmann solver for reactive flows: Is the method worth the effort for combustion? Article de journal
Dans: Physics of Fluids, vol. 33, no. 7, p. 071703, 2021.
@article{boivin:hal-03276189,
title = {Benchmarking a lattice-Boltzmann solver for reactive flows: Is the method worth the effort for combustion?},
author = {Pierre Boivin and M Tayyab and S Zhao},
url = {https://hal.archives-ouvertes.fr/hal-03276189},
doi = {10.1063/5.0057352},
year = {2021},
date = {2021-01-01},
journal = {Physics of Fluids},
volume = {33},
number = {7},
pages = {071703},
publisher = {American Institute of Physics},
abstract = {This Letter reports a validation of a lattice-Boltzmann approach following the Taylor-Green Vortex benchmark presented at the 19th International Congress on Numerical Combustion and recently reported by Abdelsamie et al. ["The Taylor-Green vortex as a benchmark for high-fidelity combustion simulations using low-Mach solvers," Comput. Fluids 223, 104935 (2021)]. The lattice-Boltzmann approach, despite having a time step bound by an acoustic Courant-Friedrichs-Lewy condition, provides results faster than the low-Mach solvers which performed to the benchmark. Such a feat is made possible by the fully explicit nature of the method and indicates very high potential for practical applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Paul Eyméoud; Fabienne Ribeiro; Rémy Besson; Guy Tréglia
How to take into account local concentration in Ising-based Monte-Carlo: illustration with zirconium hydrides Article de journal
Dans: Computational Materials Science, vol. 197, p. 110547, 2021, ISSN: 0927-0256.
@article{EYMEOUD2021110547,
title = {How to take into account local concentration in Ising-based Monte-Carlo: illustration with zirconium hydrides},
author = {Paul Eyméoud and Fabienne Ribeiro and Rémy Besson and Guy Tréglia},
url = {https://www.sciencedirect.com/science/article/pii/S0927025621002743},
doi = {https://doi.org/10.1016/j.commatsci.2021.110547},
issn = {0927-0256},
year = {2021},
date = {2021-01-01},
journal = {Computational Materials Science},
volume = {197},
pages = {110547},
abstract = {We present a detailed methodology for treating local concentration dependency of pairwise interactions in Ising-based Monte-Carlo. The procedure is described through the example of interstitial ordering processes in zirconium hydrides, studied by canonical Monte-Carlo based on a concentration-dependent Tight-Binding Ising Model. The path leads to build a phase diagram of hydrogen-vacancy ordering on interstitial tetrahedral sublattice of face-centered cubic Zr-H.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mihael Petač; Julien Lavalle; Arturo Núñez-Castiñeyra; Emmanuel Nezri
Testing the predictions of axisymmetric distribution functions of galactic dark matter with hydrodynamical simulations Article de journal
Dans: JCAP, vol. 08, p. 031, 2021.
@article{petac:hal-03262627,
title = {Testing the predictions of axisymmetric distribution functions of galactic dark matter with hydrodynamical simulations},
author = {Mihael Petač and Julien Lavalle and Arturo Núñez-Castiñeyra and Emmanuel Nezri},
url = {https://hal.archives-ouvertes.fr/hal-03262627},
doi = {10.1088/1475-7516/2021/08/031},
year = {2021},
date = {2021-01-01},
journal = {JCAP},
volume = {08},
pages = {031},
abstract = {Signal predictions for galactic dark matter (DM) searches often rely on assumptions regarding the DM phase-space distribution function (DF) in halos. This applies to both particle (e.g. p-wave suppressed or Sommerfeld-enhanced annihilation, scattering off atoms, etc.) and macroscopic DM candidates (e.g. microlensing of primordial black holes). As experiments and observations improve in precision, better assessing theoretical uncertainties becomes pressing in the prospect of deriving reliable constraints on DM candidates or trustworthy hints for detection. Most reliable predictions of DFs in halos are based on solving the steady-state collisionless Boltzmann equation (e.g. Eddington-like inversions, action-angle methods, etc.) consistently with observational constraints. One can do so starting from maximal symmetries and a minimal set of degrees of freedom, and then increasing complexity. Key issues are then whether adding complexity, which is computationally costy, improves predictions, and if so where to stop. Clues can be obtained by making predictions for zoomed-in hydrodynamical cosmological simulations in which one can access the true (coarse-grained) phase-space information. Here, we test an axisymmetric extension of the Eddington inversion to predict the full DM DF from its density profile and the total gravitational potential of the system. This permits to go beyond spherical symmetry, and is a priori well suited for spiral galaxies. We show that axisymmetry does not necessarily improve over spherical symmetry because the (observationally unconstrained) angular momentum of the DM halo is not generically aligned with the baryonic one. Theoretical errors are similar to those of the Eddington inversion though, at the 10–20% level for velocity-dependent predictions related to particle DM searches in spiral galaxies. We extensively describe the approach and comment on the results.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M Bouffard; B Favier; D Lecoanet; M Le Bars
Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell Article de journal
Dans: Geophysical Journal International, vol. 228, no. 1, p. 337-354, 2021, ISSN: 0956-540X.
@article{10.1093/gji/ggab343,
title = {Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell},
author = {M Bouffard and B Favier and D Lecoanet and M Le Bars},
url = {https://doi.org/10.1093/gji/ggab343},
doi = {10.1093/gji/ggab343},
issn = {0956-540X},
year = {2021},
date = {2021-01-01},
journal = {Geophysical Journal International},
volume = {228},
number = {1},
pages = {337-354},
abstract = {Seismic and magnetic observations have suggested the presence of a stably stratified layer atop Earth’s core. Such a layer could affect the morphology of the geomagnetic field and the evolution of the core, but the precise impact of this layer depends largely on its internal dynamics. Among other physical phenomena, stratified layers host internal gravity waves (IGW), which can be excited by adjacent convective motions. Internal waves are known to play an important role on the large-scale dynamics of the Earth’s climate and on the long-term evolution of stars. Yet, they have received relatively little attention in the Earth’s outer core so far and deserve detailed investigations in this context. Here, we make a first step in that direction by running numerical simulations of IGW in a non-rotating spherical shell in which a stratified layer lies on top of a convective region. We use a nonlinear equation of state to produce self-consistently such a two-layer system. Both propagating waves and global modes coexist in the stratified layer. We characterize the spectral properties of these waves and find that energy is distributed across a wide range of frequencies and length scales, that depends on the Prandtl number. For the control parameters considered and in the absence of rotational and magnetic effects, the mean kinetic energy in the layer is about 0.1 per cent that of the convective region. IGW produce perturbations in the gravity field that may fall within the sensitivity limit of present-day instruments and could potentially be detected in available data. We finally provide a road map for future, more geophysically realistic, studies towards a more thorough understanding of the dynamics and impact of internal waves in a stratified layer atop Earth’s core.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shang-Gui Cai; Pierre Sagaut
Explicit wall models for large eddy simulation Article de journal
Dans: Physics of Fluids, vol. 33, p. 041703, 2021.
@article{articlem,
title = {Explicit wall models for large eddy simulation},
author = {Shang-Gui Cai and Pierre Sagaut},
doi = {10.1063/5.0048563},
year = {2021},
date = {2021-01-01},
journal = {Physics of Fluids},
volume = {33},
pages = {041703},
abstract = {Algebraic explicit wall models covering the entire inner region of the turbulent boundary layer are proposed to reduce the computational effort for large eddy simulation of wall-bounded turbulent flows. The proposed formulas are given in closed forms with either logarithmic- or power-function-based laws of the wall, allowing straightforward evaluation of the friction velocity on near wall grids independent of their locations in the turbulent boundary layer. The performance of the proposed models is demonstrated by the wall modeled large eddy simulation of a turbulent plane channel flow.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Weiliang Ma; Jing Tian; Pascal Boulet; Marie-Christine Record
First-Principle Investigations on the Electronic and Transport Properties of PbBi2Te2X2 (X = S/Se/Te) Monolayers Article de journal
Dans: Nanomaterials, vol. 11, p. 2979, 2021.
@article{article,
title = {First-Principle Investigations on the Electronic and Transport Properties of PbBi2Te2X2 (X = S/Se/Te) Monolayers},
author = {Weiliang Ma and Jing Tian and Pascal Boulet and Marie-Christine Record},
doi = {10.3390/nano11112979},
year = {2021},
date = {2021-01-01},
journal = {Nanomaterials},
volume = {11},
pages = {2979},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
C Yang; Michel Mehrenberger
Highly accurate monotonicity-preserving Semi-Lagrangian scheme for Vlasov-Poisson Simulations Article de journal
Dans: Journal of Computational Physics, 2021.
@article{yang:hal-03126595,
title = {Highly accurate monotonicity-preserving Semi-Lagrangian scheme for Vlasov-Poisson Simulations},
author = {C Yang and Michel Mehrenberger},
url = {https://hal.archives-ouvertes.fr/hal-03126595},
doi = {10.1016/j.jcp.2021.110632},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Journal of Computational Physics},
publisher = {Elsevier},
abstract = {In this paper, we study a high accurate monotonicity-preserving (MP) Semi-Lagrangian scheme for Vlasov-Poisson simulations. The classical Semi-Lagrangian scheme is known to be high accurate and free from CFL condition, but it does not satisfy local maximum principle. To remedy this drawback, using the conservative form of the Semi-Lagrangian scheme, we recast existing MP schemes for the numerical flux in a common framework, and then substitute the local minimum/maximum by some "better" guess, in order to avoid as much as possible loss of accuracy and clipping near extrema, while keeping the monotonicity on monotone portions. With the limiter, on the one hand, the scheme keeps the good properties of the unlimited scheme: it is conservative, free from CFL condition and high accurate. On the other hand, for locally monotonic data, the monotonicity of the solution is preserved. Numerical tests are made on free transport equation and Vlasov-Poisson system to illustrate the robustness of our method. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damianos Agathangelou; Partha Pratim Roy; Maria del Carmen Marin; Nicolas Ferré; Massimo Olivucci; Tiago Buckup; J'er'emie L'eonard; Stefan Haacke
Sub-picosecond C=C bond photo-isomerization: evidence for the role of excited state mixing Article de journal
Dans: Comptes Rendus. Physique, vol. 22, p. 111–138, 2021.
@article{CRPHYS_2021__22_S2_111_0,
title = {Sub-picosecond C=C bond photo-isomerization: evidence for the role of excited state mixing},
author = {Damianos Agathangelou and Partha Pratim Roy and Maria del Carmen Marin and Nicolas Ferré and Massimo Olivucci and Tiago Buckup and J'er'emie L'eonard and Stefan Haacke}},
editor = {Académie des sciences, Paris},
url = {https://comptes-rendus.academie-sciences.fr/physique/articles/10.5802/crphys.41/},
doi = {10.5802/crphys.41},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Comptes Rendus. Physique},
volume = {22},
pages = {111--138},
abstract = {Sub-picosecond photo-isomerization is the major primary process of energy conversion in retinal proteins and has as such been in the focus of extensive theoretical and experimental work over the past decades. In this review article, we revisit the long-standing question as to how the protein tunes the isomerization speed and quantum yield. We focus on our recent contributions to this field, which underscore the concept of a delicate mixing of reactive and non-reactive excited states, as a result of steric properties and electrostatic interactions with the protein environment. Further avenues and new approaches are outlined which hold promise for advancing our understanding of these intimately coupled chromophore-protein systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abiola, Temitope T.; Rioux, Benjamin; Toldo, Josene M.; Alarcan, Jimmy; Woolley, Jack M.; Turner, Matthew A. P.; Coxon, Daniel J. L.; Telles do Casal, Mariana; Peyrot, Cédric; Mention, Matthieu M.; Buma, Wybren J.; Ashfold, Michael N. R.; Braeuning, Albert; Barbatti, Mario; Stavros, Vasilios G.; Allais, Florent
Towards developing novel and sustainable molecular light-to-heat converters Article de journal
Dans: Chem. Sci., vol. 12, p. 15239-15252, 2021.
@article{abiola:hal-03426788,
title = {Towards developing novel and sustainable molecular light-to-heat converters},
author = {Abiola, Temitope T. and Rioux, Benjamin and Toldo, Josene M. and Alarcan, Jimmy and Woolley, Jack M. and Turner, Matthew A. P. and Coxon, Daniel J. L. and Telles do Casal, Mariana and Peyrot, Cédric and Mention, Matthieu M. and Buma, Wybren J. and Ashfold, Michael N. R. and Braeuning, Albert and Barbatti, Mario and Stavros, Vasilios G. and Allais, Florent},
editor = {The Royal Society of Chemistry},
url = {http://dx.doi.org/10.1039/D1SC05077J},
doi = {10.1039/D1SC05077J},
year = {2021},
date = {2021-01-01},
journal = {Chem. Sci.},
volume = {12},
pages = {15239-15252},
publisher = {Chemical Science },
abstract = {Light-to-heat conversion materials generate great interest due to their widespread applications{,} notable exemplars being solar energy harvesting and photoprotection. Another more recently identified potential application for such materials is in molecular heaters for agriculture{,} whose function is to protect crops from extreme cold weather and extend both the growing season and the geographic areas capable of supporting growth{,} all of which could help reduce food security challenges. To address this demand{,} a new series of phenolic-based barbituric absorbers of ultraviolet (UV) radiation has been designed and synthesised in a sustainable manner. The photophysics of these molecules has been studied in solution using femtosecond transient electronic and vibrational absorption spectroscopies{,} allied with computational simulations and their potential toxicity assessed by in silico studies. Following photoexcitation to the lowest singlet excited state{,} these barbituric absorbers repopulate the electronic ground state with high fidelity on an ultrafast time scale (within a few picoseconds). The energy relaxation pathway includes a twisted intramolecular charge-transfer state as the system evolves out of the FranckâCondon region{,} internal conversion to the ground electronic state{,} and subsequent vibrational cooling. These barbituric absorbers display promising light-to-heat conversion capabilities{,} are predicted to be non-toxic{,} and demand further study within neighbouring application-based fields.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pierre Magnico
Molecular dynamics study on water and hydroxide transfer mechanisms in PSU-g-alkyl-TMA membranes at low hydration: Effect of side chain length Article de journal
Dans: International Journal of Hydrogen Energy, vol. 46, no. 68, p. 33915-33933, 2021, ISSN: 0360-3199.
@article{MAGNICO202133915,
title = {Molecular dynamics study on water and hydroxide transfer mechanisms in PSU-g-alkyl-TMA membranes at low hydration: Effect of side chain length},
author = {Pierre Magnico},
url = {https://www.sciencedirect.com/science/article/pii/S0360319921027221},
doi = {https://doi.org/10.1016/j.ijhydene.2021.07.081},
issn = {0360-3199},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {International Journal of Hydrogen Energy},
volume = {46},
number = {68},
pages = {33915-33933},
abstract = {Molecular dynamics simulations with anion exchange membranes (alkyl trimethyl ammonium grafted onto polysulfone) are performed to investigate the influence of the spacer length on the transport properties, on the molecular exchange mechanisms between the functional group and the aqueous phase and on the hydrogen bond network. This is especially insightful that in this work the hydration number is small. In this condition the aqueous phase must be thought as an assembly of small clusters. The results show an unexpected dependence of the water and hydroxide (OH) diffusivity on the temperature and the water uptake. The distribution of the cluster size bonded to OH explain partially the OH diffusivity. “Hopping” and “caging” motions are observed with the self-part of the Van Hove functions even at high temperature. The characteristic time of the survival probability correlation function around the functional groups is a decreasing function of the alkyl length. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Guochao Gao; Paul Cristini; Nathalie Favretto-Cristini; Carole Deumié
On the reflection of time-domain acoustic spherical waves by a sinusoidal diffraction grating Article de journal
Dans: Acta Acust., vol. 5, p. 6, 2021.
@article{refId0d,
title = {On the reflection of time-domain acoustic spherical waves by a sinusoidal diffraction grating},
author = {Guochao} {Gao and Paul} {Cristini and Nathalie} {Favretto-Cristini and Carole} {Deumié},
url = {https://doi.org/10.1051/aacus/2020033},
doi = {10.1051/aacus/2020033},
year = {2021},
date = {2021-01-01},
journal = {Acta Acust.},
volume = {5},
pages = {6},
abstract = {This work reports on some results obtained from numerical simulations of time-domain acoustic wave propagation in the presence of a periodically rough interface. Emphasis is put on the structure of the reflected signals in the presence of a sinusoidal grating. More specifically, we investigate the effect of the frequency bandwidth of the emitted signal and the effect of the incident wavefront sphericity on the signals reflected from the rough interface and associated with the different diffraction orders.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Oleg Bessonov; Sofiane Meradji
Parallel modeling of wildfires using efficient solvers for ill-conditioned linear systems Article de journal
Dans: The Journal of Supercomputing, 2021.
@article{articled,
title = {Parallel modeling of wildfires using efficient solvers for ill-conditioned linear systems},
author = {Oleg Bessonov and Sofiane Meradji},
doi = {10.1007/s11227-021-03632-8},
year = {2021},
date = {2021-01-01},
journal = {The Journal of Supercomputing},
abstract = {Numerical simulation of multi-physical processes requires a lot of processor time,
especially when solving ill-conditional linear systems arising in fluid dynamics
problems. This paper is devoted to the development of efficient parallel methods for
such systems for FireStar3D wildfire modeling code. Two alternative approaches
are discussed and analyzed, based on the MILU-preconditioned conjugate gradient
method and on the algebraic multigrid, respectively. The main difficulties of paral-
lelizing these methods are considered and solutions are presented: in the first case,
nested twisted factorization with a staircase pipelining, and in the second, a multi-
color technique for a new smoother for strongly anisotropic grids. A novel quasi-
geometric interpolation technique is presented for solving the problem of positive
off-diagonal matrix entries in the multigrid. The limits of applicability of the meth-
ods are determined depending on their flexibility, robustness and parallelization
capabilities. The performance comparison demonstrates the superiority of the new
methods over the widely used variants of the traditional conjugate gradient method.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
especially when solving ill-conditional linear systems arising in fluid dynamics
problems. This paper is devoted to the development of efficient parallel methods for
such systems for FireStar3D wildfire modeling code. Two alternative approaches
are discussed and analyzed, based on the MILU-preconditioned conjugate gradient
method and on the algebraic multigrid, respectively. The main difficulties of paral-
lelizing these methods are considered and solutions are presented: in the first case,
nested twisted factorization with a staircase pipelining, and in the second, a multi-
color technique for a new smoother for strongly anisotropic grids. A novel quasi-
geometric interpolation technique is presented for solving the problem of positive
off-diagonal matrix entries in the multigrid. The limits of applicability of the meth-
ods are determined depending on their flexibility, robustness and parallelization
capabilities. The performance comparison demonstrates the superiority of the new
methods over the widely used variants of the traditional conjugate gradient method.
2020
A Gallo; A Sepetys; Y Marandet; H Bufferand; G Ciraolo; N Fedorczak; S Brezinsek; J Bucalossi; J Coenen; F Clairet; Y Corre; C Desgranges; P Devynck; J Gaspar; R Guirlet; J Gunn; C C Klepper; J -Y Pascal; P Tamain; E Tsitrone; E A Unterberg; WEST the team
Interpretative transport modeling of the WEST boundary plasma: main plasma and light impurities Article de journal
Dans: Nuclear Fusion, vol. 60, no. 12, p. 126048, 2020.
@article{Gallo_2020,
title = {Interpretative transport modeling of the WEST boundary plasma: main plasma and light impurities},
author = {A Gallo and A Sepetys and Y Marandet and H Bufferand and G Ciraolo and N Fedorczak and S Brezinsek and J Bucalossi and J Coenen and F Clairet and Y Corre and C Desgranges and P Devynck and J Gaspar and R Guirlet and J Gunn and C C Klepper and J -Y Pascal and P Tamain and E Tsitrone and E A Unterberg and WEST the team},
url = {https://doi.org/10.1088%2F1741-4326%2Fabb95b},
doi = {10.1088/1741-4326/abb95b},
year = {2020},
date = {2020-11-01},
journal = {Nuclear Fusion},
volume = {60},
number = {12},
pages = {126048},
publisher = {IOP Publishing},
abstract = {Understanding impurity transport in tokamak plasmas is crucial to control radiative losses and material migration in future magnetic fusion reactors. In this work we deploy the SolEdge2D-EIRENE code to model the boundary plasma in a WEST discharge, satisfactorily reproducing measurements of both upstream and divertor plasma conditions. The spatial distribution of oxygen, studied here as a representative light impurity, is compared to vacuum ultraviolet spectroscopy measurements acquired with an oscillating line of sight. The simulation captures a key feature of the experiment, namely a factor of ≃2 higher oxygen brightness in the inner divertor region compared to the outer one. This spatial asymmetry in oxygen concentration is interpreted by analyzing the balance of friction forces and thermal gradient forces that the light impurity exchanges with the main plasma.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thomas Lacroix; Arturo Nunez-Castineyra; Martin Stref; Julien Lavalle; Emmanuel Nezri
Predicting the dark matter velocity distribution in galactic structures: tests against hydrodynamic cosmological simulations Article de journal
Dans: Journal of Cosmology and Astroparticle Physics, vol. 2020, no. 10, p. 031–031, 2020.
@article{Lacroix_2020,
title = {Predicting the dark matter velocity distribution in galactic structures: tests against hydrodynamic cosmological simulations},
author = {Thomas Lacroix and Arturo Nunez-Castineyra and Martin Stref and Julien Lavalle and Emmanuel Nezri},
url = {https://doi.org/10.1088%2F1475-7516%2F2020%2F10%2F031},
doi = {10.1088/1475-7516/2020/10/031},
year = {2020},
date = {2020-10-01},
journal = {Journal of Cosmology and Astroparticle Physics},
volume = {2020},
number = {10},
pages = {031--031},
publisher = {IOP Publishing},
abstract = {Reducing theoretical uncertainties in Galactic dark matter (DM) searches is an important challenge as several experiments are now delving into the parameter space relevant to popular (particle or not) candidates. Since many DM signal predictions rely on the knowledge of the DM velocity distribution—direct searches, capture by stars, p-wave-suppressed or Sommerfeld-enhanced annihilation rate, microlensing of primordial black holes, etc—it is necessary to assess the accuracy of our current theoretical handle. Beyond Maxwellian approximations or ad-hoc extrapolations of fits on cosmological simulations, approaches have been proposed to self-consistently derive the DM phase-space distribution only from the detailed mass content of the Galaxy and some symmetry assumptions (e.g. the Eddington inversion and its anisotropic extensions). Although theoretically sound, these methods are still based on simplifying assumptions and their relevance to real galaxies can be questioned. In this paper, we use zoomed-in cosmological simulations to quantify the associated uncertainties. Assuming isotropy, we predict the speed distribution and its moments from the DM and baryonic content measured in simulations, and compare them with the true ones. Taking as input galactic mass models fitted on full simulation data, we reach a predictivity down to ∼ 10% for some velocity-related observables, significantly better than some Maxwellian models. This moderate theoretical error is particularly encouraging at a time when stellar surveys like the Gaia mission should allow us to improve constraints on Galactic mass models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jing Wang; E Athanassoula; Si-Yue Yu; Christian Wolf; Li Shao; Hua Gao; T H Randriamampandry
Suppressed or Enhanced Central Star Formation Rates in Late-type Barred Galaxies Article de journal
Dans: The Astrophysical Journal, vol. 893, no. 1, p. 19, 2020, ISSN: 1538-4357.
@article{Wang_2020,
title = {Suppressed or Enhanced Central Star Formation Rates in Late-type Barred Galaxies},
author = {Jing Wang and E Athanassoula and Si-Yue Yu and Christian Wolf and Li Shao and Hua Gao and T H Randriamampandry},
url = {http://dx.doi.org/10.3847/1538-4357/ab7fad},
doi = {10.3847/1538-4357/ab7fad},
issn = {1538-4357},
year = {2020},
date = {2020-04-01},
journal = {The Astrophysical Journal},
volume = {893},
number = {1},
pages = {19},
publisher = {American Astronomical Society},
abstract = {Bars in disc-dominated galaxies are able to drive gas inflow inside the corotation radius, thus enhancing the central star formation rate (SFR). Previous work, however, has found that disc-dominated galaxies with centrally suppressed SFR frequently host a bar. Here we investigate possible causes for the suppression of central SFR in such cases. We compare physical properties of a sample of disc-dominated barred galaxies with high central SFR (HC galaxies) with those of a sample of disc-dominated barred galaxies with low central SFR (LC galaxies). We find that the two samples have on average similar HI content and bars of similar strength. But we also find that the HCs have bluer colors than LCs, and that outside the bar region they host stronger spiral arms than the LCs where closed rings are more often seen. We discuss and evaluate the possible causes for the suppression of the central SFR in the LC galaxies as opposed to its enhancement in the HC galaxies. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Paul G Chen; J M Lyu; M Jaeger; M Leonetti
Shape transition and hydrodynamics of vesicles in tube flow Article de journal
Dans: Phys. Rev. Fluids, vol. 5, p. 043602, 2020.
@article{PhysRevFluids.5.043602,
title = {Shape transition and hydrodynamics of vesicles in tube flow},
author = {Paul G Chen and J M Lyu and M Jaeger and M Leonetti},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.5.043602},
doi = {10.1103/PhysRevFluids.5.043602},
year = {2020},
date = {2020-04-01},
journal = {Phys. Rev. Fluids},
volume = {5},
pages = {043602},
publisher = {American Physical Society},
abstract = {The steady motion and deformation of a lipid-bilayer vesicle translating through a circular tube in low Reynolds number pressure-driven flow are investigated numerically using an axisymmetric boundary element method. This fluid-structure interaction problem is determined by three dimensionless parameters: reduced volume (a measure of the vesicle asphericity), geometric confinement (the ratio of the vesicle effective radius to the tube radius), and capillary number (the ratio of viscous to bending forces). The physical constraints of a vesicle—fixed surface area and enclosed volume when it is confined in a tube—determine critical confinement beyond which it cannot pass through without rupturing its membrane. The simulated results are presented in a wide range of reduced volumes [0.6, 0.98] for different degrees of confinement; the reduced volume of 0.6 mimics red blood cells. We draw a phase diagram of vesicle shapes and propose a shape transition line separating the parachutelike shape region from the bulletlike one in the reduced volume versus confinement phase space. We show that the shape transition marks a change in the behavior of vesicle mobility, especially for highly deflated vesicles. Most importantly, high-resolution simulations make it possible for us to examine the hydrodynamic interaction between the wall boundary and the vesicle surface at conditions of very high confinement, thus providing the limiting behavior of several quantities of interest, such as the thickness of lubrication film, vesicle mobility and its length, and the extra pressure drop due to the presence of the vesicle. This extra pressure drop holds implications for the rheology of dilute vesicle suspensions. Furthermore, we present various correlations and discuss a number of practical applications. The results of this work may serve as a benchmark for future studies and help devise tube-flow experiments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Daphné Lemasquerier; Giulio Facchini; Benjamin Favier ; Michael Le Bars
Remote determination of the shape of Jupiter’s vortices from laboratory experiments Article de journal
Dans: Nature Physics, 2020.
@article{Lemasquerier2020,
title = {Remote determination of the shape of Jupiter’s vortices from laboratory experiments},
author = {Daphné Lemasquerier; Giulio Facchini; Benjamin Favier ; Michael Le Bars},
url = {https://doi.org/10.1038/s41567-020-0833-9},
doi = {10.1038/s41567-020-0833-9},
year = {2020},
date = {2020-03-16},
journal = {Nature Physics},
abstract = {Jupiter’s dynamics shapes its cloud patterns but remains largely unknown below this natural observational barrier. Unravelling the underlying three-dimensional flows is thus a primary goal for NASA’s ongoing Juno mission, which was launched in 2011. Here, we address the dynamics of large Jovian vortices using laboratory experiments complemented by theoretical and numerical analyses. We determine the generic force balance responsible for their three-dimensional pancake-like shape. From this, we define scaling laws for their horizontal and vertical aspect ratios as a function of the ambient rotation, stratification and zonal wind velocity. For the Great Red Spot in particular, our predicted horizontal dimensions agree well with measurements at the cloud level since the Voyager mission in 1979. We also predict the Great Red Spot’s thickness, which is inaccessible to direct observation. It has remained surprisingly constant despite the observed horizontal shrinking. Our results now await comparison with upcoming Juno observations.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Léard; B Favier; P Le Gal; M Le Bars
Coupled convection and internal gravity waves excited in water around its density maximum at 4°C Article de journal
Dans: Phys. Rev. Fluids, vol. 5, p. 024801, 2020.
@article{PhysRevFluids.5.024801,
title = {Coupled convection and internal gravity waves excited in water around its density maximum at 4°C},
author = {P Léard and B Favier and P Le Gal and M Le Bars},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.5.024801},
doi = {10.1103/PhysRevFluids.5.024801},
year = {2020},
date = {2020-02-01},
journal = {Phys. Rev. Fluids},
volume = {5},
pages = {024801},
publisher = {American Physical Society},
abstract = {Coupled mixed convective and stratified systems are common in natural flows. To study experimentally the associated dynamics, we use a singular property of water: its nonlinear equation of state is characterized by a maximum density close to 4°C. By heating the top of a tank at 35°C and cooling the bottom at 0°C, a two-layer configuration spontaneously appears. The convective motion in the bottom layer consists mostly of a large-scale circulation and rising cold plumes. This turbulent flow generates propagating internal gravity waves in the upper stably stratified layer. Particle image velocimetry measurements are performed and spectral characteristics of the convection and internal gravity waves are presented. An horizontal large-scale reversing flow in the stratified layer is observed which is viscously driven by a third, intermediate layer. This buffer layer is located between the convective and stratified layers and is thermally coupled with the convective one, hence sustaining a strong horizontal shear. Three-dimensional direct numerical simulations with geometry and physical parameters close to the experimental ones corroborate our experimental results.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F Nespoli; P Tamain; N Fedorczak; D Galassi; Y Marandet
A new mechanism for filament disconnection at the X-point: poloidal shear in radial E texttimes B velocity Article de journal
Dans: Nuclear Fusion, vol. 60, no. 4, p. 046002, 2020.
@article{Nespoli_2020,
title = {A new mechanism for filament disconnection at the X-point: poloidal shear in radial E texttimes B velocity},
author = {F Nespoli and P Tamain and N Fedorczak and D Galassi and Y Marandet},
url = {https://doi.org/10.1088/1741-4326/ab6f1e},
doi = {10.1088/1741-4326/ab6f1e},
year = {2020},
date = {2020-02-01},
journal = {Nuclear Fusion},
volume = {60},
number = {4},
pages = {046002},
publisher = {IOP Publishing},
abstract = {Plasma filaments generated by turbulence in the scrape-off layer are sometimes observed in experiments and simulations to disconnect from the target plate in the vicinity of the X-point, resulting in a ‘quiescent zone’ with reduced fluctuations, possibly affecting the fluctuating part of the divertor heat loads. This phenomena is usually explained by the flux tubes squeezing, induced by flux expansion, down to scales where collisions dominate. In this work, we consider an additional mechanism spontaneously arising at the X-point: the poloidal shear in radial velocity. Through a simple model, tested against 3D global turbulence simulations, we quantify the effectiveness of this disconnection mechanism and identify ways to control it.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Joackim Bernier; Michel Mehrenberger
LONG-TIME BEHAVIOR OF SECOND ORDER LINEARIZED VLASOV-POISSON EQUATIONS NEAR A HOMOGENEOUS EQUILIBRIUM Article de journal
Dans: KINETIC AND RELATED MODELS, vol. 13, no. 1, p. 129-168, 2020, ISSN: 1937-5093.
@article{ISI:000500816900007,
title = {LONG-TIME BEHAVIOR OF SECOND ORDER LINEARIZED VLASOV-POISSON EQUATIONS
NEAR A HOMOGENEOUS EQUILIBRIUM},
author = {Joackim Bernier and Michel Mehrenberger},
doi = {10.3934/krm.2020005},
issn = {1937-5093},
year = {2020},
date = {2020-02-01},
journal = {KINETIC AND RELATED MODELS},
volume = {13},
number = {1},
pages = {129-168},
publisher = {AMER INST MATHEMATICAL SCIENCES-AIMS},
address = {PO BOX 2604, SPRINGFIELD, MO 65801-2604 USA},
abstract = {The asymptotic behavior of the solutions of the second order linearized
Vlasov-Poisson system around homogeneous equilibria is derived. It
provides a fine description of some nonlinear and multidimensional
phenomena such as the existence of Best frequencies. Numerical results
for the 1D x 1D and 2D x 2D Vlasov-Poisson system illustrate the
effectiveness of this approach.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vlasov-Poisson system around homogeneous equilibria is derived. It
provides a fine description of some nonlinear and multidimensional
phenomena such as the existence of Best frequencies. Numerical results
for the 1D x 1D and 2D x 2D Vlasov-Poisson system illustrate the
effectiveness of this approach.
Patrick Maget; Judith Frank; Timothee Nicolas; Olivier Agullo; Xavier Garbet; Hinrich Lutjens
Natural poloidal asymmetry and neoclassical transport of impurities in tokamak plasmas Article de journal
Dans: PLASMA PHYSICS AND CONTROLLED FUSION, vol. 62, no. 2, 2020, ISSN: 0741-3335.
@article{ISI:000500812100001,
title = {Natural poloidal asymmetry and neoclassical transport of impurities in
tokamak plasmas},
author = {Patrick Maget and Judith Frank and Timothee Nicolas and Olivier Agullo and Xavier Garbet and Hinrich Lutjens},
doi = {10.1088/1361-6587/ab53ab},
issn = {0741-3335},
year = {2020},
date = {2020-02-01},
journal = {PLASMA PHYSICS AND CONTROLLED FUSION},
volume = {62},
number = {2},
publisher = {IOP PUBLISHING LTD},
address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},
abstract = {The neoclassical transport of impurities is investigated for a plasma
without toroidal rotation nor anisotropic ion temperature. It is shown
that a natural poloidal asymmetry of the impurity density exists in this
case, and that it can be described with a simple analytical model. The
poloidal asymmetry tends naturally to cancel as the impurity profile
evolves towards its steady state, so that the main effect of the
poloidal asymmetry is to slow down the impurity flux compared to its
predicted value without poloidal asymmetry. The contribution of the
asymmetries of the electrostatic potential and of the main ion density
can be included in the analytical derivation, thus forming a
self-consistent description of the neoclassical impurity flux together
with its poloidal distribution. Numerical simulations with a non linear
fluid code confirm the analytical findings, showing that the
neoclassical transport of impurities is strongly modified by its natural
poloidal distribution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
without toroidal rotation nor anisotropic ion temperature. It is shown
that a natural poloidal asymmetry of the impurity density exists in this
case, and that it can be described with a simple analytical model. The
poloidal asymmetry tends naturally to cancel as the impurity profile
evolves towards its steady state, so that the main effect of the
poloidal asymmetry is to slow down the impurity flux compared to its
predicted value without poloidal asymmetry. The contribution of the
asymmetries of the electrostatic potential and of the main ion density
can be included in the analytical derivation, thus forming a
self-consistent description of the neoclassical impurity flux together
with its poloidal distribution. Numerical simulations with a non linear
fluid code confirm the analytical findings, showing that the
neoclassical transport of impurities is strongly modified by its natural
poloidal distribution.
Maria‐Andrea Mroginski; Suliman Adam; Gil Amoyal; Avishai Barnoy; Ana‐Nicoleta Bondar; Veniamin Borin; Jonathan Church; Tatiana Domratcheva; Bernd Ensing; Francesca Fanelli; Nicolas Ferré; Ofer Filiba; Laura Pedraza-González; Ronald González; Cristina González‐Espinoza; Rajiv Kar; Lukas Kemmler; Seung Kim; Jacob Kongsted; Igor Schapiro
Frontiers in Multiscale Modeling of Photoreceptor Proteins Article de journal
Dans: Photochemistry and Photobiology, 2020.
@article{articlee,
title = {Frontiers in Multiscale Modeling of Photoreceptor Proteins},
author = {Maria‐Andrea Mroginski and Suliman Adam and Gil Amoyal and Avishai Barnoy and Ana‐Nicoleta Bondar and Veniamin Borin and Jonathan Church and Tatiana Domratcheva and Bernd Ensing and Francesca Fanelli and Nicolas Ferré and Ofer Filiba and Laura Pedraza-González and Ronald González and Cristina González‐Espinoza and Rajiv Kar and Lukas Kemmler and Seung Kim and Jacob Kongsted and Igor Schapiro},
doi = {10.1111/php.13372},
year = {2020},
date = {2020-01-01},
journal = {Photochemistry and Photobiology},
abstract = {This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modelling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green‐fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin are presented, along with methodological developments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kankoé Sallah; Roch Giorgi; El-Hadj Ba; Martine Piarroux; Renaud Piarroux; Badara Cissé; Jean Gaudart
Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal Article de journal
Dans: International Journal of Environmental Research and Public Health, vol. 18, p. 76, 2020.
@article{articlef,
title = {Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal},
author = {Kankoé Sallah and Roch Giorgi and El-Hadj Ba and Martine Piarroux and Renaud Piarroux and Badara Cissé and Jean Gaudart},
doi = {10.3390/ijerph18010076},
year = {2020},
date = {2020-01-01},
journal = {International Journal of Environmental Research and Public Health},
volume = {18},
pages = {76},
abstract = {In central Senegal, malaria incidence declined in response to scaling-up of control measures from 2000 to 2010 and has since remained stable, making elimination unlikely in the short term. Additional control measures are needed to reduce transmission. We simulated chemoprophylaxis interventions targeting malaria hotspots using a metapopulation mathematical model, based on a differential-equation framework and incorporating human mobility. The model was fitted to weekly malaria incidence from 45 villages. Three approaches for selecting intervention targets were compared: (a) villages with malaria cases during the low transmission season of the previous year; (b) villages with highest incidence during the high transmission season of the previous year; (c) villages with highest connectivity with adjacent populations. Our results showed that intervention strategies targeting hotspots would be effective in reducing malaria incidence in both targeted and untargeted areas. Regardless of the intervention strategy used, pre-elimination (1–5 cases per 1000 per year) would not be reached without simultaneously increasing vector control by more than 10%. A cornerstone of malaria control and elimination is the effective targeting of strategic locations. Mathematical tools help to identify those locations and estimate the impact in silico.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yasaman Karami; Paul Saighi; Rémy Vanderhaegen; Denis Gerlier; Sonia Longhi; Elodie Laine; Alessandra Carbone
Predicting substitutions to modulate disorder and stability in coiled-coils Article de journal
Dans: BMC Bioinformatics, vol. 21, 2020.
@article{articleg,
title = {Predicting substitutions to modulate disorder and stability in coiled-coils},
author = {Yasaman Karami and Paul Saighi and Rémy Vanderhaegen and Denis Gerlier and Sonia Longhi and Elodie Laine and Alessandra Carbone},
doi = {10.1186/s12859-020-03867-x},
year = {2020},
date = {2020-01-01},
journal = {BMC Bioinformatics},
volume = {21},
abstract = {Background Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. Results In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Conclusions Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Boulet; Marie-Christine Record
Theoretical Investigations of the BaRh2Ge4X6 (X = S, Se, Te) Compounds Article de journal
Dans: Energies, vol. 13, p. 6434, 2020.
@article{Boulet2020TheoreticalIO,
title = {Theoretical Investigations of the BaRh2Ge4X6 (X = S, Se, Te) Compounds},
author = {P Boulet and Marie-Christine Record},
url = {https://onlinelibrary.wiley.com/doi/10.1002/jccs.202000499},
year = {2020},
date = {2020-01-01},
journal = {Energies},
volume = {13},
pages = {6434},
abstract = {The thermoelectric (TE) properties of the BaM2Ge4X6 compounds, where M = Rh and X = S, Se, Te, were investigated by computational approaches using density-functional theory and semi-classical Boltzmann theory for electronic transport. It was found that these compounds bear good TE properties, in particular BaRh2Ge4Te6, for which the figure of merit was estimated to reach 1.51 at 300 K. As this compound has not yet been proved to be stable, we also investigated BaRh2Ge4S4Te2 by assuming that replacing tellurium by sulphur could stabilize the tellurium-containing structure. It was found that the TE properties are good. The quantum theory of atoms in molecules was used to investigate the nature of the chemical interactions that prevail in these compounds. A wide variety of interactions were evidenced, from van der Waals interactions to ionic and polar-covalent ones, which could explain the good TE performance of these compounds.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shao-Long Guo; Yong-Liang Feng; Pierre Sagaut
Improved standard thermal lattice Boltzmann model with hybrid recursive regularization for compressible laminar and turbulent flows Article de journal
Dans: Physics of Fluids, vol. 32, 2020.
@article{articleh,
title = {Improved standard thermal lattice Boltzmann model with hybrid recursive regularization for compressible laminar and turbulent flows},
author = {Shao-Long Guo and Yong-Liang Feng and Pierre Sagaut},
doi = {10.1063/5.0033364},
year = {2020},
date = {2020-01-01},
journal = {Physics of Fluids},
volume = {32},
abstract = {Based on recent work by [Guo et. al, JCP,109570(2020)], an improved thermal hybrid recursive regularized lattice Boltzmann model (iHRR-ρ) on regular lattice is developed for two and three-dimensional compressible laminar and turbulent flows. To enhance the numerical stability in a broad range of Courant-Friedrichs-Lewy numbers and in under-resolved simulations, a new equilibrium density distribution function is proposed to enlarge its positivity region in Mach-temperature plane. An embedded hybridizing procedure is introduced in the quasi-symmetry correction terms, which allow for a decoupled treatment unphysical modes and physical under-resolved turbulent scales on coarse grids. To handle compressible turbulent flows, the under-resolved scales are modeled using the original hybrid recursive regularized collision model given in [Jacob et al, JoT,19,1151-1176(2018)] equipped with Vreman’s subgrid model for the Large-Eddy Simulation. The validity and accuracy of the present method for laminar and turbulent compressible flows are assessed by considering six test cases: I) viscous shock wave internal structure; II) isentropic vortex convection in supersonic regime; III) non-isothermal acoustic pulse; IV) vortex-shock wave interaction; V) supersonic flow over NACA airfoil at Re=10000 and Ma=1.5; VI) compressible Taylor-Green vortex at Ma=0.29.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Amédée Renand; Iñaki Cervera-Marzal; Laurine Gil; Chuang Dong; Alexandra Garcia; Erwan Kervagoret; Hélène Aublé; Sarah Habes; Caroline Chevalier; Fabienne Vavasseur; Béatrice Clémenceau; Anaïs Cardon; Jean-Paul Judor; Jean-François Mosnier; Florence Tanné; David-Axel Laplaud; Sophie Brouard; Jérôme Gournay; Pierre Milpied; Sophie Conchon
Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis Article de journal
Dans: Journal of Hepatology, 2020.
@article{renand:hal-02982205,
title = {Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis},
author = {Amédée Renand and Iñaki Cervera-Marzal and Laurine Gil and Chuang Dong and Alexandra Garcia and Erwan Kervagoret and Hélène Aublé and Sarah Habes and Caroline Chevalier and Fabienne Vavasseur and Béatrice Clémenceau and Anaïs Cardon and Jean-Paul Judor and Jean-François Mosnier and Florence Tanné and David-Axel Laplaud and Sophie Brouard and Jérôme Gournay and Pierre Milpied and Sophie Conchon},
editor = {The Mw 6.5 Norcia earthquake occurred on 30 October 2016, along the Mt Vettore fault (Central Apennines, Italy), it was the largest earthquake of the 2016–2017 seismic sequence that started 2 months earlier with the Mw 6.0 Amatrice earthquake (24 August). To detect potential slow slip during the sequence, we produced Interferometric Synthetic Aperture Radar (InSAR) time series using 12‐ to 6‐day repeat cycles of Sentinel‐1A/1B images. Time series indicates that centimeter‐scale surface displacements took place during the 10 weeks following the Norcia earthquake. Two areas of subsidence are detected: one in the Castelluccio basin (hanging wall of the Mt Vettore fault) and one in the southern extent of the Norcia earthquake surface rupture, near an inherited thrust. Poroelastic and viscoelastic models are unable to explain these displacements. In the Castelluccio basin, the displacement reaches 13.2 ± 1.4 mm in the ascending line of sight on 6 January 2017. South of the Norcia earthquake surface rupture (a zone between the Norcia and Amatrice earthquakes), the postseismic surface displacements affect a smaller area but reach 35.5 ± 1.7 mm in ascending line of sight by January 2017 and follow a logarithmic temporal decay consistent with postseismic afterslip. Our analysis suggests that the structurally complex area located south of the Norcia rupture (30 October) is characterized by a conditionally stable frictional regime. This geometrical and frictional barrier likely halted rupture propagation during the Amatrice (24 August) and Norcia (30 October) earthquakes at shallow depth (<3–4 km).},
url = {https://hal.archives-ouvertes.fr/hal-02982205},
doi = {10.1016/j.jhep.2020.05.053},
year = {2020},
date = {2020-01-01},
journal = {Journal of Hepatology},
publisher = {Elsevier},
abstract = {Background & Aims:In most autoimmune disorders, crosstalk of B cells andCD4 T cells results in the accumulation of autoantibodies. In autoimmunehepatitis (AIH), the presence of anti-Soluble Liver Antigen (SLA or SepSecs) autoantibodies is associated with significantly reduced overall survival, but theassociatedautoreactive CD4 T cells have not been characterized yet. Here we isolatedand deeply characterizedSLA-specific CD4 T cells in AIH patients.
Methods:We used brief ex vivorestimulation with overlapping SLA-derived peptidesto isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterize their transcriptome and TCR repertoire in n=5 AIH patients.SLA-specific CD4 T cells were tracked in peripheral blood through TCR sequencing, to identify their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content flow cytometryin an additional cohort of n=46 AIH patients and n=18non-alcoholic steatohepatitis (NASH) controls.
Results:Autoreactive SLA-specific CD4 T cells were only detected in patients with anti-SLA autoantibodiesand had a memory PD-1+CXCR5-CCR6-CD27+phenotype. ScRNA-seq revealedtheirpro-inflammatory/B-Helper profile (IL21, IFNG, TIGIT,CTLA4, NR3C1, CD109, KLRB1andCLEC2D).Autoreactive TCR clonotypes were restricted to thememory PD-1+CXCR5-CD4 T cells. This subset was significantly increased in the blood of AIH patients and supported B cell differentiationthrough IL-21.Finally, we identified a specific phenotype (PD-1+CD38+CD27+CD127-CXCR5-) of CD4 T cells linked to disease activity and IgG response during AIH.
Conclusions:This work provides for the first time a deep characterization of rare circulating autoreactive CD4 T cells andtheidentification oftheirperipheral reservoir in AIH.We alsopropose a generic phenotype of pathogenic CD4 T cellsrelated toAIHdisease activity. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Methods:We used brief ex vivorestimulation with overlapping SLA-derived peptidesto isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterize their transcriptome and TCR repertoire in n=5 AIH patients.SLA-specific CD4 T cells were tracked in peripheral blood through TCR sequencing, to identify their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content flow cytometryin an additional cohort of n=46 AIH patients and n=18non-alcoholic steatohepatitis (NASH) controls.
Results:Autoreactive SLA-specific CD4 T cells were only detected in patients with anti-SLA autoantibodiesand had a memory PD-1+CXCR5-CCR6-CD27+phenotype. ScRNA-seq revealedtheirpro-inflammatory/B-Helper profile (IL21, IFNG, TIGIT,CTLA4, NR3C1, CD109, KLRB1andCLEC2D).Autoreactive TCR clonotypes were restricted to thememory PD-1+CXCR5-CD4 T cells. This subset was significantly increased in the blood of AIH patients and supported B cell differentiationthrough IL-21.Finally, we identified a specific phenotype (PD-1+CD38+CD27+CD127-CXCR5-) of CD4 T cells linked to disease activity and IgG response during AIH.
Conclusions:This work provides for the first time a deep characterization of rare circulating autoreactive CD4 T cells andtheidentification oftheirperipheral reservoir in AIH.We alsopropose a generic phenotype of pathogenic CD4 T cellsrelated toAIHdisease activity.
Léa Pousse-Beltran; Anne Socquet; Lucilla Benedetti; Marie-Pierre Doin; Magali Rizza; Nicola D'Agostino
Localized Afterslip at Geometrical Complexities Revealed by InSAR After the 2016 Central Italy Seismic Sequence Article de journal
Dans: Journal of Geophysical Research: Solid Earth, vol. 125, no. 11, p. e2019JB019065, 2020, (e2019JB019065 2019JB019065).
@article{https://doi.org/10.1029/2019JB019065,
title = {Localized Afterslip at Geometrical Complexities Revealed by InSAR After the 2016 Central Italy Seismic Sequence},
author = {Léa Pousse-Beltran and Anne Socquet and Lucilla Benedetti and Marie-Pierre Doin and Magali Rizza and Nicola D'Agostino},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JB019065},
doi = {https://doi.org/10.1029/2019JB019065},
year = {2020},
date = {2020-01-01},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {125},
number = {11},
pages = {e2019JB019065},
abstract = {Abstract The Mw 6.5 Norcia earthquake occurred on 30 October 2016, along the Mt Vettore fault (Central Apennines, Italy), it was the largest earthquake of the 2016–2017 seismic sequence that started 2 months earlier with the Mw 6.0 Amatrice earthquake (24 August). To detect potential slow slip during the sequence, we produced Interferometric Synthetic Aperture Radar (InSAR) time series using 12- to 6-day repeat cycles of Sentinel-1A/1B images. Time series indicates that centimeter-scale surface displacements took place during the 10 weeks following the Norcia earthquake. Two areas of subsidence are detected: one in the Castelluccio basin (hanging wall of the Mt Vettore fault) and one in the southern extent of the Norcia earthquake surface rupture, near an inherited thrust. Poroelastic and viscoelastic models are unable to explain these displacements. In the Castelluccio basin, the displacement reaches 13.2 ± 1.4 mm in the ascending line of sight on 6 January 2017. South of the Norcia earthquake surface rupture (a zone between the Norcia and Amatrice earthquakes), the postseismic surface displacements affect a smaller area but reach 35.5 ± 1.7 mm in ascending line of sight by January 2017 and follow a logarithmic temporal decay consistent with postseismic afterslip. Our analysis suggests that the structurally complex area located south of the Norcia rupture (30 October) is characterized by a conditionally stable frictional regime. This geometrical and frictional barrier likely halted rupture propagation during the Amatrice (24 August) and Norcia (30 October) earthquakes at shallow depth (<3–4 km).},
note = {e2019JB019065 2019JB019065},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hailong Yang; Pascal Boulet; Marie-Christine Record
Thermoelectric Properties of Sb-S System Compounds from DFT Calculations Article de journal
Dans: Materials, vol. 13, no. 21, p. 4707, 2020.
@article{articlei,
title = {Thermoelectric Properties of Sb-S System Compounds from DFT Calculations},
author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},
url = {https://www.mdpi.com/1996-1944/13/21/4707},
doi = {10.3390/ma13214707},
year = {2020},
date = {2020-01-01},
journal = {Materials},
volume = {13},
number = {21},
pages = {4707},
abstract = {By combining density functional theory, quantum theory of atoms in molecules and transport properties calculations, we evaluated the thermoelectric properties of Sb-S system compounds and shed light on their relationships with electronic structures. The results show that, for Sb2S3, the large density of states (DOS) variation induces a large Seebeck coefficient. Taking into account the long-range weak bonds distribution, Sb2S3 should exhibit low lattice thermal conductivity. Therefore, Sb2S3 is promising for thermoelectric applications. The insertion of Be atoms into the Sb2S3 interstitial sites demonstrates the electrical properties and Seebeck coefficient anisotropy and sheds light on the understanding of the role of quasi-one-dimensional structure in the electron transport. The large interstitial sites existing in SbS2 are at the origin of phonons anharmonicity which counteracts the thermal transport. The introduction of Zn and Ga atoms into these interstitial sites could result in an enhancement of all the thermoelectric properties.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Victor Boutin; Angelo Franciosini; Franck Ruffier; Laurent Perrinet
Effect of Top-Down Connections in Hierarchical Sparse Coding Article de journal
Dans: Neural Computation, vol. 32, no. 11, p. 2279-2309, 2020, (PMID: 32946716).
@article{doi:10.1162/neco_a_01325,
title = {Effect of Top-Down Connections in Hierarchical Sparse Coding},
author = {Victor Boutin and Angelo Franciosini and Franck Ruffier and Laurent Perrinet},
url = {https://doi.org/10.1162/neco_a_01325},
doi = {10.1162/neco_a_01325},
year = {2020},
date = {2020-01-01},
journal = {Neural Computation},
volume = {32},
number = {11},
pages = {2279-2309},
abstract = {Hierarchical sparse coding (HSC) is a powerful model to efficiently represent multidimensional, structured data such as images. The simplest solution to solve this computationally hard problem is to decompose it into independent layer-wise subproblems. However, neuroscientific evidence would suggest interconnecting these subproblems as in predictive coding (PC) theory, which adds top-down connections between consecutive layers. In this study, we introduce a new model, 2-layer sparse predictive coding (2L-SPC), to assess the impact of this interlayer feedback connection. In particular, the 2L-SPC is compared with a hierarchical Lasso (Hi-La) network made out of a sequence of independent Lasso layers. The 2L-SPC and a 2-layer Hi-La networks are trained on four different databases and with different sparsity parameters on each layer. First, we show that the overall prediction error generated by 2L-SPC is lower thanks to the feedback mechanism as it transfers prediction error between layers. Second, we demonstrate that the inference stage of the 2L-SPC is faster to converge and generates a refined representation in the second layer compared to the Hi-La model. Third, we show that the 2L-SPC top-down connection accelerates the learning process of the HSC problem. Finally, the analysis of the emerging dictionaries shows that the 2L-SPC features are more generic and present a larger spatial extension.},
note = {PMID: 32946716},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Robert Darlin Mba; Juste Aristide Goungounga; Nathalie Graffeo; Roch Giorgi
Correcting inaccurate background mortality in excess hazard models through breakpoints Article de journal
Dans: BMC Medical Research Methodology, vol. 20, no. 1, p. 268, 2020.
@article{doi:10.1162/neco_a_01325b,
title = {Correcting inaccurate background mortality in excess hazard models through breakpoints},
author = {Robert Darlin Mba and Juste Aristide Goungounga and Nathalie Graffeo and Roch Giorgi},
url = {https://www.hal.inserm.fr/inserm-03104366},
doi = {10.1186/s12874-020-01139-z},
year = {2020},
date = {2020-01-01},
journal = {BMC Medical Research Methodology},
volume = {20},
number = {1},
pages = {268},
publisher = {BioMed Central},
abstract = {Methods for estimating relative survival are widely used in population-based cancer survival studies. These methods are based on splitting the observed (the overall) mortality into excess mortality (due to cancer) and background mortality (due to other causes, as expected in the general population). The latter is derived from life tables usually stratified by age, sex, and calendar year but not by other covariates (such as the deprivation level or the socioeconomic status) which may lack though they would influence background mortality. The absence of these covariates leads to inaccurate background mortality, thus to biases in estimating the excess mortality. These biases may be avoided by adjusting the background mortality for these covariates whenever available.Methods for estimating relative survival are widely used in population-based cancer survival studies. These methods are based on splitting the observed (the overall) mortality into excess mortality (due to cancer) and background mortality (due to other causes, as expected in the general population). The latter is derived from life tables usually stratified by age, sex, and calendar year but not by other covariates (such as the deprivation level or the socioeconomic status) which may lack though they would influence background mortality. The absence of these covariates leads to inaccurate background mortality, thus to biases in estimating the excess mortality. These biases may be avoided by adjusting the background mortality for these covariates whenever available.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kai Zhang; Aymeric Lamorlette
An extensive numerical study of the burning dynamics of wildland fuel using proposed configuration space Article de journal
Dans: International Journal of Heat and Mass Transfer, vol. 160, p. 120174, 2020, ISSN: 0017-9310.
@article{ZHANG2020120174,
title = {An extensive numerical study of the burning dynamics of wildland fuel using proposed configuration space},
author = {Kai Zhang and Aymeric Lamorlette},
url = {https://www.sciencedirect.com/science/article/pii/S0017931020331100},
doi = {https://doi.org/10.1016/j.ijheatmasstransfer.2020.120174},
issn = {0017-9310},
year = {2020},
date = {2020-01-01},
journal = {International Journal of Heat and Mass Transfer},
volume = {160},
pages = {120174},
abstract = {Physics-based flame models capable of predicting small-scale fire behaviors reduce computational power needed for predicting fires of large- and giga-scale. However, classical model correlations are often developed for ‘free fires’ without considering vegetation around. These models may result in inaccurate fire modeling due to wrong ‘prior’ flame shape estimated from θ ~ wind speed. To overcome this defect, three-dimensional small-scale fires with fireline intensity of 100 KW/m are numerically simulated using large eddy simulation. Fire behaviors such as flame tilt angle and heat transfer mechanisms are extensively studied using a newly proposed configuration space NC, CdLAI. The former one represents the ratio between fire to wind power, and the latter one considering the vegetation effect is for the first time introduced in flame models. Using the configuration space, two model correlations for flame tilt angle and radiative heat power reaching the unburnt fuels are proposed. The flame tilt angle θ is directly related to CdLAI (CdαsσsHF/2), while inversely related to NC (2gI/ρ0Cp,0T0U03), in contrast to the model proposed for radiative heat power. Comparisons with several classical models evidenced the capability of new flame models in predicting both free and non-free fires. The limits of the validity of the newly proposed models are also discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
S Guo; Y Feng; J Jacob; F Renard; P Sagaut
An efficient lattice Boltzmann method for compressible aerodynamics on D3Q19 lattice Article de journal
Dans: Journal of Computational Physics, vol. 418, p. 109570, 2020, ISSN: 0021-9991.
@article{GUO2020109570,
title = {An efficient lattice Boltzmann method for compressible aerodynamics on D3Q19 lattice},
author = {S Guo and Y Feng and J Jacob and F Renard and P Sagaut},
url = {https://www.sciencedirect.com/science/article/pii/S0021999120303442},
doi = {https://doi.org/10.1016/j.jcp.2020.109570},
issn = {0021-9991},
year = {2020},
date = {2020-01-01},
journal = {Journal of Computational Physics},
volume = {418},
pages = {109570},
abstract = {An efficient lattice Boltzmann (LB) model relying on a hybrid recursive regularization (HRR) collision operator on D3Q19 stencil is proposed for the simulation of three-dimensional high-speed compressible flows in both subsonic and supersonic regimes. An improved thermal equilibrium distribution function on D3Q19 lattice is derived to reduce the complexity of correcting terms. A simple shock capturing scheme and an upwind biased discretization of correction terms are implemented for supersonic flows with shocks. Mass and momentum equations are recovered by an efficient streaming, collision and forcing process on D3Q19 lattice. Then a non-conservative formulation of the entropy evolution equation is used, that is solved using a finite volume method. The proposed method is assessed considering the simulation of i) 2D isentropic vortex convection, ii) 3D non-isothermal acoustic pulse, iii) 2D supersonic flow over a bump, iv) 3D shock explosion in a box, v) 2D vortex interaction with shock wave, vi) 2D laminar flows over a flat plate at Ma of 0.5, 1.0 and 1.5.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fábris Kossoski; Mario Barbatti
Nonadiabatic dynamics in multidimensional complex potential energy surfaces Article de journal
Dans: Chem. Sci., vol. 11, p. 9827-9835, 2020.
@article{D0SC04197A,
title = {Nonadiabatic dynamics in multidimensional complex potential energy surfaces},
author = {Fábris Kossoski and Mario Barbatti},
url = {http://dx.doi.org/10.1039/D0SC04197A},
doi = {10.1039/D0SC04197A},
year = {2020},
date = {2020-01-01},
journal = {Chem. Sci.},
volume = {11},
pages = {9827-9835},
publisher = {The Royal Society of Chemistry},
abstract = {Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the π*/σ* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the π* orbital promotes CC stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the σ* orbital at the C–I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic coulombic decay, and time-dependent luminescence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jiangkun Ouyang; Anne Swartjes; Marc Geerts; Pieter J Gilissen; D Wang; Paula C P Teeuwen; paul Tinnemans; Nicolas Vanthuyne; Sara Chentouf; Floris P J T Rutjes; J -V Naubron; Jeanne Crassous; Johannes A A W Elemans; R Nolte
Absolute configuration and host-guest binding of chiral porphyrin-cages by a combined chiroptical and theoretical approach Article de journal
Dans: Nature Communications, vol. 11, no. 1, p. 4776, 2020.
@article{ouyang:hal-02959804,
title = {Absolute configuration and host-guest binding of chiral porphyrin-cages by a combined chiroptical and theoretical approach},
author = {Jiangkun Ouyang and Anne Swartjes and Marc Geerts and Pieter J Gilissen and D Wang and Paula C P Teeuwen and paul Tinnemans and Nicolas Vanthuyne and Sara Chentouf and Floris P J T Rutjes and J -V Naubron and Jeanne Crassous and Johannes A A W Elemans and R Nolte},
url = {https://hal.archives-ouvertes.fr/hal-02959804},
doi = {10.1038/s41467-020-18596-1},
year = {2020},
date = {2020-01-01},
journal = {Nature Communications},
volume = {11},
number = {1},
pages = {4776},
publisher = {Nature Publishing Group},
abstract = {Porphyrin cage-compounds are used as biomimetic models and substrate-selective catalysts in supramolecular chemistry. In this work we present the resolution of planar-chiral porphyrin cages and the determination of their absolute configuration by vibrational circular dichroism in combination with density functional theory calculations. The chiral porphyrin-cages form complexes with achiral and chiral viologen-guests and upon binding one of the axial enantiomorphs of the guest is bound selectively, as is indicated by induced-electronic-dichroism-spectra in combination with calculations. This host-guest binding also leads to unusual enhanced vibrational circular dichroism, which is the result of a combination of phenomena, such as rigidification of the host and guest structures, charge transfer, and coupling of specific vibration modes of the host and guest. The results offer insights in how the porphyrin cage-compounds may be used to construct a future molecular Turing machine that can write chiral information onto polymer chains.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
G Giorgiani; H Bufferand; F Schwander; E Serre; P Tamain
A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion Article de journal
Dans: Computer Physics Communications, vol. 254, p. 107375, 2020, ISSN: 0010-4655.
@article{GIORGIANI2020107375,
title = {A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion},
author = {G Giorgiani and H Bufferand and F Schwander and E Serre and P Tamain},
url = {https://www.sciencedirect.com/science/article/pii/S0010465520301612},
doi = {https://doi.org/10.1016/j.cpc.2020.107375},
issn = {0010-4655},
year = {2020},
date = {2020-01-01},
journal = {Computer Physics Communications},
volume = {254},
pages = {107375},
abstract = {In this work we present a hybrid discontinuous Galerkin scheme for the solution of extremely anisotropic diffusion problems arising in magnetized plasmas for fusion applications. Unstructured meshes, non-aligned with respect to the dominant diffusion direction, allow an unequalled flexibility in discretizing geometries of any shape, but may lead to spurious numerical diffusion. Curved triangles or quadrangles are used to discretize the poloidal plane of the machine, while a structured discretization is used in the toroidal direction. The proper design of the numerical fluxes guarantees the correct convergence order at any anisotropy level. Computations performed on well-designed 2D and 3D numerical tests show that non-aligned discretizations are able to provide spurious diffusion free solutions as long as high-order interpolations are used. Introducing an explicit measure of the numerical diffusion, a careful investigation is carried out showing an exponential increase of this latest with respect to the non-alignment of the mesh with the diffusion direction, as well as an exponential decrease with the polynomial degree of interpolation. A brief assessment of the method with respect to two finite-difference schemes using non-aligned discretization, but classically used in fusion modeling, is also presented.
Program summary
Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Program summary
Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme
G Giorgiani; H Bufferand; F Schwander; E Serre; P Tamain
A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion Article de journal
Dans: Computer Physics Communications, vol. 254, p. 107375, 2020, ISSN: 0010-4655.
@article{GIORGIANI2020107375b,
title = {A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion},
author = {G Giorgiani and H Bufferand and F Schwander and E Serre and P Tamain},
url = {https://www.sciencedirect.com/science/article/pii/S0010465520301612},
doi = {https://doi.org/10.1016/j.cpc.2020.107375},
issn = {0010-4655},
year = {2020},
date = {2020-01-01},
journal = {Computer Physics Communications},
volume = {254},
pages = {107375},
abstract = {In this work we present a hybrid discontinuous Galerkin scheme for the solution of extremely anisotropic diffusion problems arising in magnetized plasmas for fusion applications. Unstructured meshes, non-aligned with respect to the dominant diffusion direction, allow an unequalled flexibility in discretizing geometries of any shape, but may lead to spurious numerical diffusion. Curved triangles or quadrangles are used to discretize the poloidal plane of the machine, while a structured discretization is used in the toroidal direction. The proper design of the numerical fluxes guarantees the correct convergence order at any anisotropy level. Computations performed on well-designed 2D and 3D numerical tests show that non-aligned discretizations are able to provide spurious diffusion free solutions as long as high-order interpolations are used. Introducing an explicit measure of the numerical diffusion, a careful investigation is carried out showing an exponential increase of this latest with respect to the non-alignment of the mesh with the diffusion direction, as well as an exponential decrease with the polynomial degree of interpolation. A brief assessment of the method with respect to two finite-difference schemes using non-aligned discretization, but classically used in fusion modeling, is also presented.
Program summary
Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Program summary
Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme
Xi Deng; Pierre Boivin
Diffuse interface modelling of reactive multi-phase flows applied to a sub-critical cryogenic jet Article de journal
Dans: Applied Mathematical Modelling, vol. 84, p. 405-424, 2020, ISSN: 0307-904X.
@article{DENG2020405,
title = {Diffuse interface modelling of reactive multi-phase flows applied to a sub-critical cryogenic jet},
author = {Xi Deng and Pierre Boivin},
url = {https://www.sciencedirect.com/science/article/pii/S0307904X20301943},
doi = {https://doi.org/10.1016/j.apm.2020.04.011},
issn = {0307-904X},
year = {2020},
date = {2020-01-01},
journal = {Applied Mathematical Modelling},
volume = {84},
pages = {405-424},
abstract = {In order to simulate cryogenic H2−O2 jets under subcritical condition, a numerical model is constructed to solve compressible reactive multi-component flows which involve complex multi-physics processes such as moving material interfaces, shock waves, phase transition and combustion. The liquid and reactive gaseous mixture are described by a homogeneous mixture model with diffusion transport for heat, momentum and species. A hybrid thermodynamic closure strategy is proposed to construct an equation of state (EOS) for the mixture. The phase transition process is modeled by a recent fast relaxation method which gradually reaches the thermo-chemical equilibrium without iterative process. A simplified transport model is also implemented to ensure the accurate behavior in the limit of pure fluids and maintain computational efficiency. Last, a 12-step chemistry model is included to account for hydrogen combustion. Then the developed numerical model is solved with the finite volume method where a low dissipation AUSM (advection upstream splitting method) Riemann solver is extended for multi-component flows. A homogeneous reconstruction strategy compatible with the homogeneous mixture model is adopted to prevent numerical oscillations across material interfaces. Having included these elements, the model is validated on a number of canonical configurations, first for multiphase flows, and second for reactive flows. These tests allow recovery of the expected behavior in both the multiphase and reactive limits, and the model capability is further demonstrated on a 2D burning cryogenic H2−O2 jet, in a configuration reminiscent of rocket engine ignition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Marcel Krug; Maximilian Wagner; Tobias A Schaub; Wen-Shan Zhang; Christoph M Schüßlbauer; Johannes D R Ascherl; Peter W Münich; Rasmus R Schröder; Franziska Gröhn; Pavlo O Dral; Mario Barbatti; Dirk M Guldi; Milan Kivala
The Impact of Aggregation on the Photophysics of Spiro-Bridged Heterotriangulenes Article de journal
Dans: Angewandte Chemie International Edition, vol. 59, no. 37, p. 16233-16240, 2020.
@article{https://doi.org/10.1002/anie.202003504,
title = {The Impact of Aggregation on the Photophysics of Spiro-Bridged Heterotriangulenes},
author = {Marcel Krug and Maximilian Wagner and Tobias A Schaub and Wen-Shan Zhang and Christoph M Schüßlbauer and Johannes D R Ascherl and Peter W Münich and Rasmus R Schröder and Franziska Gröhn and Pavlo O Dral and Mario Barbatti and Dirk M Guldi and Milan Kivala},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202003504},
doi = {https://doi.org/10.1002/anie.202003504},
year = {2020},
date = {2020-01-01},
journal = {Angewandte Chemie International Edition},
volume = {59},
number = {37},
pages = {16233-16240},
abstract = {Abstract We report on the impact of the central heteroatom on structural, electronic, and spectroscopic properties of a series of spirofluorene-bridged heterotriangulenes and provide a detailed study on their aggregates. The in-depth analysis of their molecular structure by NMR spectroscopy and X-ray crystallography was further complemented by density functional theory calculations. With the aid of extensive photophysical analysis the complex fluorescence spectra were deconvoluted showing contributions from the peripheral fluorenes and the heteroaromatic cores. Beyond the molecular scale, we examined the aggregation behavior of these heterotriangulenes in THF/H2O mixtures and analyzed the aggregates by static and dynamic light scattering. The excited-state interactions within the aggregates were found to be similar to those found in the solid state. A plethora of morphologies and superstructures were observed by scanning electron microscopy of drop-casted dispersions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Katsunori Mizuno; Paul Cristini; Dimitri Komatitsch; Yann Capdeville
Numerical and Experimental Study of Wave Propagation in Water-Saturated Granular Media Using Effective Method Theories and a Full-Wave Numerical Simulation Article de journal
Dans: IEEE Journal of Oceanic Engineering, vol. 45, no. 3, p. 772 - 785, 2020.
@article{mizuno:hal-02871575,
title = {Numerical and Experimental Study of Wave Propagation in Water-Saturated Granular Media Using Effective Method Theories and a Full-Wave Numerical Simulation},
author = {Katsunori Mizuno and Paul Cristini and Dimitri Komatitsch and Yann Capdeville},
url = {https://hal.archives-ouvertes.fr/hal-02871575},
doi = {10.1109/JOE.2020.2983865},
year = {2020},
date = {2020-01-01},
journal = {IEEE Journal of Oceanic Engineering},
volume = {45},
number = {3},
pages = {772 - 785},
publisher = {Institute of Electrical and Electronics Engineers},
abstract = {In this article, the detection of an object buried in marine sediments is investigated. Using the results from a series of experiments realized in a tank filled with water and calibrated glass beads, we evaluate the performances for a wide range of the value of the ratio kd of the grain size to the wavelength (k is the wave number and d is the grain diameter) of three types of prediction tools. The first two prediction tools are based on the definition of an equivalent model. The first tool is based on the well-known Biot-Stoll theory (BM model) while the second tool uses nonperiodic homogenization to define effective velocity and anisotropy maps representing the medium (HM model). The last prediction tool implements a time-domain full-wave numerical method, which takes into account each grain separately (GM model). It is shown that a good agreement between experiments and numerical simulations can be achieved using the BM model for the low kd regime and the HM model for high kd regime. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Y Feng; S Guo; J Jacob; P Sagaut
Grid refinement in the three-dimensional hybrid recursive regularized lattice Boltzmann method for compressible aerodynamics Article de journal
Dans: Physical Review E , vol. 101, no. 6, p. 063302, 2020.
@article{feng:hal-02892273,
title = {Grid refinement in the three-dimensional hybrid recursive regularized lattice Boltzmann method for compressible aerodynamics},
author = {Y Feng and S Guo and J Jacob and P Sagaut},
url = {https://hal.archives-ouvertes.fr/hal-02892273},
doi = {10.1103/PhysRevE.101.063302},
year = {2020},
date = {2020-01-01},
journal = {Physical Review E },
volume = {101},
number = {6},
pages = {063302},
publisher = {American Physical Society (APS)},
abstract = {Grid refinement techniques are of paramount importance for computational fluid dynamics approaches relying on the use of Cartesian grids. This is especially true of solvers dedicated to aerodynamics, in which the capture of thin shear layers require the use of small cells. In this paper, a three-dimensional grid refinement technique is developed within the framework of hybrid recursive regularized lattice Boltzmann method (HRR-LBM) for compressible high-speed flows, which is an efficient collide-stream-type method on a compact D3Q19 stencil. The proposed method is successfully assessed considering several test cases, namely, an isentropic vortex propagating through transition interface, shock-vortex interaction with intersection between grid refinement interface and shock corrugation, and transonic flows over three-dimensional DLR-M6 wing with seven levels of grid refinement. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hailong Yang; Pascal Boulet; Marie-Christine Record
New insight into the structure-property relationships from chemical bonding analysis: Application to thermoelectric materials Article de journal
Dans: Journal of Solid State Chemistry, vol. 286, p. 121266, 2020, ISSN: 0022-4596.
@article{YANG2020121266,
title = {New insight into the structure-property relationships from chemical bonding analysis: Application to thermoelectric materials},
author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},
url = {https://www.sciencedirect.com/science/article/pii/S0022459620300967},
doi = {https://doi.org/10.1016/j.jssc.2020.121266},
issn = {0022-4596},
year = {2020},
date = {2020-01-01},
journal = {Journal of Solid State Chemistry},
volume = {286},
pages = {121266},
abstract = {Structure-property relationships are indisputably important to deeply understand the nature of materials. The main direction pursued to investigate these relations is based on the chemical bonding concept. The integral and local properties of chemical bonding determined from the topological analysis of electron density by combining the quantum theory of atoms in molecules (AIM) and DFT calculations can aid to build a bridge between the atomic structure and the intrinsic properties of materials. In this paper, the electronic and thermal transport properties of thermoelectric materials in the Cu–Sb–Se system have been analysed by coupling energy densities relationships and corresponding electron density Laplacian distribution for specific interactions. The asset of this method is to directly highlight the influence of lone pair electrons and atomic fluctuations on interatomic interactions as well as the coupling effect of weak bonds, which offers a new approach to design and search for materials with low thermal conductivity at low calculation cost.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hailong Yang; Pascal Boulet; Marie-Christine Record
A rapid method for analyzing the chemical bond from energy densities calculations at the bond critical point Article de journal
Dans: Computational and Theoretical Chemistry, vol. 1178, p. 112784, 2020, ISSN: 2210-271X.
@article{YANG2020112784,
title = {A rapid method for analyzing the chemical bond from energy densities calculations at the bond critical point},
author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},
url = {https://www.sciencedirect.com/science/article/pii/S2210271X20300840},
doi = {https://doi.org/10.1016/j.comptc.2020.112784},
issn = {2210-271X},
year = {2020},
date = {2020-01-01},
journal = {Computational and Theoretical Chemistry},
volume = {1178},
pages = {112784},
abstract = {The quantum theory atoms in molecules (QTAIM) method has been used in this paper to characterize various bonding interactions in molecules and solid compounds. By using DFT-PAW calculations, complete electron density Laplacian distributions have been obtained and related to energies densities calculated at the bond critical points. From the analysis of these results a simple and rapid method, based solely on local energies densities calculations, is proposed to diagnose the bonding state, the polarizability and the deformation of the charge distribution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
T Cartier-Michaud; D Galassi; Ph Ghendrih; P Tamain; F Schwander; E Serre
A posteriori error estimate in fluid simulations of turbulent edge plasmas for magnetic fusion in tokamak using the data mining iPoPe method Article de journal
Dans: Physics of Plasmas, 2020.
@article{cartiermichaud:hal-02613800,
title = {A posteriori error estimate in fluid simulations of turbulent edge plasmas for magnetic fusion in tokamak using the data mining iPoPe method},
author = {T Cartier-Michaud and D Galassi and Ph Ghendrih and P Tamain and F Schwander and E Serre},
url = {https://hal.archives-ouvertes.fr/hal-02613800},
year = {2020},
date = {2020-01-01},
journal = {Physics of Plasmas},
publisher = {American Institute of Physics},
abstract = {Progressing towards more reliable numerical solutions in the simulation of plasma for magnetic confinement fusion has become a critical issue for the success of the ITER operation. This requires developing rigorous and efficient methods of verification of the numerical simulations in any relevant flow regimes of the operation. The paper introduces a new formulation of the PoPe 1 method, namely the independent Projection on Proper elements method (iPoPe) to quantify the numerical error by performing a data-driven identification of the mathematical model from the simulation outputs. Based on a statistical postprocessing of the outputs database, the method provides a measure of the error by estimating the distance between the (numerical) effective and (analytical) theoretical weights of each operator implemented in the mathematical model. The efficiency of the present method is illustrated on turbulent edge plasma simulations based on a drift-reduced Braginskii fluid model in realistic magnetic geometries. Results show the effective order of the numerical method in these multiscale flow regimes as well as the values of the plasma parameters which can be safely simulated with respect to a given discretization. In this sense, the method goes one step further than the Method of Manufactured Solution (MMS 2-4), recently introduced in fusion, and provides an efficient verification procedure of the numerical simulations in any regimes, including turbulent ones that could be generalized to other scientific domains. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Farhan Siddique; Mario Barbatti; Zhonghua Cui; Hans Lischka; Adélia Aquino
Nonadiabatic Dynamics of Charge-Transfer States Using the Anthracene-Tetracyanoethylene Complex as Prototype Article de journal
Dans: Journal of Physical Chemistry A, vol. 124, no. 17, p. 3347-3357, 2020.
@article{siddique:hal-02612347,
title = {Nonadiabatic Dynamics of Charge-Transfer States Using the Anthracene-Tetracyanoethylene Complex as Prototype},
author = {Farhan Siddique and Mario Barbatti and Zhonghua Cui and Hans Lischka and Adélia Aquino},
url = {https://hal-amu.archives-ouvertes.fr/hal-02612347},
doi = {10.1021/acs.jpca.0c01900},
year = {2020},
date = {2020-01-01},
journal = {Journal of Physical Chemistry A},
volume = {124},
number = {17},
pages = {3347-3357},
publisher = {American Chemical Society},
abstract = {Surface hopping quantum mechanical/molecular dynamics simulations have been performed for the tetracyanoethylene–anthracene complex to investigate the evolution of charge-transfer (CT) states after excitation into a locally excited (LE) state of anthracene. The scaled opposite-spin (SOS) second-order algebraic diagrammatic construction (SOS-ADC(2)) has been used to achieve a balanced description of LE and CT states. The calculations have been performed for two media, the gas phase and water (described by molecular mechanics, MM). The two dynamics variants show strongly different behaviors. Even though in both cases the conversion from the LE state to lower-lying CT states occurs with 100 fs, in the gas phase, the system remains in the excited state for longer than 2 ps, while in water, it returns to the ground state within 0.5 ps. Moreover, while in the gas phase the original neutral equilibrium structure should be recovered, in water, the ion-pair (IPr) CT state is strongly stabilized, creating a new competing ground-state isomer. Thus, we predict that the ground state of the complex in water should be composed of two species, the original neutral state and an IPr state. The existence of an IPr ground state in strongly polar environments opens interesting possibilities for the design of efficient charge-separating organic donor–acceptor interfaces. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Ritam Mansour; Ljiljana Stojanovi'c; Josene Toldo; Mario Barbatti
On the Origin of the Shift Between Vertical Excitation and Band Maximum in Molecular Photoabsorption Article de journal
Dans: Journal of Molecular Modeling, vol. 26, no. 5, 2020.
@article{bai:hal-02612358,
title = {On the Origin of the Shift Between Vertical Excitation and Band Maximum in Molecular Photoabsorption},
author = {Shuming Bai and Ritam Mansour and Ljiljana Stojanovi{'c} and Josene Toldo and Mario Barbatti},
url = {https://hal-amu.archives-ouvertes.fr/hal-02612358},
doi = {10.1007/s00894-020-04355-y},
year = {2020},
date = {2020-01-01},
journal = {Journal of Molecular Modeling},
volume = {26},
number = {5},
publisher = {Springer Verlag (Germany)},
abstract = {The analysis of the photoabsorption spectra of molecules shows that the band maximum is usually redshifted in comparison to the vertical excitation. We conducted a throughout analysis of this shift based on low-dimensional analytical and numerical model systems, showing that its origin is rooted in the frequency changing between the ground and the excited states in multidimensional systems. Moreover, we deliver a benchmark of ab initio results for the shift based on a comparison of vertical excitations and band maxima calculated with the nuclear ensemble approach for the 28 organic molecules in the Mülheim molecular dataset. The mean value of the shift calculated over 60 transitions is 0.11 ± 0.08 eV. The mean value of the band width is 0.32 ± 0.14 eV. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pingping Jiang; Marie-Christine Record; Pascal Boulet
First-principles calculations on CuInSe2/AlP heterostructures Article de journal
Dans: J. Mater. Chem. C, vol. 8, p. 4732-4742, 2020.
@article{D0TC00131G,
title = {First-principles calculations on CuInSe2/AlP heterostructures},
author = {Pingping Jiang and Marie-Christine Record and Pascal Boulet},
url = {http://dx.doi.org/10.1039/D0TC00131G},
doi = {10.1039/D0TC00131G},
year = {2020},
date = {2020-01-01},
journal = {J. Mater. Chem. C},
volume = {8},
pages = {4732-4742},
publisher = {The Royal Society of Chemistry},
abstract = {Heterostructures based on a CuInSe2 absorber with an AlP buffer have been modeled for the first time using different stacking schemes and interfacial terminations. Mechanical, electronic and topological properties of CuInSe2/AlP heterostructures along the [001] direction were investigated using the full potential linear augmented plane wave (FP-LAPW) method. Optimal interfacial distance, thermodynamic stability and band alignment have been computed systematically. A heterointerface with “on-top” stacking is thermodynamically the most stable compared with other stackings. The magnitudes of core level binding energy differences are in accordance with interfacial adhesion energies. Absolute deformation potentials (ADPs) of band energies as a function of (001) biaxial strain were determined. With redressing of ADPs, the revised valence and conduction band offsets have increased and decreased, respectively. AlP has strong resistance to biaxial strain in the evolution of band energy edges. Topological properties and density of states were used to investigate the relationship between interatomic interactions and energy band evolution. The most stable CuInSe2/AlP heterostructures have “spike-like” band offsets, with the one terminated as Se–Al characterized by a flat conduction band offset of 12 meV. This comes from the strong “Cu d-Se p” states hybridization. The theoretical maximum conversion efficiency of the AlP-based “absorber-buffer” heterostructure is 27.39% at 0.5 μm thickness.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hans Lischka; Ron Shepard; Thomas Mueller; Péter Szalay; Russell Pitzer; Adélia Aquino; Mayzza Nascimento; Mario Barbatti; Lachlan Belcher; Jean Blaudeau; Itamar Jr; Scott Brozell; Emily Carter; Anita Das; Gergely Gidofalvi; Leticia González; William Hase; Gary Kedziora; Miklos Kertesz; Zhiyong Zhang
The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry Article de journal
Dans: The Journal of Chemical Physics, vol. 152, p. 134110, 2020.
@article{articlej,
title = {The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry},
author = {Hans Lischka and Ron Shepard and Thomas Mueller and Péter Szalay and Russell Pitzer and Adélia Aquino and Mayzza Nascimento and Mario Barbatti and Lachlan Belcher and Jean Blaudeau and Itamar Jr and Scott Brozell and Emily Carter and Anita Das and Gergely Gidofalvi and Leticia González and William Hase and Gary Kedziora and Miklos Kertesz and Zhiyong Zhang},
doi = {10.1063/1.5144267},
year = {2020},
date = {2020-01-01},
journal = {The Journal of Chemical Physics},
volume = {152},
pages = {134110},
abstract = {The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zeyd Benseghier; Pablo Cuéllar; Li-Hua Luu; Stéphane Bonelli; Pierre Philippe
A parallel GPU-based computational framework for the micromechanical analysis of geotechnical and erosion problems Article de journal
Dans: Computers and Geotechnics, vol. 120, p. 103404, 2020, ISSN: 0266-352X.
@article{BENSEGHIER2020103404,
title = {A parallel GPU-based computational framework for the micromechanical analysis of geotechnical and erosion problems},
author = {Zeyd Benseghier and Pablo Cuéllar and Li-Hua Luu and Stéphane Bonelli and Pierre Philippe},
url = {https://www.sciencedirect.com/science/article/pii/S0266352X19304689},
doi = {https://doi.org/10.1016/j.compgeo.2019.103404},
issn = {0266-352X},
year = {2020},
date = {2020-01-01},
journal = {Computers and Geotechnics},
volume = {120},
pages = {103404},
abstract = {This article deals with the relevance and practical feasibility of micromechanical simulations for their application to general geomechanical problems involving fluid-saturated granular assemblies, whether frictional or cohesive. A set of conceptual and numerical tools is here presented, advocating for a parallel computation using graphical processing units (GPUs) to treat large numbers of degrees of freedom with conventional desktop computers. The fluid phase is here simulated with a particle-resolved approach in the frame of the Lattice Botzmann Method (LBM) while the granular solid phase is modelled as a collection of discrete particles from a Molecular Dynamics DEM perspective. The range of possible material behaviours for the solid granular phase is intended here to cover a broad spectrum from purely frictional to viscous cohesive materials with either brittle or transient debonding features. Specific details of the implementation and some validation cases are put forward. Finally, some exemplary applications in the fields of soil erosion and geotechnical profile installation are provided along with a discussion on the parallel performance of the presented models. The results show that a micromechanical approach can be feasible and useful in practice, providing meaningful insights into complex engineering problems like the erosion kinetics of a soil under an impinging jet or the penetration resistance of a deep foundation in a layered soil profile.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hung Truong; Thomas Engels; Dmitry Kolomenskiy; Kai Schneider
A mass-spring fluid-structure interaction solver: Application to flexible revolving wings Article de journal
Dans: Computers & Fluids, vol. 200, p. 104426, 2020, ISSN: 0045-7930.
@article{TRUONG2020104426,
title = {A mass-spring fluid-structure interaction solver: Application to flexible revolving wings},
author = {Hung Truong and Thomas Engels and Dmitry Kolomenskiy and Kai Schneider},
url = {https://www.sciencedirect.com/science/article/pii/S0045793020300025},
doi = {https://doi.org/10.1016/j.compfluid.2020.104426},
issn = {0045-7930},
year = {2020},
date = {2020-01-01},
journal = {Computers & Fluids},
volume = {200},
pages = {104426},
abstract = {The secret to the spectacular flight capabilities of flapping insects lies in their wings, which are often approximated as flat, rigid plates. Real wings are however delicate structures, composed of veins and membranes, and can undergo significant deformation. In the present work, we present detailed numerical simulations of such deformable wings. Our results are obtained with a fluid–structure interaction solver, coupling a mass–spring model for the flexible wing with a pseudo-spectral code solving the incompressible Navier–Stokes equations. We impose the no-slip boundary condition through the volume penalization method; the time-dependent complex geometry is then completely described by a mask function. This allows solving the governing equations of the fluid on a regular Cartesian grid. Our implementation for massively parallel computers allows us to perform high resolution computations with up to 500 million grid points. The mass–spring model uses a functional approach, thus modeling the different mechanical behaviors of the veins and the membranes of the wing. We perform a series of numerical simulations of a flexible revolving bumblebee wing at a Reynolds number Re=1800. In order to assess the influence of wing flexibility on the aerodynamics, we vary the elasticity parameters and study rigid, flexible and highly flexible wing models. Code validation is carried out by computing classical benchmarks.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thomas Engels; Henja-Niniane Wehmann; Fritz-Olaf Lehmann
Three-dimensional wing structure attenuates aerodynamic efficiency in flapping fly wings Article de journal
Dans: Journal of The Royal Society Interface, vol. 17, p. 20190804, 2020.
@article{articlek,
title = {Three-dimensional wing structure attenuates aerodynamic efficiency in flapping fly wings},
author = {Thomas Engels and Henja-Niniane Wehmann and Fritz-Olaf Lehmann},
doi = {10.1098/rsif.2019.0804},
year = {2020},
date = {2020-01-01},
journal = {Journal of The Royal Society Interface},
volume = {17},
pages = {20190804},
abstract = {The aerial performance of flying insects ultimately depends on how flapping wings interact with the surrounding air. It has previously been suggested that the wing's three-dimensional camber and corrugation help to stiffen the wing against aerodynamic and inertial loading during flapping motion. Their contribution to aerodynamic force production, however, is under debate. Here, we investigated the potential benefit of three-dimensional wing shape in three different-sized species of flies using models of micro-computed tomography-scanned natural wings and models in which we removed either the wing's camber, corrugation, or both properties. Forces and aerodynamic power requirements during root flapping were derived from three-dimensional computational fluid dynamics modelling. Our data show that three-dimensional camber has no benefit for lift production and attenuates Rankine–Froude flight efficiency by up to approximately 12% compared to a flat wing. Moreover, we did not find evidence for lift-enhancing trapped vortices in corrugation valleys at Reynolds numbers between 137 and 1623. We found, however, that in all tested insect species, aerodynamic pressure distribution during flapping is closely aligned to the wing's venation pattern. Altogether, our study strongly supports the assumption that the wing's three-dimensional structure provides mechanical support against external forces rather than improving lift or saving energetic costs associated with active wing flapping.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Noudjoud Attaf; Iñaki Cervera-Marzal; Chuang Dong; Laurine Gil; Amédée Renand; Lionel Spinelli; Pierre Milpied
Corrigendum: FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells Article de journal
Dans: Frontiers in Immunology, vol. 11, p. 2047, 2020.
@article{articlel,
title = {Corrigendum: FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells},
author = {Noudjoud Attaf and Iñaki Cervera-Marzal and Chuang Dong and Laurine Gil and Amédée Renand and Lionel Spinelli and Pierre Milpied},
doi = {10.3389/fimmu.2020.02047},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in Immunology},
volume = {11},
pages = {2047},
abstract = {The aerial performance of flying insects ultimately depends on how flapping wings interact with the surrounding air. It has previously been suggested that the wing's three-dimensional camber and corrugation help to stiffen the wing against aerodynamic and inertial loading during flapping motion. Their contribution to aerodynamic force production, however, is under debate. Here, we investigated the potential benefit of three-dimensional wing shape in three different-sized species of flies using models of micro-computed tomography-scanned natural wings and models in which we removed either the wing's camber, corrugation, or both properties. Forces and aerodynamic power requirements during root flapping were derived from three-dimensional computational fluid dynamics modelling. Our data show that three-dimensional camber has no benefit for lift production and attenuates Rankine–Froude flight efficiency by up to approximately 12% compared to a flat wing. Moreover, we did not find evidence for lift-enhancing trapped vortices in corrugation valleys at Reynolds numbers between 137 and 1623. We found, however, that in all tested insect species, aerodynamic pressure distribution during flapping is closely aligned to the wing's venation pattern. Altogether, our study strongly supports the assumption that the wing's three-dimensional structure provides mechanical support against external forces rather than improving lift or saving energetic costs associated with active wing flapping.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kai Zhang; Salman Verma; Arnaud Trouvé; Aymeric Lamorlette
A study of the canopy effect on fire regime transition using an objectively defined Byram convective number Article de journal
Dans: Fire Safety Journal, vol. 112, p. 102950, 2020, ISSN: 0379-7112.
@article{ZHANG2020102950,
title = {A study of the canopy effect on fire regime transition using an objectively defined Byram convective number},
author = {Kai Zhang and Salman Verma and Arnaud Trouvé and Aymeric Lamorlette},
url = {https://www.sciencedirect.com/science/article/pii/S0379711219304497},
doi = {https://doi.org/10.1016/j.firesaf.2020.102950},
issn = {0379-7112},
year = {2020},
date = {2020-01-01},
journal = {Fire Safety Journal},
volume = {112},
pages = {102950},
abstract = {Forest fires can be classified into two regimes, depending on Byram convective number NC: a plume-dominated and wind-driven regime. This classification is often based on two-dimensional (2D) studies without considering flame front structures, and is associated with the change of governing heat transfer mechanism. Studies based on three-dimensional (3D) considerations suggest the dependency of the fire regime transition on canopy characteristics CdLAI (CdαsσsHF/2) through which the atmosphere boundary layer (ABL) flow changes to mixing layer (ML) flow. Hence, the primary objective of the present study is to investigate the fire regime transition and its associated heat transfer mechanisms with the aid of drawing a dimensionless configuration space NC, CdLAI. This requires an objective definition of the Byram convective number; the 2 m or 10 m high open wind speed (U∞=U2 or U10) often used to define it being arbitrary. Therefore, the present study introduces a scaling method for the reference height (Yref) at which the wind speed Uref is chosen to define a new Byram convective number NC’. A mathematical expression for Yref as a function of canopy/vegetation height is proposed for a small-scale, stationary fire. The new configuration space NC’, CdLAI is considered more suitable for investigating the fire regime transition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bjørn Ursin; Nathalie Favretto-Cristini; Paul Cristini
Amplitude and phase changes for reflected and transmitted waves from a curved interface in anisotropic media Article de journal
Dans: Geophysical Journal International, vol. 224, no. 1, p. 719-737, 2020, ISSN: 0956-540X.
@article{10.1093/gji/ggaa456,
title = {Amplitude and phase changes for reflected and transmitted waves from a curved interface in anisotropic media},
author = {Bjørn Ursin and Nathalie Favretto-Cristini and Paul Cristini},
url = {https://doi.org/10.1093/gji/ggaa456},
doi = {10.1093/gji/ggaa456},
issn = {0956-540X},
year = {2020},
date = {2020-01-01},
journal = {Geophysical Journal International},
volume = {224},
number = {1},
pages = {719-737},
abstract = {It is well known that seismic data that have been recorded in complex geological environments must be compensated for geometrical spreading before AVO/AVA (amplitude-versus-offset/amplitude-versus-angle) analysis, in order to avoid erroneous imaging interpretation. By investigating analytically both the effect of the geometrical spreading and the effect of the reflector curvature on amplitude and phase changes for reflected and transmitted waves between anisotropic media, using ray theory, we show that these data should be compensated for interface effects as well. In order to gain insight more specifically in the focusing effect of the interface, the special case of homogeneous isotropic media separated by a curved interface of syncline type is discussed and compared to the case of a plane interface. 3-D numerical simulations of wave reflection from curved interfaces using a spectral element method validate our analytical derivations. In particular, numerical seismograms obtained at a vertical receiver array highlight that the effect of interface curvature on the reflected events is much more pronounced in a restricted area associated with the existence of caustics, which is consistent with our analytical predictions. Moreover, comparisons between the numerical and the analytical results confirm the fact that using plane-wave reflection coefficients without correction for the interface effect may lead to wrong interpretation of AVA/AVO analysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stéphane Ayache; Ronan Sicre; Thierry Arti`eres
Transfer Learning by Weighting Convolution Proceedings Article
Dans: International Joint Conference on Neural Networks (IJCNN), Glasgow, United Kingdom, 2020.
@inproceedings{ayache:hal-02544099,
title = {Transfer Learning by Weighting Convolution},
author = {Stéphane Ayache and Ronan Sicre and Thierry Arti{`e}res},
url = {https://hal.archives-ouvertes.fr/hal-02544099},
year = {2020},
date = {2020-01-01},
booktitle = {International Joint Conference on Neural Networks (IJCNN)},
address = {Glasgow, United Kingdom},
abstract = {Transferring pretrained deep architectures to datasets with few labels is still a challenge in many real-world situations. This paper presents a new framework to understand convolutional neural networks, by establishing connections between Kronecker factorization and convolutional layers. We then introduce Convolution Weighting Layers that learn a vector of weights for each channel, allowing efficient transfer learning in small training settings, as well as enabling pruning the transferred models. Experiments are conducted on two main settings with few labeled data: transfer learning for classification and transfer learning for retrieval. Two well known convolutional architectures are evaluated on five public datasets. We show that weighting convolutions is efficient to adapt pretrained models to new tasks and that pruned networks conserve good performance. },
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Akrem Sellami; François-Xavier Dupé; Bastien Cagna; Hachem Kadri; Stéphane Ayache; Thierry Artières; Sylvain Takerkart
Mapping individual differences in cortical architecture using multi-view representation learning Divers
2020.
@misc{sellami2020mapping,
title = {Mapping individual differences in cortical architecture using multi-view representation learning},
author = {Akrem Sellami and François-Xavier Dupé and Bastien Cagna and Hachem Kadri and Stéphane Ayache and Thierry Artières and Sylvain Takerkart},
url = {https://arxiv.org/abs/2004.02804},
year = {2020},
date = {2020-01-01},
abstract = {In neuroscience, understanding inter-individual differences has recently emerged as a major challenge, for which functional magnetic resonance imaging (fMRI) has proven invaluable. For this, neuroscientists rely on basic methods such as univariate linear correlations between single brain features and a score that quantifies either the severity of a disease or the subject's performance in a cognitive task. However, to this date, task-fMRI and resting-state fMRI have been exploited separately for this question, because of the lack of methods to effectively combine them. In this paper, we introduce a novel machine learning method which allows combining the activation-and connectivity-based information respectively measured through these two fMRI protocols to identify markers of individual differences in the functional organization of the brain. It combines a multi-view deep autoencoder which is designed to fuse the two fMRI modalities into a joint representation space within which a predictive model is trained to guess a scalar score that characterizes the patient. Our experimental results demonstrate the ability of the proposed method to outperform competitive approaches and to produce interpretable and biologically plausible results.},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Benjamin Kadoch; Wouter Bos; Kai Schneider
Efficiency of laminar and turbulent mixing in wall-bounded flows Article de journal
Dans: Physical Review E, vol. 101, 2020.
@article{articlec,
title = {Efficiency of laminar and turbulent mixing in wall-bounded flows},
author = {Benjamin Kadoch and Wouter Bos and Kai Schneider},
doi = {10.1103/PhysRevE.101.043104},
year = {2020},
date = {2020-01-01},
journal = {Physical Review E},
volume = {101},
abstract = {A turbulent flow mixes in general more rapidly a passive scalar than a laminar flow does. From an energetic point of view, for statistically homogeneous or periodic flows, the laminar regime is more efficient. However, the presence of walls may change this picture. We consider in this investigation mixing in two-dimensional laminar and turbulent wall-bounded flows using direct numerical simulation. We show that for sufficiently large Schmidt number, turbulent flows more efficiently mix a wall-bounded scalar field than a chaotic or laminar flow does. The mixing efficiency is shown to be a function of the Péclet number, and a phenomenological explanation yields a scaling law, consistent with the observations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Benjamin Favier; Edgar Knobloch
Robust wall states in rapidly rotating Rayleigh–Bénard convection Article de journal
Dans: Journal of Fluid Mechanics, vol. 895, p. R1, 2020.
@article{favier_knobloch_2020,
title = {Robust wall states in rapidly rotating Rayleigh–Bénard convection},
author = {Benjamin Favier and Edgar Knobloch},
doi = {10.1017/jfm.2020.310},
year = {2020},
date = {2020-01-01},
journal = {Journal of Fluid Mechanics},
volume = {895},
pages = {R1},
publisher = {Cambridge University Press},
abstract = {We show, using direct numerical simulations with experimentally realizable boundary conditions, that wall modes in Rayleigh–Bénard convection in a rapidly rotating cylinder persist even very far from their linear onset. These nonlinear wall states survive in the presence of turbulence in the bulk and are robust with respect to changes in the shape of the boundary of the container. In this sense, these states behave much like the topologically protected states present in two-dimensional chiral systems even though rotating convection is a three-dimensional nonlinear driven dissipative system. We suggest that the robustness of this nonlinear state may provide an explanation for the strong zonal flows observed recently in experiments and simulations of rapidly rotating convection at high Rayleigh number.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Karno Schwinn; Nicolas Ferré; Miquel Huix-Rotllant
UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 22, p. 12447-12455, 2020.
@article{D0CP01714K,
title = {UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein},
author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant},
url = {http://dx.doi.org/10.1039/D0CP01714K},
doi = {10.1039/D0CP01714K},
year = {2020},
date = {2020-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {22},
pages = {12447-12455},
publisher = {The Royal Society of Chemistry},
abstract = {Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Karno Schwinn; Nicolas Ferré; Miquel Huix-Rotllant
Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 16, no. 6, p. 3816-3824, 2020.
@article{doi:10.1021/acs.jctc.9b01145,
title = {Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome},
author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant},
url = {https://doi.org/10.1021/acs.jctc.9b01145},
doi = {10.1021/acs.jctc.9b01145},
year = {2020},
date = {2020-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {16},
number = {6},
pages = {3816-3824},
abstract = {Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an environment represented as a classical electrostatic potential. The main bottleneck of EE-QM/MM second derivatives is the solution of coupled perturbed equations for each MM atom perturbation. Here, we exploit the Q-vector method [J. Chem. Phys., 2019, 151, 041102] to workaround this bottleneck. We derive the full analytic second derivative of the EE-QM/MM energy, which allows us to compute QM, MM, and QM-MM Hessian blocks in an efficient and easy to implement manner. To show the capabilities of our method, we compute the normal modes for the full Arabidopsis thaliana plant cryptochrome. We show that the flavin adenine dinucleotide vibrations (QM subsystem) strongly mix with protein modes. We compute approximate vibronic couplings for the lowest bright transition, from which we extract spectral densities and the homogeneous broadening of FAD absorption spectrum in protein using vibrationally resolved electronic spectrum simulations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Y Wang; E Athanassoula; S Mao
Basis function expansions for galactic dynamics: Spherical versus cylindrical coordinates Article de journal
Dans: A&A, vol. 639, p. A38, 2020.
@article{refId0c,
title = {Basis function expansions for galactic dynamics: Spherical versus cylindrical coordinates},
author = {Y } {Wang and E } {Athanassoula and S } {Mao},
url = {https://doi.org/10.1051/0004-6361/202038225},
doi = {10.1051/0004-6361/202038225},
year = {2020},
date = {2020-01-01},
journal = {A&A},
volume = {639},
pages = {A38},
abstract = {Aims. The orbital structure of galaxies is strongly influenced by the accuracy of the force calculation during orbit integration. We explore the accuracy of force calculations for two expansion methods and determine which one is preferable for orbit integration.
Methods. We specifically compare two methods, one was introduced by Hernquist & Ostriker (HO), which uses a spherical coordinate system and was built specifically for the Hernquist model, and the other by Vasiliev & Athanassoula (CylSP) has a cylindrical coordinate system. Our comparisons include the Dehnen profile, its triaxial extension (of which the Hernquist profile is a special case) and a multicomponent system including a bar and disk density distributions for both analytical models and N-body realizations.
Results. For the generalized Dehnen density, the CylSP method is more accurate than the HO method for nearly all inner power-law indices and shapes at all radii. For N-body realizations of the Dehnen model, or snapshots of an N-body simulation, the CylSP method is more accurate than the HO method in the central region for the oblate, prolate, and triaxial Hernquist profiles if the particle number is more than 5 × 105. For snapshots of the Hernquist models with spherical shape, the HO method is preferred. For the Ferrers bar model, the force from the CylSP method is more accurate than the HO method. The CPU time required for the initialization of the HO method is significantly shorter than that for the CylSP method, while the HO method costs subsequently much more CPU time than the CylSP method if the input corresponds to particle positions. From surface of section analyses, we find that the HO method creates more chaotic orbits than the CylSP method in the bar model. This could be understood to be due to a spurious peak in the central region when the force is calculated with the HO expansion.
Conclusions. For an analytical model, the CylSP method with an inner cutoff radius of interpolation Rmin as calculated by the AGAMA software, is preferred due to its accuracy. For snapshots or N-body realizations not including a disk or a bar component, a detailed comparison between these two methods is needed if a density model other than the Dehnen model is used. For multicomponent systems, including a disk and a bar, the CylSP method is preferable.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Methods. We specifically compare two methods, one was introduced by Hernquist & Ostriker (HO), which uses a spherical coordinate system and was built specifically for the Hernquist model, and the other by Vasiliev & Athanassoula (CylSP) has a cylindrical coordinate system. Our comparisons include the Dehnen profile, its triaxial extension (of which the Hernquist profile is a special case) and a multicomponent system including a bar and disk density distributions for both analytical models and N-body realizations.
Results. For the generalized Dehnen density, the CylSP method is more accurate than the HO method for nearly all inner power-law indices and shapes at all radii. For N-body realizations of the Dehnen model, or snapshots of an N-body simulation, the CylSP method is more accurate than the HO method in the central region for the oblate, prolate, and triaxial Hernquist profiles if the particle number is more than 5 × 105. For snapshots of the Hernquist models with spherical shape, the HO method is preferred. For the Ferrers bar model, the force from the CylSP method is more accurate than the HO method. The CPU time required for the initialization of the HO method is significantly shorter than that for the CylSP method, while the HO method costs subsequently much more CPU time than the CylSP method if the input corresponds to particle positions. From surface of section analyses, we find that the HO method creates more chaotic orbits than the CylSP method in the bar model. This could be understood to be due to a spurious peak in the central region when the force is calculated with the HO expansion.
Conclusions. For an analytical model, the CylSP method with an inner cutoff radius of interpolation Rmin as calculated by the AGAMA software, is preferred due to its accuracy. For snapshots or N-body realizations not including a disk or a bar component, a detailed comparison between these two methods is needed if a density model other than the Dehnen model is used. For multicomponent systems, including a disk and a bar, the CylSP method is preferable.
Paul Eyméoud; Philippe Maugis
Magnetic behavior of transition metal solutes in α-iron: A classification Article de journal
Dans: Journal of Magnetism and Magnetic Materials, vol. 513, p. 167223, 2020, ISSN: 0304-8853.
@article{EYMEOUD2020167223,
title = {Magnetic behavior of transition metal solutes in α-iron: A classification},
author = {Paul Eyméoud and Philippe Maugis},
url = {http://www.sciencedirect.com/science/article/pii/S0304885320311902},
doi = {https://doi.org/10.1016/j.jmmm.2020.167223},
issn = {0304-8853},
year = {2020},
date = {2020-01-01},
journal = {Journal of Magnetism and Magnetic Materials},
volume = {513},
pages = {167223},
abstract = {For several transition metals M, we have computed atomic magnetic moments for the body-centered cubic substitutional solid solution Fe1-xMx, by two comparative first-principle approaches for atomic disorder: Korringa-Kohn-Rostoker Coherent Potential Approximation (KKR-CPA) and Density Functional Theory applied to Special Quasirandom Structures (SQS-DFT). Our results, compared with experimental and numerical literature, led to a classification of transition metal solutes in α-iron with respect to their magnetic behavior.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2019
Nuno Manuel Almeida de Barbosa; Madjid Zemmouche; Pauline Gosset; Cristina Garcia-Iriepa; Vincent Ledentu; Isabelle Navizet; Pascal Didier; Nicolas Ferre
pH-Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate Article de journal
Dans: CHEMPHOTOCHEM, 2019, ISSN: 2367-0932.
@article{ISI:000493158900001,
title = {pH-Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate},
author = {Nuno Manuel Almeida de Barbosa and Madjid Zemmouche and Pauline Gosset and Cristina Garcia-Iriepa and Vincent Ledentu and Isabelle Navizet and Pascal Didier and Nicolas Ferre},
doi = {10.1002/cptc.201900150, Early Access Date = OCT 2019},
issn = {2367-0932},
year = {2019},
date = {2019-12-13},
journal = {CHEMPHOTOCHEM},
publisher = {WILEY-V C H VERLAG GMBH},
address = {POSTFACH 101161, 69451 WEINHEIM, GERMANY},
abstract = {The photophysical properties of oxyluciferin, the light emitter
responsible for firefly bioluminescence, are pH-dependent. One of the
potential proton acceptor/donor is adenosine monophosphate (AMP). We
have studied three oxyluciferin synthetic analogues with or without AMP, in water, in the pH=5 to 11 range, using both experimental steady-state
absorption spectroscopy or the recently developed computational protocol
that uses constant pH molecular dynamics and then hybrid QM/MM
calculations (CpHMD-then-QM/MM). The latter features a systematic
investigation of all the protonation microstates using molecular
dynamics simulations coupled to thousands hybrid QM/MM vertical
excitation energies. Our results demonstrate that AMP does not
significantly modify the visible light absorption of the analogues,
whatever the pH value. We also show that CpHMD-then-QM/MM is capable to
qualitatively reproduce the pH-dependent absorption spectrum of the
analogues, despite the employed low QM level of theory.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
responsible for firefly bioluminescence, are pH-dependent. One of the
potential proton acceptor/donor is adenosine monophosphate (AMP). We
have studied three oxyluciferin synthetic analogues with or without AMP, in water, in the pH=5 to 11 range, using both experimental steady-state
absorption spectroscopy or the recently developed computational protocol
that uses constant pH molecular dynamics and then hybrid QM/MM
calculations (CpHMD-then-QM/MM). The latter features a systematic
investigation of all the protonation microstates using molecular
dynamics simulations coupled to thousands hybrid QM/MM vertical
excitation energies. Our results demonstrate that AMP does not
significantly modify the visible light absorption of the analogues,
whatever the pH value. We also show that CpHMD-then-QM/MM is capable to
qualitatively reproduce the pH-dependent absorption spectrum of the
analogues, despite the employed low QM level of theory.
Marianthi Karageorgi; Simon C Groen; Fidan Sumbul; Julianne N Pelaez; Kirsten I Verster; Jessica M Aguilar; Amy P Hastings; Susan L Bernstein; Teruyuki Matsunaga; Michael Astourian; Geno Guerra; Felix Rico; Susanne Dobler; Anurag A Agrawal; Noah K Whiteman
Genome editing retraces the evolution of toxin resistance in the monarch butterfly Article de journal
Dans: NATURE, vol. 574, no. 7778, p. 409+, 2019, ISSN: 0028-0836.
@article{ISI:000490988300066,
title = {Genome editing retraces the evolution of toxin resistance in the monarch
butterfly},
author = {Marianthi Karageorgi and Simon C Groen and Fidan Sumbul and Julianne N Pelaez and Kirsten I Verster and Jessica M Aguilar and Amy P Hastings and Susan L Bernstein and Teruyuki Matsunaga and Michael Astourian and Geno Guerra and Felix Rico and Susanne Dobler and Anurag A Agrawal and Noah K Whiteman},
doi = {10.1038/s41586-019-1610-8},
issn = {0028-0836},
year = {2019},
date = {2019-10-01},
journal = {NATURE},
volume = {574},
number = {7778},
pages = {409+},
publisher = {NATURE PUBLISHING GROUP},
address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
abstract = {Identifying the genetic mechanisms of adaptation requires the
elucidation of links between the evolution of DNA sequence, phenotype,
and fitness(1). Convergent evolution can be used as a guide to identify
candidate mutations that underlie adaptive traits(2-4), and new genome
editing technology is facilitating functional validation of these
mutations in whole organisms(1,5). We combined these approaches to study
a classic case of convergence in insects from six orders, including the
monarch butterfly (Danaus plexippus), that have independently evolved to
colonize plants that produce cardiac glycoside toxins(6-11). Many of
these insects evolved parallel amino acid substitutions in the
alpha-subunit (ATP alpha) of the sodium pump (Na+/K+-ATPase)(7-11), the
physiological target of cardiac glycosides(12). Here we describe
mutational paths involving three repeatedly changing amino acid sites
(111, 119 and 122) in ATP alpha that are associated with cardiac
glycoside specialization(13,14). We then performed CRISPR-Cas9 base
editing on the native Atp alpha gene in Drosophila melanogaster flies
and retraced the mutational path taken across the monarch
lineage(11,15). We show in vivo, in vitro and in silico that the path
conferred resistance and target-site insensitivity to cardiac
glycosides(16), culminating in triple mutant `monarch flies' that were
as insensitive to cardiac glycosides as monarch butterflies. `Monarch
flies' retained small amounts of cardiac glycosides through
metamorphosis, a trait that has been optimized in monarch butterflies to
deter predators(17-19.) The order in which the substitutions evolved was
explained by amelioration of antagonistic pleiotropy through
epistasis(13,14,20-22). Our study illuminates how the monarch butterfly
evolved resistance to a class of plant toxins, eventually becoming
unpalatable, and changing the nature of species interactions within
ecological communities(2,6-11,15,17-19).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
elucidation of links between the evolution of DNA sequence, phenotype,
and fitness(1). Convergent evolution can be used as a guide to identify
candidate mutations that underlie adaptive traits(2-4), and new genome
editing technology is facilitating functional validation of these
mutations in whole organisms(1,5). We combined these approaches to study
a classic case of convergence in insects from six orders, including the
monarch butterfly (Danaus plexippus), that have independently evolved to
colonize plants that produce cardiac glycoside toxins(6-11). Many of
these insects evolved parallel amino acid substitutions in the
alpha-subunit (ATP alpha) of the sodium pump (Na+/K+-ATPase)(7-11), the
physiological target of cardiac glycosides(12). Here we describe
mutational paths involving three repeatedly changing amino acid sites
(111, 119 and 122) in ATP alpha that are associated with cardiac
glycoside specialization(13,14). We then performed CRISPR-Cas9 base
editing on the native Atp alpha gene in Drosophila melanogaster flies
and retraced the mutational path taken across the monarch
lineage(11,15). We show in vivo, in vitro and in silico that the path
conferred resistance and target-site insensitivity to cardiac
glycosides(16), culminating in triple mutant `monarch flies' that were
as insensitive to cardiac glycosides as monarch butterflies. `Monarch
flies' retained small amounts of cardiac glycosides through
metamorphosis, a trait that has been optimized in monarch butterflies to
deter predators(17-19.) The order in which the substitutions evolved was
explained by amelioration of antagonistic pleiotropy through
epistasis(13,14,20-22). Our study illuminates how the monarch butterfly
evolved resistance to a class of plant toxins, eventually becoming
unpalatable, and changing the nature of species interactions within
ecological communities(2,6-11,15,17-19).
Flavio Ronetti; Luca Vannucci; Dario Ferraro; Thibaut Jonckheere; Jér^ome Rech; Thierry Martin; Maura Sassetti
Hong-Ou-Mandel heat noise in the quantum Hall regime Article de journal
Dans: Phys. Rev. B, vol. 99, p. 205406, 2019.
@article{PhysRevB.99.205406,
title = {Hong-Ou-Mandel heat noise in the quantum Hall regime},
author = {Flavio Ronetti and Luca Vannucci and Dario Ferraro and Thibaut Jonckheere and Jér^ome Rech and Thierry Martin and Maura Sassetti},
url = {https://link.aps.org/doi/10.1103/PhysRevB.99.205406},
doi = {10.1103/PhysRevB.99.205406},
year = {2019},
date = {2019-05-01},
journal = {Phys. Rev. B},
volume = {99},
pages = {205406},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pingping Jiang; Pascal Boulet; Marie-Christine Record
A DFT study of the electronic, optical and topological properties of free and biaxially strained CuIn1-xAlxSe2 Article de journal
Dans: JOURNAL OF MATERIALS CHEMISTRY C, vol. 7, no. 19, p. 5803-5815, 2019, ISSN: 2050-7526.
@article{ISI:000472444000028,
title = {A DFT study of the electronic, optical and topological properties of
free and biaxially strained CuIn1-xAlxSe2},
author = {Pingping Jiang and Pascal Boulet and Marie-Christine Record},
doi = {10.1039/c9tc00277d},
issn = {2050-7526},
year = {2019},
date = {2019-05-01},
journal = {JOURNAL OF MATERIALS CHEMISTRY C},
volume = {7},
number = {19},
pages = {5803-5815},
publisher = {ROYAL SOC CHEMISTRY},
address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS,
ENGLAND},
abstract = {The electronic and optical properties of free and biaxially strained
CuIn1-xAlxSe2 were calculated by using the full potential linear
augmented plane wave (FP-LAPW) method. The results show that
CuIn1-xAlxSe2 has a direct band gap with increasing value as x
increases. CuIn0.75Al0.25Se2 has been recognized as the optimally
substituted compound in terms of band gap and conversion efficiency. The
geometry optimized bond length and bond angle between nuclei terminal
atoms (M and Se) and the bond critical point, the electron density , the
local energy density, and Laplacian delta(2) for nonequivalent pairwise
M-Se were examined. High bond deflection with a small bond angle
provides a high possibility of electron transition, which mainly occurs
between In and Se orbitals. Under biaxial strains, the optical
properties are improved along the lengthened deformation direction.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
CuIn1-xAlxSe2 were calculated by using the full potential linear
augmented plane wave (FP-LAPW) method. The results show that
CuIn1-xAlxSe2 has a direct band gap with increasing value as x
increases. CuIn0.75Al0.25Se2 has been recognized as the optimally
substituted compound in terms of band gap and conversion efficiency. The
geometry optimized bond length and bond angle between nuclei terminal
atoms (M and Se) and the bond critical point, the electron density , the
local energy density, and Laplacian delta(2) for nonequivalent pairwise
M-Se were examined. High bond deflection with a small bond angle
provides a high possibility of electron transition, which mainly occurs
between In and Se orbitals. Under biaxial strains, the optical
properties are improved along the lengthened deformation direction.
S Baschetti; H Bufferand; G Ciraolo; N Fedorczak; P Ghendrih; P Tamain; E Serre; EUROfusion MST1 Team; TCV Team
A kappa - epsilon model for plasma anomalous transport in tokamaks: closure via the scaling of the global confinement Article de journal
Dans: NUCLEAR MATERIALS AND ENERGY, vol. 19, p. 200-204, 2019.
@article{ISI:000470746100032,
title = {A kappa - epsilon model for plasma anomalous transport in tokamaks:
closure via the scaling of the global confinement},
author = {S Baschetti and H Bufferand and G Ciraolo and N Fedorczak and P Ghendrih and P Tamain and E Serre and EUROfusion MST1 Team and TCV Team},
doi = {10.1016/j.nme.2019.02.032},
year = {2019},
date = {2019-05-01},
journal = {NUCLEAR MATERIALS AND ENERGY},
volume = {19},
pages = {200-204},
publisher = {ELSEVIER SCIENCE BV},
address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
abstract = {A reduced model for radial anomalous transport of plasma in tokamaks,
inspired by the Reynolds-Averaged Navier-Stokes (RANS) approach, is
presented assuming diffusion as governing mechanism. In order to
self-consistently calculate transport coefficients, an empirical
equation is built for the turbulent kinetic energy and the system is
closed via the scaling law of global confinement. In such way the SOL
width appears to recover experimental dependencies with respect to
machine parameters and interestingly, when the model is implemented in a
2D transport code for a realistic study-case, mean fields retrieve some
features already observed in 1st-principle turbulent codes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
inspired by the Reynolds-Averaged Navier-Stokes (RANS) approach, is
presented assuming diffusion as governing mechanism. In order to
self-consistently calculate transport coefficients, an empirical
equation is built for the turbulent kinetic energy and the system is
closed via the scaling law of global confinement. In such way the SOL
width appears to recover experimental dependencies with respect to
machine parameters and interestingly, when the model is implemented in a
2D transport code for a realistic study-case, mean fields retrieve some
features already observed in 1st-principle turbulent codes.
J Denis; J Bucalossi; G Ciraolo; E A Hodille; B Pegourie; H Bufferand; C Grisolia; T Loarer; Y Marandet; E Serre; JET Contributors
Dynamic modelling of local fuel inventory and desorption in the whole tokamak vacuum vessel for auto-consistent plasma-wall interaction simulations Article de journal
Dans: NUCLEAR MATERIALS AND ENERGY, vol. 19, p. 550-557, 2019.
@article{ISI:000470746100086,
title = {Dynamic modelling of local fuel inventory and desorption in the whole
tokamak vacuum vessel for auto-consistent plasma-wall interaction
simulations},
author = {J Denis and J Bucalossi and G Ciraolo and E A Hodille and B Pegourie and H Bufferand and C Grisolia and T Loarer and Y Marandet and E Serre and JET Contributors},
doi = {10.1016/j.nme.2019.03.019},
year = {2019},
date = {2019-05-01},
journal = {NUCLEAR MATERIALS AND ENERGY},
volume = {19},
pages = {550-557},
publisher = {ELSEVIER SCIENCE BV},
address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
abstract = {An extension of the SolEdge2D-EIRENE code package, named D-WEE, has been
developed to add the dynamics of thermal desorption of hydrogen isotopes
from the surface of plasma facing materials. To achieve this purpose,
D-WEE models hydrogen isotopes implantation, transport and retention in
those materials. Before launching autoconsistent simulation (with
feedback of D-WEE on SolEdge2D-EIRENE), D-WEE has to be initialised to
ensure a realistic wall behaviour in terms of dynamics (pumping or
fuelling areas) and fuel content. A methodology based on modelling is
introduced to perform such initialisation. A synthetic plasma pulse is
built from consecutive SolEdge2D-EIRENE simulations. This synthetic
pulse is used as a plasma background for the D-WEE module. A sequence of
plasma pulses is simulated with D-WEE to model a tokamak operation. This
simulation enables to extract at a desired time during a pulse the local
fuel inventory and the local desorption flux density which could be used
as initial condition for coupled plasma-wall simulations. To assess the
relevance of the dynamic retention behaviour obtained in the simulation,
a confrontation to post-pulse experimental pressure measurement is
performed. Such confrontation reveals a qualitative agreement between
the temporal pressure drop obtained in the simulation and the one
observed experimentally. The simulated dynamic retention during the
consecutive pulses is also studied.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
developed to add the dynamics of thermal desorption of hydrogen isotopes
from the surface of plasma facing materials. To achieve this purpose,
D-WEE models hydrogen isotopes implantation, transport and retention in
those materials. Before launching autoconsistent simulation (with
feedback of D-WEE on SolEdge2D-EIRENE), D-WEE has to be initialised to
ensure a realistic wall behaviour in terms of dynamics (pumping or
fuelling areas) and fuel content. A methodology based on modelling is
introduced to perform such initialisation. A synthetic plasma pulse is
built from consecutive SolEdge2D-EIRENE simulations. This synthetic
pulse is used as a plasma background for the D-WEE module. A sequence of
plasma pulses is simulated with D-WEE to model a tokamak operation. This
simulation enables to extract at a desired time during a pulse the local
fuel inventory and the local desorption flux density which could be used
as initial condition for coupled plasma-wall simulations. To assess the
relevance of the dynamic retention behaviour obtained in the simulation,
a confrontation to post-pulse experimental pressure measurement is
performed. Such confrontation reveals a qualitative agreement between
the temporal pressure drop obtained in the simulation and the one
observed experimentally. The simulated dynamic retention during the
consecutive pulses is also studied.
G Giorgiani; H Bufferand; G Ciraolo; E Serre; P Tamain
A magnetic-field independent approach for strongly anisotropic equations arising plasma-edge transport simulations Article de journal
Dans: NUCLEAR MATERIALS AND ENERGY, vol. 19, p. 340-345, 2019.
@article{ISI:000470746100054,
title = {A magnetic-field independent approach for strongly anisotropic equations
arising plasma-edge transport simulations},
author = {G Giorgiani and H Bufferand and G Ciraolo and E Serre and P Tamain},
doi = {10.1016/j.nme.2019.03.002},
year = {2019},
date = {2019-05-01},
journal = {NUCLEAR MATERIALS AND ENERGY},
volume = {19},
pages = {340-345},
publisher = {ELSEVIER SCIENCE BV},
address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
abstract = {A [Summary] The control of the power exhaust in tokamaks is still an
open issue for the future fusion operations. The heat loads on divertor
and limiter PFCs is largely determined by the physics of the Scrape-Off
Layer (SOL), and therefore it depends mainly on the geometry of the
magnetic surfaces and on the geometry of wall components. A better
characterization of the heat exhaust mechanisms requires therefore to
improve the capabilities of the transport codes in terms of geometrical
description of the wall components and in terms of the description of
the magnetic geometry. The possibility of dealing with evolving magnetic
configurations becomes also critical: during start-up or control
operations, for example, the evolution of particles and heat fluxes is
little known, although being critical for the safety of the machine.
Hence, among the new capabilities of future transport codes will be the
possibility of accurately describe the reactor chamber, and the
flexibility with respect the magnetic configuration. In particular,
avoiding expensive re-meshing of the computational domain in case of
evolving equilibrium is mandatory.
In order to fulfill these requirements, in this work a fluid solver
based on non-aligned discretization is used to solve the plasma-edge
transport equations for density, momentum and energies. Preliminary
tests on non-structured meshes and realistic geometries/physical
parameters show the pertinency of this novel approach.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
open issue for the future fusion operations. The heat loads on divertor
and limiter PFCs is largely determined by the physics of the Scrape-Off
Layer (SOL), and therefore it depends mainly on the geometry of the
magnetic surfaces and on the geometry of wall components. A better
characterization of the heat exhaust mechanisms requires therefore to
improve the capabilities of the transport codes in terms of geometrical
description of the wall components and in terms of the description of
the magnetic geometry. The possibility of dealing with evolving magnetic
configurations becomes also critical: during start-up or control
operations, for example, the evolution of particles and heat fluxes is
little known, although being critical for the safety of the machine.
Hence, among the new capabilities of future transport codes will be the
possibility of accurately describe the reactor chamber, and the
flexibility with respect the magnetic configuration. In particular,
avoiding expensive re-meshing of the computational domain in case of
evolving equilibrium is mandatory.
In order to fulfill these requirements, in this work a fluid solver
based on non-aligned discretization is used to solve the plasma-edge
transport equations for density, momentum and energies. Preliminary
tests on non-structured meshes and realistic geometries/physical
parameters show the pertinency of this novel approach.
B Favier; J Purseed; L Duchemin
Rayleigh–Bénard convection with a melting boundary Article de journal
Dans: Journal of Fluid Mechanics, vol. 858, p. 437–473, 2019.
@article{favier_purseed_duchemin_2019b,
title = {Rayleigh–Bénard convection with a melting boundary},
author = {B Favier and J Purseed and L Duchemin},
doi = {10.1017/jfm.2018.773},
year = {2019},
date = {2019-01-01},
journal = {Journal of Fluid Mechanics},
volume = {858},
pages = {437–473},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hassan Denawi; Mathieu Abel; Roland Hayn
Magnetic Polymer Chains of Transition Metal Atoms and Zwitterionic Quinone Article de journal
Dans: The Journal of Physical Chemistry C, vol. 123, no. 7, p. 4582-4589, 2019.
@article{doi:10.1021/acs.jpcc.8b12433,
title = {Magnetic Polymer Chains of Transition Metal Atoms and Zwitterionic Quinone},
author = {Hassan Denawi and Mathieu Abel and Roland Hayn},
url = {https://doi.org/10.1021/acs.jpcc.8b12433},
doi = {10.1021/acs.jpcc.8b12433},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {123},
number = {7},
pages = {4582-4589},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M Valentinuzzi; Y Marandet; H Bufferand; G Ciraolo; P Tamain
Two-phases hybrid model for neutrals Article de journal
Dans: Nuclear Materials and Energy, vol. 18, p. 41 - 45, 2019, ISSN: 2352-1791.
@article{VALENTINUZZI201941,
title = {Two-phases hybrid model for neutrals},
author = {M Valentinuzzi and Y Marandet and H Bufferand and G Ciraolo and P Tamain},
url = {http://www.sciencedirect.com/science/article/pii/S2352179118301856},
doi = {https://doi.org/10.1016/j.nme.2018.12.003},
issn = {2352-1791},
year = {2019},
date = {2019-01-01},
journal = {Nuclear Materials and Energy},
volume = {18},
pages = {41 - 45},
abstract = {A new hybrid fluid-kinetic code for the atoms has been developed and implemented in Soledge2D. The new code package is able to simulate the evolution of ions, electrons, molecules and two different populations (or phases) of atoms in realistic 2D geometry. Simulations in ITER geometry show that, with a fluid breakdown parameter of up to 0.1÷0.5, only negligible differences are found with respect to fully-kinetic Soledge2D–Eirene cases, while at the same time improving the computational performances of the code package.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
D M Fan; Y Marandet; P Tamain; H Bufferand; G Ciraolo; Ph. Ghendrih; E Serre
Effect of turbulent fluctuations on neutral particles transport with the TOKAM3X-EIRENE turbulence code Article de journal
Dans: Nuclear Materials and Energy, vol. 18, p. 105 - 110, 2019, ISSN: 2352-1791.
@article{FAN2019105,
title = {Effect of turbulent fluctuations on neutral particles transport with the TOKAM3X-EIRENE turbulence code},
author = {D M Fan and Y Marandet and P Tamain and H Bufferand and G Ciraolo and Ph. Ghendrih and E Serre},
url = {http://www.sciencedirect.com/science/article/pii/S2352179118301200},
doi = {https://doi.org/10.1016/j.nme.2018.12.011},
issn = {2352-1791},
year = {2019},
date = {2019-01-01},
journal = {Nuclear Materials and Energy},
volume = {18},
pages = {105 - 110},
abstract = {The effect of turbulent fluctuations on the transport of neutral particles (atoms, molecules) in tokamak plasmas is investigated with the 3D global turbulence code TOKAM3X-EIRENE in limiter geometry. The statistical properties of turbulent fields relevant to this work are discussed, including the recycling flux. The neutral particle transport is recalculated on the mean field plasma, and compared to the mean neutral particle density/flows obtained from the turbulent simulation, so as to assess the effects of the fluctuations, in particular on the ionization balance. The latter effects are remarkably modest in the simulation presented here, but are expected to become more and more pronounced as the high recycling regime is approached, in particular because the plasma temperature becomes low enough so that ionization is strongly non-linear. However, the turbulent fluctuations in the SOL do have a substantial effect on the neutral densities on the low field side of the limiter, including in the confined plasma. These effects are traced back to non-linearities in the plasma flux at the wall, and the fluctuations in the latter are identified as an important contributor both to neutral particle density fluctuations and to deviations from mean neutral particle density/flows in the turbulent simulation with respect to the same quantities recalculated on the mean plasma fields.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F Nespoli; H Bufferand; M Valentinuzzi; N Fedorczak; G Ciraolo; E Serre; Y Marandet; R Maurizio; De H Oliveira; B Labit; M Komm; M Faitsch; S Elmore
Application of a two-fluid two-point model to SolEdge2D-EIRENE simulations of TCV H-mode plasma Article de journal
Dans: Nuclear Materials and Energy, vol. 18, p. 29 - 34, 2019, ISSN: 2352-1791.
@article{NESPOLI201929,
title = {Application of a two-fluid two-point model to SolEdge2D-EIRENE simulations of TCV H-mode plasma},
author = {F Nespoli and H Bufferand and M Valentinuzzi and N Fedorczak and G Ciraolo and E Serre and Y Marandet and R Maurizio and De H Oliveira and B Labit and M Komm and M Faitsch and S Elmore},
url = {http://www.sciencedirect.com/science/article/pii/S2352179118301819},
doi = {https://doi.org/10.1016/j.nme.2018.11.026},
issn = {2352-1791},
year = {2019},
date = {2019-01-01},
journal = {Nuclear Materials and Energy},
volume = {18},
pages = {29 - 34},
abstract = {The edge and scrape-off layer (SOL) plasma of the inter-ELM phase of an H-mode discharge from the TCV tokamak is modeled with the transport code SolEdge2D-EIRENE (Bufferand et al. Nuclear Fusion 55 (2015)). The numerical simulations, in presence and in absence of C impurities sputtered from the first wall, are presented and compared with the experiments, finding an overall good agreement. The application of the standard two-point model to the simulation results leads to an apparent momentum gain along the divertor leg. A two-fluid two-point model featuring thermally decoupled ions and electrons is introduced and applied to the simulation results, overcoming this apparent discrepancy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
H Bufferand; P Tamain; S Baschetti; J Bucalossi; G Ciraolo; N Fedorczak; Ph. Ghendrih; F Nespoli; F Schwander; E Serre; Y Marandet
Three-dimensional modelling of edge multi-component plasma taking into account realistic wall geometry Article de journal
Dans: Nuclear Materials and Energy, vol. 18, p. 82 - 86, 2019, ISSN: 2352-1791.
@article{BUFFERAND201982,
title = {Three-dimensional modelling of edge multi-component plasma taking into account realistic wall geometry},
author = {H Bufferand and P Tamain and S Baschetti and J Bucalossi and G Ciraolo and N Fedorczak and Ph. Ghendrih and F Nespoli and F Schwander and E Serre and Y Marandet},
url = {http://www.sciencedirect.com/science/article/pii/S2352179118302035},
doi = {https://doi.org/10.1016/j.nme.2018.11.025},
issn = {2352-1791},
year = {2019},
date = {2019-01-01},
journal = {Nuclear Materials and Energy},
volume = {18},
pages = {82 - 86},
abstract = {A 3D multispecies fluid model has been implemented in the SOLEDGE-TOKAM suite of codes to address Scrape-off layer turbulent impurity transport. Zhdanov closure is used to address multi-component plasma modeling without any mass ordering or trace impurity assumption. Thanks to immersed boundary conditions, up to the wall simulations with non-axisymmetric plasma facing components are performed, in particular in the WEST configuration. A first proof of principle of interchange turbulence simulation of a Deuterium+Carbon plasma is also reported.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cédric Maury; Teresa Bravo; Daniel Mazzoni
The use of microperforations to attenuate the cavity pressure fluctuations induced by a low-speed flow Article de journal
Dans: Journal of Sound and Vibration, vol. 439, p. 1 - 16, 2019, ISSN: 0022-460X.
@article{MAURY20191,
title = {The use of microperforations to attenuate the cavity pressure fluctuations induced by a low-speed flow},
author = {Cédric Maury and Teresa Bravo and Daniel Mazzoni},
url = {http://www.sciencedirect.com/science/article/pii/S0022460X18306400},
doi = {https://doi.org/10.1016/j.jsv.2018.09.045},
issn = {0022-460X},
year = {2019},
date = {2019-01-01},
journal = {Journal of Sound and Vibration},
volume = {439},
pages = {1 - 16},
abstract = {The paper describes experimental and numerical studies on the use of micro-perforated panels to reduce the flow cavity pressure fluctuations under a low-speed turbulent boundary layer. This passive strategy has been hardly studied in shallow cavities with length-to-depth ratios of the order of 10, for which flow reattachment might occur at the cavity floor. This implies the formation of a localized recirculation bubble upstream in the cavity, which is referred to as a closed cavity flow regime. An open flow regime takes place when the cavity is separated from the main flow by a shear layer over the full length. For a transitional case with a length-to-depth ratio of 10.6, micro-perforating the cavity floor reduces by up to 8 dB the dominant spectral peaks related to the bottom wall-pressure fluctuations in the first half of the cavity. For the closed regime with a length-to-depth ratio of 17.6, up to 6 dB reduction is found. The broadband fluctuations that are dominating in the downstream part of the cavity are not affected by the presence of the micro-perforations. Reduction of the peak pressure levels by the apertures is confirmed by two-dimensional Lattice Boltzmann simulations. Maximum dissipation occurs when outflow conditions are established within and at the inlet-outlet of the orifices. The impedance of the micro-perforated floor has been optimised and its effect on the bottom wall-pressures has been assessed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Christine D Wilson; Laura C Parker; Ryan Chown; Niu Li; Cheng Li; Houjun Mo; E Athanassoula; Lin Lin; Ting Xiao
Linking bar- and interaction-driven molecular gas concentration with centrally enhanced star formation in EDGE–CALIFA galaxies Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 484, no. 4, p. 5192-5211, 2019, ISSN: 0035-8711.
@article{10.1093/mnras/stz349,
title = {Linking bar- and interaction-driven molecular gas concentration with centrally enhanced star formation in EDGE–CALIFA galaxies},
author = {Christine D Wilson and Laura C Parker and Ryan Chown and Niu Li and Cheng Li and Houjun Mo and E Athanassoula and Lin Lin and Ting Xiao},
url = {https://doi.org/10.1093/mnras/stz349},
doi = {10.1093/mnras/stz349},
issn = {0035-8711},
year = {2019},
date = {2019-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {484},
number = {4},
pages = {5192-5211},
abstract = {We study the spatially resolved star formation history (SFH) and molecular gas distribution of 58 nearby galaxies, using integral field spectroscopy from the CALIFA survey and CO J = 1–0 intensity mapping from the CARMA EDGE survey. We use the 4000 Å break (Dn(4000)), the equivalent width (EW) of the H δ absorption line (EW(H δA)), and the EW of the H α emission line (EW(H α)) to measure the recent SFH of these galaxies. We measure radial profiles of the three SFH indicators and molecular gas mass surface density, from which we measure the level of centrally enhanced star formation and the molecular gas concentration. When we separate our galaxies into categories of barred (17 galaxies), unbarred (24 galaxies), and merging/paired (17 galaxies), we find that the galaxies that have centrally enhanced star formation (19/58) are either barred (13/19) or in mergers/pairs (6/19) with relatively high molecular gas concentrations. A comparison between our barred galaxies and a snapshot of a hydrodynamic N-body simulation of a barred galaxy shows that the current theory of bar formation and evolution can qualitatively reproduce the main features of the observed galaxies in our sample, including both the sharp decrease of stellar age in the galactic centre and the gradual decrease of age with increasing distance from centre. These findings provide substantial evidence for a picture in which cold gas is transported inwards by a bar or tidal interaction, which leads to the growth and rejuvenation of star formation in the central region.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ran Liu; Xing Gao; Mario Barbatti; Jun Jiang; Guozhen Zhang
Promoting Intersystem Crossing of a Fluorescent Molecule via Single Functional Group Modification Article de journal
Dans: The Journal of Physical Chemistry Letters, vol. 10, no. 6, p. 1388-1393, 2019.
@article{doi:10.1021/acs.jpclett.9b00286,
title = {Promoting Intersystem Crossing of a Fluorescent Molecule via Single Functional Group Modification},
author = {Ran Liu and Xing Gao and Mario Barbatti and Jun Jiang and Guozhen Zhang},
url = {https://doi.org/10.1021/acs.jpclett.9b00286},
doi = {10.1021/acs.jpclett.9b00286},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {10},
number = {6},
pages = {1388-1393},
abstract = {Pure light-atom organic phosphorescent molecules have been under scientific scrutiny because they are inexpensive, flexible, and environment friendly. The development of such materials, however, faces a bottleneck problem of intrinsically small spin–orbit couplings, which can be addressed by seeking a proper balance between intersystem crossing (ISC) and fluorescence rates. Using N-substituted naphthalimides as the prototype molecule, we applied chemical modifications with several electrophilic and nucleophilic functional groups, to approach the goal. The selected electron donating groups actively restrain the fluorescence, enabling an efficient ISC to the triplet manifold. Electron withdrawing groups do not change the luminescent properties of the parent species. The changes in ISC and fluorescence rates are related to the nature of the lowest singlet state, which changes from localized excitation into charge-transfer excitation upon configuration change of excited molecules. This finding opens an alternative strategy for designing pure light-atom organic phosphorescent molecules for emerging luminescent materials applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gessenildo Pereira Rodrigues; Thayana Maria Lopes de Lima; Railton Barbosa de Andrade; Elizete Ventura; Silmar Andrade do Monte; Mario Barbatti
Photoinduced Formation of H-Bonded Ion Pair in HCFC-133a Article de journal
Dans: The Journal of Physical Chemistry A, vol. 123, no. 10, p. 1953-1961, 2019, (PMID: 30786711).
@article{doi:10.1021/acs.jpca.8b12482,
title = {Photoinduced Formation of H-Bonded Ion Pair in HCFC-133a},
author = {Gessenildo Pereira Rodrigues and Thayana Maria Lopes de Lima and Railton Barbosa de Andrade and Elizete Ventura and Silmar Andrade do Monte and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jpca.8b12482},
doi = {10.1021/acs.jpca.8b12482},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Physical Chemistry A},
volume = {123},
number = {10},
pages = {1953-1961},
abstract = {High-level multireference electronic structure calculations have been performed to study the Cl– yield from photoexcited CF3CH2Cl (HCFC-133a). The analysis of this process tells that it relates to an electron transfer from the carbon to the Cl atom, forming a highly polar contact ion-pair complex, CF3HCH+···Cl–, in the excited (S3) state. This complex has a strong binding energy of 3.53 eV, from which 0.47 eV is due to an underlying hydrogen bond. Through comparison with the results obtained for the prototype CH3Cl system, where a similar ion-pair state associated with Cl– formation has also been observed, it is suggested that photodissociation of HCFC-133a can also yield Cl– through an analogous process. This hypothesis is further supported by nonadiabatic dynamics simulations, which shows formation of the ion-pair complex in the subpicosecond time scale.},
note = {PMID: 30786711},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 15, no. 3, p. 1503-1513, 2019, (PMID: 30735372).
@article{doi:10.1021/acs.jctc.8b00923,
title = {Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings},
author = {Shuming Bai and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jctc.8b00923},
doi = {10.1021/acs.jctc.8b00923},
year = {2019},
date = {2019-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {15},
number = {3},
pages = {1503-1513},
abstract = {Spin-exchange internal conversion (SEIC) is a general class of reactions having singlet fission and triplet fusion as particular cases. Based on a charge transfer (CT) mediated mechanism and analytical derivation with a model Hamiltonian, we propose proxies for estimating the coupling strength in both diabatic and adiabatic pictures for general SEIC reactions. In the diabatic picture, we demonstrated the existence of a bilinear relationship between the coupling strength and molecular orbital overlap, which provides a practical way to predict diabatic couplings. In the adiabatic picture, we showed that nonadiabatic couplings can be approximated by simple functions of the wave function CT coefficients. These approaches were verified through the investigation of singlet oxygen photosensitization, where both 1Δg and 1Σg oxygen states can be competitively generated by a triplet fusion reaction. The interplay between the CT-mediated mechanism, the spatial factors of the bimolecular complex, and the electronic structure of the oxygen molecule during the reaction explains the curiously small coupling to the 1Σg state along specific incidence directions. The results from both the diabatic and adiabatic pictures provide a comprehensive understanding of the reaction mechanism, which applies to general SEIC problems.},
note = {PMID: 30735372},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pierre Thureau; Simone Sturniolo; Miri Zilka; Fabio Ziarelli; Stéphane Viel; Jonathan R Yates; Giulia Mollica
Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings Article de journal
Dans: Magnetic Resonance in Chemistry, vol. 57, no. 5, p. 256-264, 2019.
@article{doi:10.1002/mrc.4848,
title = {Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings},
author = {Pierre Thureau and Simone Sturniolo and Miri Zilka and Fabio Ziarelli and Stéphane Viel and Jonathan R Yates and Giulia Mollica},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrc.4848},
doi = {10.1002/mrc.4848},
year = {2019},
date = {2019-01-01},
journal = {Magnetic Resonance in Chemistry},
volume = {57},
number = {5},
pages = {256-264},
abstract = {Abstract Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed 1H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using 13C-13C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although 13C-13C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2018
Je K š; Y Marandet; H Bufferand; J P Gunn; H J van der Meiden; G Ciraolo
Studying divertor relevant plasmas in the Pilot-PSI linear plasma device: experiments versus modelling Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 60, no. 12, p. 125009, 2018.
@article{Je_ko_2018,
title = {Studying divertor relevant plasmas in the Pilot-PSI linear plasma device: experiments versus modelling},
author = {Je K š and Y Marandet and H Bufferand and J P Gunn and H J van der Meiden and G Ciraolo},
url = {https://doi.org/10.1088%2F1361-6587%2Faae80d},
doi = {10.1088/1361-6587/aae80d},
year = {2018},
date = {2018-11-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {60},
number = {12},
pages = {125009},
publisher = {IOP Publishing},
abstract = {Predictions for the operation of tokamak divertors are reliant on edge plasma simulations typically consisting of a fluid plasma code in combination with a Monte-Carlo (MC) code for neutral species. Pilot-PSI is a linear device operating with a cascaded arc plasma source that produces plasmas comparable to those expected during the inter-ELM phase in the ITER divertor (T
e
∼ 1 eV, n
e
∼ 1020 m−3). In this study, plasma discharges in Pilot-PSI have been modelled using the Soledge2D fluid plasma code (Bufferand et al 2015 Nucl. Fusion 55) coupled to the Eirene neutral MC code (Reiter et al 2005 Fusion Sci. Technol. 47, 172–186) in order to (a) investigate which phenomena need to be included in the modelling to reproduce experimental trends and (b) provide new insights to the interpretation of experiments. The simulations highlight the key role of ion/molecule elastic collisions in determining the ion flux reaching the target. Recombination is likely to play a role at high molecular background pressure. However, even with the most advanced atomic and molecular model used in this work, T
e
at the target is overestimated with respect to the measurements using TS and spectroscopy. T
e
in the simulations appears to saturate at 0.7 eV for a wide range of parameters, while experimentally values of 0.1–0.3 eV are found. As a consequence, in the simulations the volume recombination is underestimated, which is a strong function of T
e
when it is below 1 eV. Further analysis of simulation results using a two-point formalism shows that inelastic collisions between electrons and neutral background particles remove most of the energy flux, mainly via dissociation of molecules and molecular ions. However this happens mostly in the upstream region of the beam where T
e
> 1 eV. For T
e
< 1 eV, there seems to be no significant energy removal mechanism in the simulated cases. The results also indicate that conclusions on the importance of volume processes, e.g. recombination, cannot be solely based on T
e
or the dominance of certain reaction rate coefficients over others, but rather the complete transport picture, including macroscopic flow, has to be taken into account. In the cases studied here, the plasma is typically advected to the wall too fast for recombination to remove a significant fraction of the particle flux.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
e
∼ 1 eV, n
e
∼ 1020 m−3). In this study, plasma discharges in Pilot-PSI have been modelled using the Soledge2D fluid plasma code (Bufferand et al 2015 Nucl. Fusion 55) coupled to the Eirene neutral MC code (Reiter et al 2005 Fusion Sci. Technol. 47, 172–186) in order to (a) investigate which phenomena need to be included in the modelling to reproduce experimental trends and (b) provide new insights to the interpretation of experiments. The simulations highlight the key role of ion/molecule elastic collisions in determining the ion flux reaching the target. Recombination is likely to play a role at high molecular background pressure. However, even with the most advanced atomic and molecular model used in this work, T
e
at the target is overestimated with respect to the measurements using TS and spectroscopy. T
e
in the simulations appears to saturate at 0.7 eV for a wide range of parameters, while experimentally values of 0.1–0.3 eV are found. As a consequence, in the simulations the volume recombination is underestimated, which is a strong function of T
e
when it is below 1 eV. Further analysis of simulation results using a two-point formalism shows that inelastic collisions between electrons and neutral background particles remove most of the energy flux, mainly via dissociation of molecules and molecular ions. However this happens mostly in the upstream region of the beam where T
e
> 1 eV. For T
e
< 1 eV, there seems to be no significant energy removal mechanism in the simulated cases. The results also indicate that conclusions on the importance of volume processes, e.g. recombination, cannot be solely based on T
e
or the dominance of certain reaction rate coefficients over others, but rather the complete transport picture, including macroscopic flow, has to be taken into account. In the cases studied here, the plasma is typically advected to the wall too fast for recombination to remove a significant fraction of the particle flux.
Falahati Konstantin; Tamura Hiroyuki; Burghardt Irene; Huix-Rotllant Miquel
2018.
@book{Falahati2018,
title = {Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics},
author = {Falahati Konstantin and Tamura Hiroyuki and Burghardt Irene and Huix-Rotllant Miquel},
editor = {Nature Communications},
url = {https://doi.org/10.1038/s41467-018-06615-1},
doi = {10.1038/s41467-018-06615-1},
year = {2018},
date = {2018-10-29},
abstract = {Light absorption of myoglobin triggers diatomic ligand photolysis and a spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond timescale. The microscopic origin of these reactions remains controversial. Here, we apply quantum wavepacket dynamics to elucidate the ultrafast photochemical mechanism for a heme–carbon monoxide (heme–CO) complex. We observe coherent oscillations of the Fe–CO bond distance with a period of 42 fs and an amplitude of ∼1 Å. These nuclear motions induce pronounced geometric reorganization, which makes the CO dissociation irreversible. The reaction is initially dominated by symmetry breaking vibrations inducing an electron transfer from porphyrin to iron. Subsequently, the wavepacket relaxes to the triplet manifold in ∼75 fs and to the quintet manifold in ∼430 fs. Our results highlight the central role of nuclear vibrations at the origin of the ultrafast photodynamics of organometallic complexes.},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
Xiaoliang He; Sourabh Apte; Kai Schneider; Benjamin Kadoch
Angular multiscale statistics of turbulence in a porous bed Article de journal
Dans: Phys. Rev. Fluids, vol. 3, p. 084501, 2018.
@article{PhysRevFluids.3.084501,
title = {Angular multiscale statistics of turbulence in a porous bed},
author = {Xiaoliang He and Sourabh Apte and Kai Schneider and Benjamin Kadoch},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.3.084501},
doi = {10.1103/PhysRevFluids.3.084501},
year = {2018},
date = {2018-08-01},
journal = {Phys. Rev. Fluids},
volume = {3},
pages = {084501},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
S Cabanes; B Favier; M Le Bars
Some statistical properties of three-dimensional zonostrophic turbulence Article de journal
Dans: Geophysical and Astrophysical Fluid Dynamics, vol. 112, no. 3, p. 207-221, 2018.
@article{cabanes:hal-01904597,
title = {Some statistical properties of three-dimensional zonostrophic turbulence},
author = {S Cabanes and B Favier and M Le Bars},
url = {https://hal.archives-ouvertes.fr/hal-01904597},
doi = {10.1080/03091929.2018.1467413},
year = {2018},
date = {2018-01-01},
journal = {Geophysical and Astrophysical Fluid Dynamics},
volume = {112},
number = {3},
pages = {207-221},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sandeep K Reddy; Benjamin Favier; Michael Le Bars
Turbulent Kinematic Dynamos in Ellipsoids Driven by Mechanical Forcing Article de journal
Dans: Geophysical Research Letters, vol. 45, no. 4, p. 1741-1750, 2018.
@article{doi:10.1002/2017GL076542,
title = {Turbulent Kinematic Dynamos in Ellipsoids Driven by Mechanical Forcing},
author = {Sandeep K Reddy and Benjamin Favier and Michael Le Bars},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GL076542},
doi = {10.1002/2017GL076542},
year = {2018},
date = {2018-01-01},
journal = {Geophysical Research Letters},
volume = {45},
number = {4},
pages = {1741-1750},
abstract = {Abstract Dynamo action in planetary cores has been extensively studied in the context of convectively driven flows. We show in this letter that mechanical forcings, namely, tides, libration, and precession, are also able to kinematically sustain a magnetic field against ohmic diffusion. Previous attempts published in the literature focused on the laminar response or considered idealized spherical configurations. In contrast, we focus here on the developed turbulent regime and we self-consistently solve the magnetohydrodynamic equations in an ellipsoidal container. Our results open new avenues of research in dynamo theory where both convection and mechanical forcing can play a role, independently or simultaneously.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thomas Le Reun; Benjamin Favier; Michael Le Bars
Parametric instability and wave turbulence driven by tidal excitation of internal waves Article de journal
Dans: Journal of Fluid Mechanics, vol. 840, p. 498–529, 2018.
@article{lereun_favier_lebars_2018,
title = {Parametric instability and wave turbulence driven by tidal excitation of internal waves},
author = {Thomas Le Reun and Benjamin Favier and Michael Le Bars},
doi = {10.1017/jfm.2018.18},
year = {2018},
date = {2018-01-01},
journal = {Journal of Fluid Mechanics},
volume = {840},
pages = {498–529},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yongliang Feng; Muhammad Tayyab; Pierre Boivin
A Lattice-Boltzmann model for low-Mach reactive flows Article de journal
Dans: Combustion and Flame, vol. 196, p. 249 - 254, 2018, ISSN: 0010-2180.
@article{FENG2018249,
title = {A Lattice-Boltzmann model for low-Mach reactive flows},
author = {Yongliang Feng and Muhammad Tayyab and Pierre Boivin},
url = {http://www.sciencedirect.com/science/article/pii/S0010218018302803},
doi = {https://doi.org/10.1016/j.combustflame.2018.06.027},
issn = {0010-2180},
year = {2018},
date = {2018-01-01},
journal = {Combustion and Flame},
volume = {196},
pages = {249 - 254},
abstract = {A new Lattice-Boltzmann model for low-Mach reactive flows is presented. Based on standard lattices, the model is easy to implement, and is the first, to the authors’ knowledge, to pass the classical freely propagating flame test case as well as the counterflow diffusion flame, with strains up to extinction. For this presentation, simplified transport properties are considered, each species being assigned a separate Lewis number. In addition, the gas mixture is assumed to be calorically perfect. Comparisons with reference solutions show excellent agreement for mass fraction profiles, flame speed in premixed mixtures, as well as maximum temperature dependence with strain rate in counterflow diffusion flames.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Elisa Pieri; Vincent Ledentu; Miquel Huix-Rotllant; Nicolas Ferré
Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 20, p. 23252-23261, 2018.
@article{C8CP03557A,
title = {Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad},
author = {Elisa Pieri and Vincent Ledentu and Miquel Huix-Rotllant and Nicolas Ferré},
url = {http://dx.doi.org/10.1039/C8CP03557A},
doi = {10.1039/C8CP03557A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {23252-23261},
publisher = {The Royal Society of Chemistry},
abstract = {When a chromophore interacts with several titratable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine–tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to help in the interpretation of the experimental tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that radical tryptophan probably contributes to the peptide spectrum, thanks to a UV-induced electron transfer from tyrosine to tryptophan, ultimately shedding light on the complex pH-dependent behavior of the peptide spectrum.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cristina García-Iriepa; Pauline Gosset; Romain Berraud-Pache; Madjid Zemmouche; Grégory Taupier; Kokou Dodzi Dorkenoo; Pascal Didier; Jérémie Léonard; Nicolas Ferré; Isabelle Navizet
Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 14, no. 4, p. 2117-2126, 2018, (PMID: 29509419).
@article{doi:10.1021/acs.jctc.7b01240,
title = {Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water},
author = {Cristina García-Iriepa and Pauline Gosset and Romain Berraud-Pache and Madjid Zemmouche and Grégory Taupier and Kokou Dodzi Dorkenoo and Pascal Didier and Jérémie Léonard and Nicolas Ferré and Isabelle Navizet},
url = {https://doi.org/10.1021/acs.jctc.7b01240},
doi = {10.1021/acs.jctc.7b01240},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {4},
pages = {2117-2126},
abstract = {Firefly bioluminescence is a quite efficient process largely used for numerous applications. However, some fundamental photochemical properties of the light emitter are still to be analyzed. Indeed, the light emitter, oxyluciferin, can be in six different forms due to interexchange reactions. In this work, we present the simulation of the absorption and emission spectra of the possible natural oxyluciferin forms in water and some of their analogues considering both the solvent/oxyluciferin interactions and the dynamical effects by using MD simulations and QM/MM methods. On the one hand, the absorption band shapes have been rationalized by analyzing the electronic nature of the transitions involved. On the other hand, the simulated and experimental emission spectra have been compared. In this case, an ultrafast excited state proton transfer (ESPT) occurs in oxyluciferin and its analogues, which impairs the detection of the emission from the protonated state by steady-state fluorescence spectroscopy. Transient absorption spectroscopy was used to evidence this ultrafast ESPT and rationalize the comparison between simulated and experimental steady-state emission spectra. Finally, this work shows the suitability of the studied oxyluciferin analogues to mimic the corresponding natural forms in water solution, as an elegant way to block the desired interexchange reactions allowing the study of each oxyluciferin form separately.},
note = {PMID: 29509419},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Grégoire David; Frank Wennmohs; Frank Neese; Nicolas Ferré
Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory Article de journal
Dans: Inorganic Chemistry, vol. 57, no. 20, p. 12769-12776, 2018.
@article{doi:10.1021/acs.inorgchem.8b01970,
title = {Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory},
author = {Grégoire David and Frank Wennmohs and Frank Neese and Nicolas Ferré},
url = {https://doi.org/10.1021/acs.inorgchem.8b01970},
doi = {10.1021/acs.inorgchem.8b01970},
year = {2018},
date = {2018-01-01},
journal = {Inorganic Chemistry},
volume = {57},
number = {20},
pages = {12769-12776},
abstract = {With broken-symmetry Kohn–Sham density functional theory calculations, it is demonstrated that the ferromagnetic or anti-ferromagnetic character of two prototypical binuclear copper complexes can be modified, both in the sign and in magnitude, by means of chemical substitutions operated on the bridges connecting the two magnetic centers. The level of detail provided by the magnetic exchange decomposition in terms of direct exchange, kinetic exchange, and core polarization puts forward the relative importance of the different bridges. At variance with the principal bridge for which chemical substitutions modify both the direct and the kinetic exchange contributions, modifications of the secondary bridge only affect the magnitude of the anti-ferromagnetic kinetic exchange mechanism, ultimately allowing for a direct control of the magnetic character of the modified compound.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transport and Mixing Induced by Beating Cilia in Human Airways Article de journal
Dans: Frontiers in Physiology, vol. 9, p. 161, 2018, ISSN: 1664-042X.
@article{10.3389/fphys.2018.00161,
title = {Transport and Mixing Induced by Beating Cilia in Human Airways},
url = {https://www.frontiersin.org/article/10.3389/fphys.2018.00161},
doi = {10.3389/fphys.2018.00161},
issn = {1664-042X},
year = {2018},
date = {2018-01-01},
journal = {Frontiers in Physiology},
volume = {9},
pages = {161},
abstract = {The fluid transport and mixing induced by beating cilia, present in the bronchial airways, are studied using a coupled lattice Boltzmann – Immersed Boundary solver. This solver allows the simulation of both single and multi-component fluid flows around moving solid boundaries. The cilia are modeled by a set of Lagrangian points, and Immersed Boundary forces are computed onto these points in order to ensure the no-slip velocity conditions between the cilia and the fluids. The cilia are immersed in a two-layer environment: the periciliary layer (PCL) and the mucus above it. The motion of the cilia is prescribed, as well as the phase lag between two cilia in order to obtain a typical collective motion of cilia, known as metachronal waves. The results obtained from a parametric study show that antiplectic metachronal waves are the most efficient regarding the fluid transport. A specific value of phase lag, which generates the larger mucus transport, is identified. The mixing is studied using several populations of tracers initially seeded into the pericilary liquid, in the mucus just above the PCL-mucus interface, and in the mucus far away from the interface. We observe that each zone exhibits different chaotic mixing properties. The larger mixing is obtained in the PCL layer where only a few beating cycles of the cilia are required to obtain a full mixing, while above the interface, the mixing is weaker and takes more time. Almost no mixing is observed within the mucus, and almost all the tracers do not penetrate the PCL layer. Lyapunov exponents are also computed for specific locations to assess how the mixing is performed locally. Two time scales are introduced to allow a comparison between mixing induced by fluid advection and by molecular diffusion. These results are relevant in the context of respiratory flows to investigate the transport of drugs for patients suffering from chronic respiratory diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicolas Cavassilas; Demetrio Logoteta; Youseung Lee; Fabienne Michelini; Michel Lannoo; Marc Bescond; Mathieu Luisier
Dual-Gated WTe2/MoSe2 van der Waals Tandem Solar Cells Article de journal
Dans: The Journal of Physical Chemistry C, vol. 122, no. 50, p. 28545-28549, 2018.
@article{doi:10.1021/acs.jpcc.8b09905,
title = {Dual-Gated WTe2/MoSe2 van der Waals Tandem Solar Cells},
author = {Nicolas Cavassilas and Demetrio Logoteta and Youseung Lee and Fabienne Michelini and Michel Lannoo and Marc Bescond and Mathieu Luisier},
url = {https://doi.org/10.1021/acs.jpcc.8b09905},
doi = {10.1021/acs.jpcc.8b09905},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28545-28549},
abstract = {We propose and numerically investigate, through a multiscale approach, a tandem solar cell based on a van der Waals heterostructure comprising of two monolayers of transition-metal dichalcogenides. The electronic connection between the two subcells is obtained via tunneling through the van der Waals heterojunction, which is electrostatically controlled by means of a dual gate. Furthermore, by adjusting the dual-gate voltages, the photocurrents in the two subcells can be matched and the tandem cell performances can be optimized. Assuming an optimal absorptance, as expected in light-trapping systems, we predict that a power conversion efficiency of 30.7%, largely exceeding that of the single subcells, can be achieved. The proposed design being suitable for other van der Waals heterojunctions shows that it represents a viable option for future high-efficiency photovoltaic systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alexis Bottero; Paul Cristini; Dimitri Komatitsch; Quentin Brissaud
Broadband transmission losses and time dispersion maps from time-domain numerical simulations in ocean acoustics Article de journal
Dans: Journal of the Acoustical Society of America, vol. 144, no. 3, p. EL222 - EL228, 2018.
@article{bottero:hal-01793392,
title = {Broadband transmission losses and time dispersion maps from time-domain numerical simulations in ocean acoustics},
author = {Alexis Bottero and Paul Cristini and Dimitri Komatitsch and Quentin Brissaud},
url = {https://hal.archives-ouvertes.fr/hal-01793392},
doi = {10.1121/1.5055787},
year = {2018},
date = {2018-01-01},
journal = {Journal of the Acoustical Society of America},
volume = {144},
number = {3},
pages = {EL222 - EL228},
publisher = {Acoustical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M L M Rocco; M Häming; C E V de Moura; M Barbatti; A B Rocha; A Schöll; E Umbach
High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes Article de journal
Dans: The Journal of Physical Chemistry C, vol. 122, no. 50, p. 28692-28701, 2018.
@article{doi:10.1021/acs.jpcc.8b08945,
title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},
author = {M L M Rocco and M Häming and C E V de Moura and M Barbatti and A B Rocha and A Schöll and E Umbach},
url = {https://doi.org/10.1021/acs.jpcc.8b08945},
doi = {10.1021/acs.jpcc.8b08945},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28692-28701},
abstract = {We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Deniz Tuna; Lasse Spörkel; Mario Barbatti; Walter Thiel
Nonadiabatic dynamics simulations of photoexcited urocanic acid Article de journal
Dans: Chemical Physics, vol. 515, p. 521 - 534, 2018, ISSN: 0301-0104, (Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)).
@article{TUNA2018521,
title = {Nonadiabatic dynamics simulations of photoexcited urocanic acid},
author = {Deniz Tuna and Lasse Spörkel and Mario Barbatti and Walter Thiel},
url = {http://www.sciencedirect.com/science/article/pii/S0301010418306542},
doi = {https://doi.org/10.1016/j.chemphys.2018.09.036},
issn = {0301-0104},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {521 - 534},
abstract = {Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations. We find that UA has an ultrashort excited-state lifetime, which is due to ultrafast radiationless excited-state deactivation driven by E↔Z photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes. The computed S1 excited-state lifetimes for the E and Z isomers of the N1H and N3H tautomers range from 271 to 506 fs. The photoisomerization quantum yield is calculated to be 43% (32%) for the combined E (Z) isomers of both tautomers. The shorter lifetime and the lower photoisomerization quantum yield of the Z isomers can be rationalized by the larger number of available excited-state deactivation processes: the Z isomers can undergo ESIPT and photoisomerization, whereas the E isomers can only deactivate via the latter process. The intramolecular hydrogen bond that is present in many Z conformers can prevent successful photoisomerization to an E isomer. We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, which has previously been detected spectroscopically in aqueous solution. However, we do find an EEDQY-PI as well as a complementary excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT) for the N1H-Z isomers, which demonstrates the competition of the photoisomerization and ESIPT processes. The present comprehensive study lays the groundwork for future photodynamics simulations of UA in the aqueous phase.},
note = {Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pavlo O Dral; Mario Barbatti; Walter Thiel
Nonadiabatic Excited-State Dynamics with Machine Learning Article de journal
Dans: The Journal of Physical Chemistry Letters, vol. 9, no. 19, p. 5660-5663, 2018, (PMID: 30200766).
@article{doi:10.1021/acs.jpclett.8b02469,
title = {Nonadiabatic Excited-State Dynamics with Machine Learning},
author = {Pavlo O Dral and Mario Barbatti and Walter Thiel},
url = {https://doi.org/10.1021/acs.jpclett.8b02469},
doi = {10.1021/acs.jpclett.8b02469},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {9},
number = {19},
pages = {5660-5663},
abstract = {We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points. We investigate the feasibility of this approach by using adiabatic spin-boson Hamiltonian models of various dimensions as reference methods.},
note = {PMID: 30200766},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A Mohamadzade; S Bai; M Barbatti; S Ullrich
Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position Article de journal
Dans: Chemical Physics, vol. 515, p. 572-579, 2018.
@article{2018CP....515..572M,
title = {Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position},
author = {A {Mohamadzade} and S {Bai} and M {Barbatti} and S {Ullrich}},
doi = {10.1016/j.chemphys.2018.08.011},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {572-579},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vanessa C de Medeiros; Railton B de Andrade; Gessenildo P. Rodrigues; Glauco F Bauerfeldt; Elizete Ventura; Mario Barbatti; Silmar A do Monte
Photochemistry of CF3Cl: Quenching of Charged Fragments Is Caused by Nonadiabatic Effects Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 14, no. 9, p. 4844-4855, 2018, (PMID: 30080978).
@article{doi:10.1021/acs.jctc.8b00457,
title = {Photochemistry of CF3Cl: Quenching of Charged Fragments Is Caused by Nonadiabatic Effects},
author = {Vanessa C de Medeiros and Railton B de Andrade and Gessenildo P. Rodrigues and Glauco F Bauerfeldt and Elizete Ventura and Mario Barbatti and Silmar A do Monte},
url = {https://doi.org/10.1021/acs.jctc.8b00457},
doi = {10.1021/acs.jctc.8b00457},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {9},
pages = {4844-4855},
abstract = {For the first time, high-level multireference electronic structure calculations have been performed to study the photochemistry of CF3Cl, allowing a comprehensive interpretation and assignment of experimental data concerning fluorescence, ion-pair formation, and generation of CF3 fragments in several electronic states. All studied dissociation channels correlate either with Cl or Cl– in the ground state. On the other hand, a CF3 fragment can be generated either in the ground or excited state. A rationalization for the nonadiabatic relaxation of CF3Cl, including the formation of an (n4s) stable state and internal conversion at multiple-state intersections, has been provided. Our results explain the anomalous quenching of a charged fragment after low-energy excitation, a fact experimentally observed by separate groups. We show that the CF3+···Cl– ion pair undergoes an internal conversion to the ground state, producing neutral CF3 and Cl fragments. The results also allow understanding as to why CF3Cl is usually a nonemitting species and how UV emission could be induced.},
note = {PMID: 30080978},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Li-li Jiang; Dan Luo; Xiong Lu; Qin-yong Zhang; Fang-gong Cai; Jun Chen
Comparative Study on Chemical Reduction of Free-standing Flexible GO Films and Their Cyclic Voltammetry Performance Article de journal
Dans: Colloids and Surfaces A: Physicochemical and Engineering Aspects, vol. 555, 2018.
@article{articleb,
title = {Comparative Study on Chemical Reduction of Free-standing Flexible GO Films and Their Cyclic Voltammetry Performance},
author = {Li-li Jiang and Dan Luo and Xiong Lu and Qin-yong Zhang and Fang-gong Cai and Jun Chen},
doi = {10.1016/j.colsurfa.2018.07.050},
year = {2018},
date = {2018-01-01},
journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
volume = {555},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hans Lischka; Dana Nachtigallová; Adélia J A Aquino; Péter G Szalay; Felix Plasser; Francisco B C Machado; Mario Barbatti
Multireference Approaches for Excited States of Molecules Article de journal
Dans: Chemical Reviews, vol. 118, no. 15, p. 7293-7361, 2018, (PMID: 30040389).
@article{doi:10.1021/acs.chemrev.8b00244,
title = {Multireference Approaches for Excited States of Molecules},
author = {Hans Lischka and Dana Nachtigallová and Adélia J A Aquino and Péter G Szalay and Felix Plasser and Francisco B C Machado and Mario Barbatti},
url = {https://doi.org/10.1021/acs.chemrev.8b00244},
doi = {10.1021/acs.chemrev.8b00244},
year = {2018},
date = {2018-01-01},
journal = {Chemical Reviews},
volume = {118},
number = {15},
pages = {7293-7361},
abstract = {Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.},
note = {PMID: 30040389},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
Mechanism of enhanced triplet decay of thionucleobase by glycosylation and rate-modulating strategies Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 20, p. 16428-16436, 2018.
@article{C8CP02306A,
title = {Mechanism of enhanced triplet decay of thionucleobase by glycosylation and rate-modulating strategies},
author = {Shuming Bai and Mario Barbatti},
url = {http://dx.doi.org/10.1039/C8CP02306A},
doi = {10.1039/C8CP02306A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {16428-16436},
publisher = {The Royal Society of Chemistry},
abstract = {The decay of the triplet state of photosensitizers is essential to their performance in singlet-oxygen generation. Experiments have shown that in thionucleosides, this decay is enhanced compared to that in the corresponding thionucleobases. In this work, we applied quantum-chemical methods and chemical-kinetic modeling to investigate the effects of the sugar substituent on the triplet decay of thionucleosides. The computed rates for the energetically favored conformers of thiothymidine, thiouridine, and thioguanosine (and the respective thionucleobases) show a remarkable quantitative agreement with the experimental results. We additionally show that the triplet decay enhancement is caused by the repulsion interaction between the sugar group and the sulfur atom, which reduces the activation energy for intersystem crossing by destabilizing the T1 minimum. In some instances, an intramolecular hydrogen bond stabilizes the energy of the T1/S0 crossing point, also reducing the activation energy. This molecular understanding of the mechanism of enhanced triplet decay provides a guideline to control the triplet decay rate, which was tested in new thiothymidine derivatives.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fábris Kossoski; Mario Barbatti
Nuclear Ensemble Approach with Importance Sampling Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 14, no. 6, p. 3173-3183, 2018, (PMID: 29694040).
@article{doi:10.1021/acs.jctc.8b00059,
title = {Nuclear Ensemble Approach with Importance Sampling},
author = {Fábris Kossoski and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jctc.8b00059},
doi = {10.1021/acs.jctc.8b00059},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {6},
pages = {3173-3183},
abstract = {We show that the importance sampling technique can effectively augment the range of problems where the nuclear ensemble approach can be applied. A sampling probability distribution function initially determines the collection of initial conditions for which calculations are performed, as usual. Then, results for a distinct target distribution are computed by introducing compensating importance sampling weights for each sampled point. This mapping between the two probability distributions can be performed whenever they are both explicitly constructed. Perhaps most notably, this procedure allows for the computation of temperature dependent observables. As a test case, we investigated the UV absorption spectra of phenol, which has been shown to have a marked temperature dependence. Application of the proposed technique to a range that covers 500 K provides results that converge to those obtained with conventional sampling. We further show that an overall improved rate of convergence is obtained when sampling is performed at intermediate temperatures. The comparison between calculated and the available measured cross sections is very satisfactory, as the main features of the spectra are correctly reproduced. As a second test case, one of Tully’s classical models was revisited, and we show that the computation of dynamical observables also profits from the importance sampling technique. In summary, the strategy developed here can be employed to assess the role of temperature for any property calculated within the nuclear ensemble method, with the same computational cost as doing so for a single temperature.},
note = {PMID: 29694040},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rachel Crespo-Otero; Mario Barbatti
Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics Article de journal
Dans: Chemical Reviews, vol. 118, no. 15, p. 7026-7068, 2018, (PMID: 29767966).
@article{doi:10.1021/acs.chemrev.7b00577,
title = {Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics},
author = {Rachel Crespo-Otero and Mario Barbatti},
url = {https://doi.org/10.1021/acs.chemrev.7b00577},
doi = {10.1021/acs.chemrev.7b00577},
year = {2018},
date = {2018-01-01},
journal = {Chemical Reviews},
volume = {118},
number = {15},
pages = {7026-7068},
abstract = {Nonadiabatic mixed quantum–classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods—mean-field Ehrenfest, trajectory surface hopping, and multiple spawning—this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.},
note = {PMID: 29767966},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M L M Rocco; M Häming; C E V de Moura; M Barbatti; A B Rocha; A Schöll; E Umbach
High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes Article de journal
Dans: The Journal of Physical Chemistry C, vol. 122, no. 50, p. 28692-28701, 2018.
@article{doi:10.1021/acs.jpcc.8b08945b,
title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},
author = {M L M Rocco and M Häming and C E V de Moura and M Barbatti and A B Rocha and A Schöll and E Umbach},
url = {https://doi.org/10.1021/acs.jpcc.8b08945},
doi = {10.1021/acs.jpcc.8b08945},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28692-28701},
abstract = {We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hans Lischka; Mario Barbatti; Farhan Siddique; Anita Das; Adelia J A Aquino
The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster Article de journal
Dans: Chemical Physics, vol. 515, p. 472 - 479, 2018, ISSN: 0301-0104, (Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)).
@article{LISCHKA2018472,
title = {The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster},
author = {Hans Lischka and Mario Barbatti and Farhan Siddique and Anita Das and Adelia J A Aquino},
url = {http://www.sciencedirect.com/science/article/pii/S0301010418305500},
doi = {https://doi.org/10.1016/j.chemphys.2018.07.050},
issn = {0301-0104},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {472 - 479},
abstract = {Surface hopping photodynamics simulations have been performed on a cluster of thymine interacting with six water molecules (T(H2O)6). The second-order algebraic diagrammatic construction method (ADC(2)) has been used for calculating the required electronic energies and excited state gradients. Comparison with the previously performed photodynamics for the isolated thymine (Molecules 21 (2016) 1603) shows a similar global behavior and the central role of the S1(nπ∗) minimum for further long-term dynamics. The main difference comes from the destabilization of the nπ∗ state by hydrogen bonding, which leads to a significantly enhanced conversion rate from the bright S2(ππ∗) state to S1(nπ∗) for the T(H2O)6 cluster. On the other hand, the decay time to S0 and the trapping in S1 is significantly increased. Due to the localized character of the lone pair orbital involved in the nπ∗ transition at one oxygen atom, specific changes in the structure of the hydrogen bonded network are observed. Since the hydrogen bonding of the water molecules connected to that oxygen atom is specifically weakened, they show dissociations from thymine during the photodynamics, starting within 30 fs after electronic excitation of thymine.},
note = {Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Konstantin Falahati; Carsten Hamerla; Miquel Huix-Rotllant; Irene Burghardt
Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 20, p. 12483-12492, 2018.
@article{C8CP00657A,
title = {Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states},
author = {Konstantin Falahati and Carsten Hamerla and Miquel Huix-Rotllant and Irene Burghardt},
url = {http://dx.doi.org/10.1039/C8CP00657A},
doi = {10.1039/C8CP00657A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {12483-12492},
publisher = {The Royal Society of Chemistry},
abstract = {We examine the mechanism of ultrafast internal conversion between the B band (Soret band) and the Q band in porphine (H2P), the prototypical free-base porphyrin, using electronic structure studies and on-the-fly surface-hopping nonadiabatic dynamics. Our study highlights the crucial role of dark states within the N band which are found to mediate B/Q state transfer, necessitating a treatment beyond Gouterman's classic four-orbital model. The sequential B → N → Q pathway dominates largely over the direct B → Q pathway which is found to be energetically unfavorable. Potential energy surface cuts and conical intersections between excited states are determined by TDDFT and validated by CASSCF/CASPT2 and XMCQDPT2 calculations. Both the static analysis and on-the-fly surface-hopping calculations suggest a pathway which involves minor structural deformations via in-plane vibrations. The B → N conversion is a barrierless adiabatic process occurring within ∼20 fs, while the subsequent N → Q conversion occurs via a conical intersection within ∼100 fs, in agreement with time-resolved experiments for porphine and related free base porphyrins. Furthermore, evidence for both sequential and direct transfer to the Qx and Qy states},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicolas Frangieh; Dominique Morvan; Sofiane Meradji; G ACCARY; O Bessonov
Numerical simulation of grassland fires behavior using an implicit physical multiphase model Article de journal
Dans: Fire Safety Journal, vol. 102, p. 37-47, 2018.
@article{frangieh:hal-01978037,
title = {Numerical simulation of grassland fires behavior using an implicit physical multiphase model},
author = {Nicolas Frangieh and Dominique Morvan and Sofiane Meradji and G ACCARY and O Bessonov},
url = {https://hal.archives-ouvertes.fr/hal-01978037},
year = {2018},
date = {2018-01-01},
journal = {Fire Safety Journal},
volume = {102},
pages = {37-47},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dominique Morvan; Gilbert Accary; Sofiane Meradji; Nicolas Frangieh; Oleg BESSONOV
A 3D physical model to study the behavior of vegetation fires at laboratory scale Article de journal
Dans: Fire Safety Journal, vol. 101, p. 39-52, 2018.
@article{morvan:hal-01946956,
title = {A 3D physical model to study the behavior of vegetation fires at laboratory scale},
author = {Dominique Morvan and Gilbert Accary and Sofiane Meradji and Nicolas Frangieh and Oleg BESSONOV},
url = {https://hal.archives-ouvertes.fr/hal-01946956},
year = {2018},
date = {2018-01-01},
journal = {Fire Safety Journal},
volume = {101},
pages = {39-52},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dmytro Kandaskalov; Philippe Maugis
Thermodynamic stabilities in the Fe-Fe16C2 system: Influence of carbon-carbon interactions studied by DFT Article de journal
Dans: Computational Materials Science, vol. 150, p. 524 - 534, 2018, ISSN: 0927-0256.
@article{KANDASKALOV2018524,
title = {Thermodynamic stabilities in the Fe-Fe16C2 system: Influence of carbon-carbon interactions studied by DFT},
author = {Dmytro Kandaskalov and Philippe Maugis},
url = {http://www.sciencedirect.com/science/article/pii/S0927025618302672},
doi = {https://doi.org/10.1016/j.commatsci.2018.04.025},
issn = {0927-0256},
year = {2018},
date = {2018-01-01},
journal = {Computational Materials Science},
volume = {150},
pages = {524 - 534},
abstract = {Low-temperature decomposition of ferrous martensite leads to the formation of alternate C-rich and Fe-rich nanodomains. From experimental results, the Fe-rich domains consist of α-ferrite, while the C-rich domains are often supposed to be the ordered α″-Fe16C2 phase. The aim of our theoretical study was to investigate the thermodynamic and structural parameters of intermediate compounds α″-Fe128Cn, to find the possible composition of the C-rich domains. We used DFT calculations coupled to statistical thermodynamics to build the energy landscape in the Fe-Fe16C2 system. The paper also includes the study of α-Fe|α″-Fe16C2 interfaces to identify the optimal orientation relationship between the two phases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2017
A Pivano; V O Dolocan
Systematic motion of magnetic domain walls in notched nanowires under ultrashort current pulses Article de journal
Dans: Phys. Rev. B, vol. 96, p. 224431, 2017.
@article{PhysRevB.96.224431,
title = {Systematic motion of magnetic domain walls in notched nanowires under ultrashort current pulses},
author = {A Pivano and V O Dolocan},
url = {https://link.aps.org/doi/10.1103/PhysRevB.96.224431},
doi = {10.1103/PhysRevB.96.224431},
year = {2017},
date = {2017-12-01},
journal = {Phys. Rev. B},
volume = {96},
pages = {224431},
publisher = {American Physical Society},
abstract = {The precise manipulation of transverse magnetic domain walls in finite/infinite nanowires with artificial defects under the influence of very short spin-polarized current pulses is investigated. We show that for a classical 3d ferromagnet material like nickel, the exact positioning of the domain walls at room temperature is possible only for pulses with very short rise and fall time that move the domain wall reliably to nearest neighboring pinning position. The influence of the shape of the current pulse and of the transient effects on the phase diagram current-pulse length are discussed. We show that large transient effects appear even when α=β, below a critical value, due to the domain wall distortion caused by the current pulse shape and the presence of the notches. The transient effects can oppose or amplify the spin-transfer torque (STT), depending on the ratio β/α. This enlarges the physical comprehension of the domain wall (DW) motion under STT and opens the route to the DW displacement in both directions with unipolar currents.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
L -A Couston; D Lecoanet; B Favier; M Le Bars
Dynamics of mixed convectivechar21stably-stratified fluids Article de journal
Dans: Phys. Rev. Fluids, vol. 2, p. 094804, 2017.
@article{PhysRevFluids.2.094804,
title = {Dynamics of mixed convectivechar21stably-stratified fluids},
author = {L -A Couston and D Lecoanet and B Favier and M Le Bars},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.2.094804},
doi = {10.1103/PhysRevFluids.2.094804},
year = {2017},
date = {2017-09-01},
journal = {Phys. Rev. Fluids},
volume = {2},
pages = {094804},
publisher = {American Physical Society},
abstract = {We study the dynamical regimes of a density-stratified fluid confined between isothermal no-slip top and bottom boundaries (at temperatures Tt and Tb) via direct numerical simulation. The thermal expansion coefficient of the fluid is temperature dependent and chosen such that the fluid density is maximum at the inversion temperature Tb>Ti>Tt. Thus, the lower layer of the fluid is convectively unstable while the upper layer is stably stratified. We show that the characteristics of the convection change significantly depending on the degree of stratification of the stable layer. For strong stable stratification, the convection zone coincides with the fraction of the fluid that is convectively unstable (i.e., where T>Ti), and convective motions consist of rising and sinking plumes of large density anomaly, as is the case in canonical Rayleigh-Bénard convection; internal gravity waves are generated by turbulent fluctuations in the convective layer and propagate in the upper layer. For weak stable stratification, we demonstrate that a large fraction of the stable fluid (i.e., with temperature T<Ti) is instead destabilized and entrained by buoyant plumes emitted from the bottom boundary. The convection thus mixes cold patches of low density-anomaly fluid with hot upward plumes and the end result is that the Ti isotherm sinks within the bottom boundary layer and that the convection is entrainment dominated. We provide a phenomenological description of the transition between the regimes of plume-dominated and entrainment-dominated convection through analysis of the differences in the heat transfer mechanisms, kinetic energy density spectra, and probability density functions for different stratification strengths. Importantly, we find that the effect of the stable layer on the convection decreases only weakly with increasing stratification strength, meaning that the dynamics of the stable layer and convection should be studied self-consistently in a wide range of applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thomas Le Reun; Benjamin Favier; Adrian J Barker; Michael Le Bars
Inertial Wave Turbulence Driven by Elliptical Instability Article de journal
Dans: Phys. Rev. Lett., vol. 119, p. 034502, 2017.
@article{PhysRevLett.119.034502,
title = {Inertial Wave Turbulence Driven by Elliptical Instability},
author = {Thomas Le Reun and Benjamin Favier and Adrian J Barker and Michael Le Bars},
url = {https://link.aps.org/doi/10.1103/PhysRevLett.119.034502},
doi = {10.1103/PhysRevLett.119.034502},
year = {2017},
date = {2017-07-01},
journal = {Phys. Rev. Lett.},
volume = {119},
pages = {034502},
publisher = {American Physical Society},
abstract = {The combination of elliptical deformation of streamlines and vorticity can lead to the destabilization of any rotating flow via the elliptical instability. Such a mechanism has been invoked as a possible source of turbulence in planetary cores subject to tidal deformations. The saturation of the elliptical instability has been shown to generate turbulence composed of nonlinearly interacting waves and strong columnar vortices with varying respective amplitudes, depending on the control parameters and geometry. In this Letter, we present a suite of numerical simulations to investigate the saturation and the transition from vortex-dominated to wave-dominated regimes. This is achieved by simulating the growth and saturation of the elliptical instability in an idealized triply periodic domain, adding a frictional damping to the geostrophic component only, to mimic its interaction with boundaries. We reproduce several experimental observations within one idealized local model and complement them by reaching more extreme flow parameters. In particular, a wave-dominated regime that exhibits many signatures of inertial wave turbulence is characterized for the first time. This regime is expected in planetary interiors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Minh Chien Nguyen; Marc Medale; Olivier Asserin; Stephane Gounand; Philippe Gilles
Sensitivity to welding positions and parameters in GTA welding with a 3D multiphysics numerical model Article de journal
Dans: Numerical Heat Transfer, Part A: Applications, vol. 0, no. 0, p. 1-17, 2017.
@article{doi:10.1080/10407782.2016.1264747,
title = {Sensitivity to welding positions and parameters in GTA welding with a 3D multiphysics numerical model},
author = {Minh Chien Nguyen and Marc Medale and Olivier Asserin and Stephane Gounand and Philippe Gilles},
url = {http://dx.doi.org/10.1080/10407782.2016.1264747},
doi = {10.1080/10407782.2016.1264747},
year = {2017},
date = {2017-02-13},
urldate = {0000-01-01},
journal = {Numerical Heat Transfer, Part A: Applications},
volume = {0},
number = {0},
pages = {1-17},
abstract = {ABSTRACTA three-dimensional numerical model of Gas Tungsten Arc welding has been developed to predict weld a bead shape, fluid flow in the weld pool, as well as thermal field in the workpiece. This model accounts for coupled electromagnetism, heat transfer, and fluid flow with a moving free surface to simulate different welding positions. The solution strategy of the coupled non-linear equations that has been implemented in the CastɜM finite-element code is also discussed. The capabilities of our numerical model are first assessed by comparison to the experimental results. Then, as fluid flows in a weld pool play a prominent role in the weld quality as well as in the final shape of the weld bead seam, the effect of various welding positions on the weld pool shape has been investigated. This constitutes the main novelty of this work. The performed computations point out a strong sensitivity to gravity on the weld pool shape depending on assisting or opposing the weld direction with respect to gravity. This study contributes to assessing the model capabilities that provide a deeper physical insight into a more efficient optimization of welding processes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Simon Cabanes, Jonathan Aurnou, Benjamin Favier & Michael Le Bars
A laboratory model for deep-seated jets on the gas giants Article de journal
Dans: Nature Physics, 2017.
@article{Cabanes2017,
title = {A laboratory model for deep-seated jets on the gas giants},
author = {Simon Cabanes, Jonathan Aurnou, Benjamin Favier & Michael Le Bars},
editor = {Nature Physics},
url = {http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys4001.html},
doi = {10.1038/nphys4001},
year = {2017},
date = {2017-01-23},
journal = {Nature Physics},
abstract = {The strong east–west jet flows on the gas giants, Jupiter1 and Saturn2, have persisted for hundreds of years. Yet, experimental studies cannot reach the planetary regime and similarly strong and quasi-steady jets have been reproduced in numerical models only under simplifying assumptions and limitations. Two models have been proposed: a shallow model where jets are confined to the weather layer and a deep model where the jets extend into the planetary molecular envelope. Here we show that turbulent laboratory flows naturally generate multiple, alternating jets in a rapidly rotating cylindrical container. The observed properties of gas giants’ jets are only now reproduced in a laboratory experiment emulating the deep model. Our findings demonstrate that long-lived jets can persist at high latitudes even under conditions including viscous dissipation and friction and bear relevance to the shallow versus deep models debate in the context of the ongoing Juno mission.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P. Tamain; C. Colin; L. Colas; C. Baudoin; G. Ciraolo; R. Futtersack; D. Galassi; Ph Ghendrih; N. Nace; F. Schwander; E. Serre
Numerical analysis of the impact of an RF sheath on the Scrape-Off Layer in 2D and 3D turbulence simulations Article de journal
Dans: Nuclear Materials and Energy, p. -, 2017, ISSN: 2352-1791.
@article{Tamain2017,
title = {Numerical analysis of the impact of an RF sheath on the Scrape-Off Layer in 2D and 3D turbulence simulations},
author = {P. Tamain and C. Colin and L. Colas and C. Baudoin and G. Ciraolo and R. Futtersack and D. Galassi and Ph Ghendrih and N. Nace and F. Schwander and E. Serre},
url = {http://www.sciencedirect.com/science/article/pii/S2352179116302757},
doi = {http://dx.doi.org/10.1016/j.nme.2016.12.022},
issn = {2352-1791},
year = {2017},
date = {2017-01-01},
journal = {Nuclear Materials and Energy},
pages = {-},
abstract = {Abstract Motivated by Radio Frequency (RF) heating studies, the response of the plasma of tokamaks to the presence of a locally polarized limiter is studied. In a first part, we use the TOKAM3X 3D global edge turbulence code to analyse the impact of such biasing in a realistic geometry. Key features of experimental observations are qualitatively recovered, especially the extension of a potential and density perturbation on long, but finite, distances along connected field lines. The perturbation is also found to extend in the transverse direction. Both observations demonstrate the influence of perpendicular current loops on the plasma confirming the need for an accurate description in reduced models. In a second part, we use the TOKAM2D slab turbulence code to determine the validity of using a transverse Ohm's law for this purpose. Results indicate that a local Ohm's law with a constant and uniform perpendicular resistivity appears at least as an oversimplified description of perpendicular charge transport in a turbulent Scrape-Off Layer.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
H. Bufferand; C. Baudoin; J. Bucalossi; G. Ciraolo; J. Denis; N. Fedorczak; D. Galassi; Ph. Ghendrih; R. Leybros; Y. Marandet; N. Mellet; J. Morales; N. Nace; E. Serre; P. Tamain; M. Valentinuzzi
Implementation of drift velocities and currents in SOLEDGE2D–EIRENE Article de journal
Dans: Nuclear Materials and Energy, p. -, 2017, ISSN: 2352-1791.
@article{Bufferand2017,
title = {Implementation of drift velocities and currents in SOLEDGE2D–EIRENE},
author = {H. Bufferand and C. Baudoin and J. Bucalossi and G. Ciraolo and J. Denis and N. Fedorczak and D. Galassi and Ph. Ghendrih and R. Leybros and Y. Marandet and N. Mellet and J. Morales and N. Nace and E. Serre and P. Tamain and M. Valentinuzzi},
url = {http://www.sciencedirect.com/science/article/pii/S2352179116301946},
doi = {http://dx.doi.org/10.1016/j.nme.2016.11.031},
issn = {2352-1791},
year = {2017},
date = {2017-01-01},
journal = {Nuclear Materials and Energy},
pages = {-},
abstract = {Abstract In order to improve cross-field transport description, drifts and currents have been implemented in SOLEDGE2D–EIRENE. The derivation of an equation for the electric potential is recalled. The resolution of current equation is tested in a simple slab case. WEST divertor simulations in forward-B and reverse-B fields are also discussed. A significant increase of ExB shear is observed in the forward-B configuration that could explain a favorable L-H transition in this case.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
G. Ciraolo; H. Bufferand; J. Bucalossi; Ph. Ghendrih; P. Tamain; Y. Marandet; M. Valentinuzzi; J. Denis; N. Fedorczak; E. Hodille; N. Mellet; B. Pegourie; C. Grisolia; C. Bourdelle; E. Tsitrone; D. Galassi; R. Leybros; G. Giorgiani; E. Serre
H-mode WEST tungsten divertor operation: deuterium and nitrogen seeded simulations with SOLEDGE2D-EIRENE Article de journal
Dans: Nuclear Materials and Energy, p. -, 2017, ISSN: 2352-1791.
@article{Ciraolo2017,
title = {H-mode WEST tungsten divertor operation: deuterium and nitrogen seeded simulations with SOLEDGE2D-EIRENE},
author = {G. Ciraolo and H. Bufferand and J. Bucalossi and Ph. Ghendrih and P. Tamain and Y. Marandet and M. Valentinuzzi and J. Denis and N. Fedorczak and E. Hodille and N. Mellet and B. Pegourie and C. Grisolia and C. Bourdelle and E. Tsitrone and D. Galassi and R. Leybros and G. Giorgiani and E. Serre},
url = {http://www.sciencedirect.com/science/article/pii/S235217911630271X},
doi = {http://dx.doi.org/10.1016/j.nme.2016.12.025},
issn = {2352-1791},
year = {2017},
date = {2017-01-01},
journal = {Nuclear Materials and Energy},
pages = {-},
abstract = {Abstract Simulations of WEST H-mode divertor scenarios have been performed with SOLEDGE2D-EIRENE edge plasma transport code, both for pure deuterium and nitrogen seeded discharge. In the pure deuterium case, a target heat flux of 8 MW/m2 is reached, but misalignment between heat and the particle outflux yields 50 eV plasma temperature at the target plates. With nitrogen seeding, the heat and particle outflux are observed to be aligned so that lower plasma temperatures at the target plates are achieved together with the required high heat fluxes. This change in heat and particle outflux alignment is analysed with respect to the role of divertor geometry and the impact of vertical vs horizontal target plates on neutrals spreading.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Athanassoula, E.; Rodionov, S. A.; Prantzos, N.
Metallicity-dependent kinematics and morphology of the Milky Way bulge Article de journal
Dans: Monthly Notices of the Royal Astronomical Society: Letters, vol. 467, no. 1, p. L46, 2017.
@article{doi:10.1093/mnrasl/slw255,
title = {Metallicity-dependent kinematics and morphology of the Milky Way bulge},
author = {Athanassoula, E. and Rodionov, S. A. and Prantzos, N.},
url = {+ http://dx.doi.org/10.1093/mnrasl/slw255},
doi = {10.1093/mnrasl/slw255},
year = {2017},
date = {2017-01-01},
journal = {Monthly Notices of the Royal Astronomical Society: Letters},
volume = {467},
number = {1},
pages = {L46},
abstract = {We use N-body chemo-dynamic simulations to study the coupling between morphology, kinematics and metallicity of the bar/bulge region of our Galaxy. We make qualitative comparisons of our results with available observations and find very good agreement. We conclude that this region is complex, since it comprises several stellar components with different properties -- i.e. a boxy/peanut bulge, thin and thick disc components, and, to lesser extents, a disky pseudobulge, a stellar halo and a small classical bulge -- all cohabiting in dynamical equilibrium. Our models show strong links between kinematics and metallicity, or morphology and metallicity, as already suggested by a number of recent observations. We discuss and explain these links. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gao, Xing; Bai, Shuming; Fazzi, Daniele; Niehaus, Thomas; Barbatti, Mario; Thiel, Walter
Evaluation of Spin-Orbit Couplings with Linear-Response Time-Dependent Density Functional Methods Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 13, no. 2, p. 515-524, 2017, (PMID: 27959528).
@article{doi:10.1021/acs.jctc.6b00915,
title = {Evaluation of Spin-Orbit Couplings with Linear-Response Time-Dependent Density Functional Methods},
author = {Gao, Xing and Bai, Shuming and Fazzi, Daniele and Niehaus, Thomas and Barbatti, Mario and Thiel, Walter},
url = {http://dx.doi.org/10.1021/acs.jctc.6b00915},
doi = {10.1021/acs.jctc.6b00915},
year = {2017},
date = {2017-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
number = {2},
pages = {515-524},
abstract = {A new versatile code based on Python scripts was developed to calculate spin–orbit coupling (SOC) elements between singlet and triplet states. The code, named PySOC, is interfaced to third-party quantum chemistry packages, such as Gaussian 09 and DFTB+. SOCs are evaluated using linear-response (LR) methods based on time-dependent density functional theory (TDDFT), the Tamm-Dancoff approximation (TDA), and time-dependent density functional tight binding (TD-DFTB). The evaluation employs Casida-type wave functions and the Breit-Pauli (BP) spin–orbit Hamiltonian with an effective charge approximation. For validation purposes, SOCs calculated with PySOC are benchmarked for several organic molecules, with SOC values spanning several orders of magnitude. The computed SOCs show little variation with the basis set, but are sensitive to the chosen density functional. The benchmark results are in good agreement with reference data obtained using higher-level spin–orbit Hamiltonians and electronic structure methods, such as CASPT2 and DFT/MRCI. PySOC can be easily interfaced to other third-party codes and other methods yielding CI-type wave functions.},
note = {PMID: 27959528},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dmytro Kandaskalov; Philippe Maugis
A first-principle study of the structural, elastic, lattice dynamical and thermodynamic properties of and phases Article de journal
Dans: Computational Materials Science, vol. 128, p. 278 - 286, 2017, ISSN: 0927-0256.
@article{Kandaskalov2017278,
title = {A first-principle study of the structural, elastic, lattice dynamical and thermodynamic properties of and phases},
author = {Dmytro Kandaskalov and Philippe Maugis},
url = {http://www.sciencedirect.com/science/article/pii/S0927025616305730},
doi = {http://dx.doi.org/10.1016/j.commatsci.2016.11.022},
issn = {0927-0256},
year = {2017},
date = {2017-01-01},
journal = {Computational Materials Science},
volume = {128},
pages = {278 - 286},
abstract = {Abstract Low temperature decomposition of ferrous martensite leads to the formation of alternate C-rich and Fe-rich domains. Although some contradictions exist in the experimental results, the C-rich domains are often supposed to be the ordered α ″ - Fe 16 C 2 phase. The aim of our theoretical study is to investigate the fundamental properties of the α ″ - Fe 16 C 2 phase and to compare it to the isomorphic known phase α ″ - Fe 16 N 2 . In this paper, we present the structural, electronic, magnetic, vibrational and elastic properties of α ″ - Fe 16 C 2 and Fe 16 N 2 phases, calculated within the formalism of the DFT theory. This study is used to discuss the relative properties and stabilities of these two phases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bilel Sanhaji
Testing for Nonlinearity in Conditional Covariances Article de journal
Dans: 2017, ISSN: 21946507.
@article{Sanhaji2017,
title = {Testing for Nonlinearity in Conditional Covariances},
author = {Bilel Sanhaji},
editor = {Journal of Time Series Econometrics},
url = {https://doi.org/10.1515/jtse-2016-0010},
doi = {jtse-2016-0010},
issn = {21946507},
year = {2017},
date = {2017-01-01},
abstract = {We propose two Lagrange multiplier tests for nonlinearity in conditional covariances in multivariate GARCH models. The null hypothesis is the scalar BEKK model in which covolatilities of time series are driven by a linear function of their own lags and lagged squared innovations. The alternative hypothesis is an extension of the model in which covolatilities are modeled by a nonlinear function of the lagged squared innovations, represented by an exponential or a logistic transition function. Moreover, on the same basis we develop two other tests that are robust to leverage effects. We investigate the size and power of these tests through Monte Carlo experiments, and we provide empirical illustrations in many of which cases these tests encourage the use of nonlinearity in conditional covariances.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
E Constant; J Favier; M Meldi; P Meliga; E Serre
An immersed boundary method in OpenFOAM : Verification and validation Article de journal
Dans: Computers & Fluids, vol. 157, p. 55 - 72, 2017, ISSN: 0045-7930.
@article{CONSTANT201755,
title = {An immersed boundary method in OpenFOAM : Verification and validation},
author = {E Constant and J Favier and M Meldi and P Meliga and E Serre},
url = {http://www.sciencedirect.com/science/article/pii/S004579301730275X},
doi = {https://doi.org/10.1016/j.compfluid.2017.08.001},
issn = {0045-7930},
year = {2017},
date = {2017-01-01},
journal = {Computers & Fluids},
volume = {157},
pages = {55 - 72},
abstract = {The present work proposes a modified Pressure-Implicit Split-Operator (PISO) solver integrating the recent Immersed Boundary Method (IBM) proposed by [1] in order to perform reliable simulations of incompressible flows around bluff bodies using the open source toolbox OpenFOAM version 2.2 ([2]). The (IBM) allows for a precise representation of fixed and moving solid obstacles embedded in the physical domain, using uniform or stretched Cartesian meshes. Owing to this feature, the maximum level of accuracy and scalability of the numerical solvers can be systematically achieved. An iterative scheme based on sub-iterations between (IBM) and pressure correction has been implemented in the native (PISO) solver of OpenFOAM. This allows one to use fast optimized Poisson solvers while satisfying simultaneously the divergence-free flow state and the no-slip condition at the body surface. To compute the divergence of the momentum equation (in the PISO loop) and the interpolation of the fluxes, we propose an hybrid calculation with an analytical resolution (using the kernel function equation) of the quantities involving the force term (singular quantities). A careful and original verification study has been carried out which allows to estimate three different errors related to the discretization and to the (IBM). Various 2D and 3D well-documented test cases of academic flows around fixed or moving solid bodies (cylinder and sphere) have been simulated and carefully validated against existing data from the literature in a large range of Reynolds number},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Manas; Y Camenen; S Benkadda; H Weisen; C Angioni; F J Casson; C Giroud; M Gelfusa; M Maslov
Gyrokinetic modeling of impurity peaking in JET H-mode plasmas Article de journal
Dans: Physics Of Plasmas, vol. 24, no. 6, p. 12. 062511, 2017.
@article{Manas:230792,
title = {Gyrokinetic modeling of impurity peaking in JET H-mode plasmas},
author = {P Manas and Y Camenen and S Benkadda and H Weisen and C Angioni and F J Casson and C Giroud and M Gelfusa and M Maslov},
url = {https://aip.scitation.org/doi/abs/10.1063/1.4985330?journalCode=php},
year = {2017},
date = {2017-01-01},
journal = {Physics Of Plasmas},
volume = {24},
number = {6},
pages = {12. 062511},
publisher = {Amer Inst Physics},
address = {Melville},
abstract = {Quantitative comparisons are presented between gyrokinetic simulations and experimental values of the carbon impurity peaking factor in a database of JET H-modes during the carbon wall era. These plasmas feature strong NBI heating and hence high values of toroidal rotation and corresponding gradient. Furthermore, the carbon profiles present particularly interesting shapes for fusion devices, i.e., hollow in the core and peaked near the edge. Dependencies of the experimental carbon peaking factor (R/L-nC) on plasma parameters are investigated via multilinear regressions. A marked correlation between R/L-nC and the normalised toroidal rotation gradient is observed in the core, which suggests an important role of the rotation in establishing hollow carbon profiles. The carbon peaking factor is then computed with the gyrokinetic code GKW, using a quasi-linear approach, supported by a few non-linear simulations. The comparison of the quasi-linear predictions to the experimental values at mid-radius reveals two main regimes. At low normalised collisionality, nu*, and T-e/T-i < 1, the gyrokinetic simulations quantitatively recover experimental carbon density profiles, provided that rotodiffusion is taken into account. In contrast, at higher nu* and T-e/T-i > 1, the very hollow experimental carbon density profiles are never predicted by the simulations and the carbon density peaking is systematically over estimated. This points to a possible missing ingredient in this regime.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Migliano; D Zarzoso; F J Artola; Y Camenen; X Garbet
An improved approximation for the analytical treatment of the local linear gyro-kinetic plasma dispersion relation in toroidal geometry Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 59, no. 9, p. 095004, 2017.
@article{0741-3335-59-9-095004,
title = {An improved approximation for the analytical treatment of the local linear gyro-kinetic plasma dispersion relation in toroidal geometry},
author = {P Migliano and D Zarzoso and F J Artola and Y Camenen and X Garbet},
url = {http://stacks.iop.org/0741-3335/59/i=9/a=095004},
year = {2017},
date = {2017-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {59},
number = {9},
pages = {095004},
abstract = {The analytical treatment of plasma kinetic linear instabilities in toroidal geometry is commonly tackled employing a power series expansion of the resonant part of the dispersion relation. This expansion is valid under the assumption that the modulus of the mode frequency is smaller than the magnitude of the frequencies characterising the system (the drift, bounce and transit frequencies for example). We will refer to this approximation as high frequency approximation (HFA). In this paper the linear plasma dispersion relation is derived in the framework of the gyro-kinetic model, for the electrostatic case, in the local limit, in the absence of collisions, for a non rotating plasma, considering adiabatic electrons, in toroidal circular geometry, neglecting the parallel dynamics effect. A systematic analysis of the meaning and limitations of the HFA is performed. As already known, the HFA is not valid for tokamak relevant parameters. A new way to approximate the resonant part of the dispersion relation, called here Improved high frequency approximation (IHFA), is therefore proposed. A quantitative analysis of the ion temperature gradient (ITG) instability is presented. The IHFA is shown to be applicable to the treatment of the ITG instability in tokamaks.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M Muraglia; O Agullo; A Poyé; S Benkadda; N Dubuit; X Garbet; A Sen
Amplification of a turbulence driven seed magnetic island by bootstrap current Article de journal
Dans: Nuclear Fusion, vol. 57, no. 7, p. 072010, 2017.
@article{0029-5515-57-7-072010,
title = {Amplification of a turbulence driven seed magnetic island by bootstrap current},
author = {M Muraglia and O Agullo and A Poyé and S Benkadda and N Dubuit and X Garbet and A Sen},
url = {http://stacks.iop.org/0029-5515/57/i=7/a=072010},
year = {2017},
date = {2017-01-01},
journal = {Nuclear Fusion},
volume = {57},
number = {7},
pages = {072010},
abstract = {The amplification of a turbulence driven seed magnetic island by the bootstrap current is investigated numerically in a reduced magnetohydrodynamic model as a possible additional channel for the excitation and development of a neoclassical tearing mode (NTM) in a tokamak. The novel mechanism for such an excitation involves a two-step process, namely, the formation of a seed island due to a nonlinear beating of interchange turbulence modes followed by an amplification of the seed island by the bootstrap current leading to a large saturated island. Our study indicates that the level of turbulence controls both the critical seed island size and the saturated island size.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O Agullo; M Muraglia; S Benkadda; A Poyé; N Dubuit; X Garbet; A Sen
Nonlinear dynamics of turbulence driven magnetic islands. II. Numerical simulations Article de journal
Dans: Physics of Plasmas, vol. 24, no. 4, p. 042309, 2017.
@article{doi:10.1063/1.4981230,
title = {Nonlinear dynamics of turbulence driven magnetic islands. II. Numerical simulations},
author = {O Agullo and M Muraglia and S Benkadda and A Poyé and N Dubuit and X Garbet and A Sen},
url = {https://doi.org/10.1063/1.4981230},
doi = {10.1063/1.4981230},
year = {2017},
date = {2017-01-01},
journal = {Physics of Plasmas},
volume = {24},
number = {4},
pages = {042309},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O Agullo; M Muraglia; S Benkadda; A Poyé; N Dubuit; X Garbet; A Sen
Nonlinear dynamics of turbulence driven magnetic islands. I. Theoretical aspects Article de journal
Dans: Physics of Plasmas, vol. 24, no. 4, p. 042308, 2017.
@article{doi:10.1063/1.4981229,
title = {Nonlinear dynamics of turbulence driven magnetic islands. I. Theoretical aspects},
author = {O Agullo and M Muraglia and S Benkadda and A Poyé and N Dubuit and X Garbet and A Sen},
url = {https://doi.org/10.1063/1.4981229},
doi = {10.1063/1.4981229},
year = {2017},
date = {2017-01-01},
journal = {Physics of Plasmas},
volume = {24},
number = {4},
pages = {042308},
abstract = {The nonlinear dynamics of a turbulence driven magnetic island (TDMI) is investigated numerically in a reduced magnetohydrodynamic fluid model. The significance of identifying a characteristic signature of a TDMI for its experimental observation is discussed. The principal focus of our simulations is on the nature of the pressure profile flattening inside a TDMI, and we show that, in agreement with analytical predictions, a partial flattening occurs when the island size exceeds a critical value that is a function of the small scale interchange dynamics. We also present a model and test it numerically, which links explicitly the interchange turbulence and the island pressure flattening.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Michael Stenrup; Elisa Pieri; Vincent Ledentu; Nicolas Ferre
pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 19, p. 14073-14084, 2017.
@article{C7CP00991G,
title = {pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin},
author = {Michael Stenrup and Elisa Pieri and Vincent Ledentu and Nicolas Ferre},
url = {http://dx.doi.org/10.1039/C7CP00991G},
doi = {10.1039/C7CP00991G},
year = {2017},
date = {2017-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {19},
pages = {14073-14084},
publisher = {The Royal Society of Chemistry},
abstract = {A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH. It relies on the existence of a protein structure, the prediction of titratable amino-acid pKa values and a very limited set of parameters. Applied to the case of the photochromic Anabaena sensory rhodopsin protein, the model succeeds in reproducing qualitatively the reported experimental data, confirming the importance of aspartic acid 217 in the observed blue shift in the [small lambda]max of ASR at neutral pH. It also suggests for the first time the role of two other amino acids, glutamic acid 36 at basic pH and aspartic acid 120 at acidic pH.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A M Grannan; B Favier; M Le Bars; J M Aurnou
Tidally forced turbulence in planetary interiors Article de journal
Dans: Geophysical Journal International, vol. 208, no. 3, p. 1690-1703, 2017.
@article{doi:10.1093/gji/ggw479,
title = {Tidally forced turbulence in planetary interiors},
author = {A M Grannan and B Favier and M Le Bars and J M Aurnou},
doi = {10.1093/gji/ggw479},
year = {2017},
date = {2017-01-01},
journal = {Geophysical Journal International},
volume = {208},
number = {3},
pages = {1690-1703},
abstract = {The turbulence generated in the liquid metal cores and subsurface oceans of planetary bodies may be due to the role of mechanical forcing through precession/nutation, libration, tidal forcing and collisions. Here, we model the response of an enclosed constant density fluid to tidal forcing by combining laboratory equatorial velocity measurements with selected high-resolution numerical simulations to show, for the first time, the generation of bulk filling turbulence. The transition to saturated turbulence is characterized by an elliptical instability that first excites primary inertial modes of the system, then secondary inertial modes forced by the primary inertial modes, and then bulk filling turbulence. The amplitude of this saturated turbulence scales with the body's elliptical distortion, U ∼ β, while a time- and radially averaged azimuthal zonal flow scales with β2. The results of the current tidal experiments are compared with recent studies of the libration-driven turbulent flows studied by Grannan et al. and Favier et al. Tides and libration correspond to two end-member types of geophysical mechanical forcings. For satellites dominated by tidal forcing, the ellipsoidal boundary enclosing the internal fluid layers is elastically deformed while, for librational forcing, the core-mantle boundary possesses an inherently rigid, frozen-in ellipsoidal shape. We find striking similarities between tidally and librationally driven flow transitions to bulk turbulence and zonal flows. This suggests a generic fluid response independent of the style of mechanical forcing. Since β ≲ 10−4 in planetary bodies, it is often argued that mechanically driven zonal velocities will be small. In contrast, our linear scaling for mechanically driven bulk turbulence, U ∼ β, suggests geophysically significant velocities that can play a significant role in planetary processes including tidal dissipation and magnetic field generation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Simon Cabanes; Jonathan M Aurnou; Benjamin Favier; Michael Le Bars
A laboratory model for deep-seated jets on the gas giants Article de journal
Dans: Nature Physics, 2017.
@article{cabanes:hal-01478957,
title = {A laboratory model for deep-seated jets on the gas giants},
author = {Simon Cabanes and Jonathan M Aurnou and Benjamin Favier and Michael Le Bars},
url = {https://hal.archives-ouvertes.fr/hal-01478957},
doi = {10.1038/nphys4001},
year = {2017},
date = {2017-01-01},
journal = {Nature Physics},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O Février; P Maget; H Lütjens; P Beyer
Comparison of magnetic island stabilization strategies from magneto-hydrodynamic simulations Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 59, no. 4, p. 044002, 2017.
@article{0741-3335-59-4-044002,
title = {Comparison of magnetic island stabilization strategies from magneto-hydrodynamic simulations},
author = {O Février and P Maget and H Lütjens and P Beyer},
url = {http://stacks.iop.org/0741-3335/59/i=4/a=044002},
year = {2017},
date = {2017-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {59},
number = {4},
pages = {044002},
abstract = {The degradation of plasma confinement in tokamaks caused by magnetic islands motivates to better understand their possible suppression using electron cyclotron current drive (ECCD) and to investigate the various strategies relevant for this purpose. In this work, we evaluate the efficiency of several control methods through nonlinear simulations of this process with the toroidal magneto-hydro-dynamic (MHD) code XTOR-2F (Lütjens and Luciani 2010 J. Comput. Phys. 229 [http://https://doi.org/10.1016/j.jcp.2010.07.013] 8130–43 ), which has been extended to incorporate in Ohm’s law a source term modeling the driven current resulting from the interaction of the EC waves with the plasma. A basic control system has been implemented in the code, allowing testing of advanced strategies that require feedback on island position or phase. We focus in particular on the robustness of the control strategies towards uncertainties that apply to the control and ECCD systems, such as the risk of misalignment of the current deposition or the possible inability to generate narrow current deposition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O A. Bessonov
Analysis of mixed convection in the Czochralski model in a wide range of Prandtl numbers Article de journal
Dans: Fluid Dynamics, vol. 52, p. 375-387, 2017.
@article{articleb,
title = {Analysis of mixed convection in the Czochralski model in a wide range of Prandtl numbers},
author = {O A. Bessonov},
url = {https://www.researchgate.net/publication/317912710_Analysis_of_mixed_convection_in_the_Czochralski_model_in_a_wide_range_of_Prandtl_numbers},
doi = {10.1134/S001546281703005X},
year = {2017},
date = {2017-01-01},
booktitle = {Fluid Dynamics},
journal = {Fluid Dynamics},
volume = {52},
pages = {375-387},
abstract = {The results of the calculations and analysis of the effect of separate and joint rotation of the crystal and the crucible on the flow stability are presented for a wide range of Prandtl numbers (from 0.01 to 10). The regimes with a high stability threshold are determined for different combinations of the rotation velocities. It is shown that for high Prandtl numbers, simultaneous rotation of the crystal and the crucible makes it possible to increase the critical Grashof number in 9–12 times. A resultant diagram (map) of the limiting regimes of natural and mixed convection is constructed. Themethodology of control and analysis of 2D and 3D instability modes is discussed.
Analysis of mixed convection in the Czochralski model in a.... Available from: https://www.researchgate.net/publication/317912710_Analysis_of_mixed_convection_in_the_Czochralski_model_in_a_wide_range_of_Prandtl_numbers [accessed Apr 03 2018].},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Analysis of mixed convection in the Czochralski model in a.... Available from: https://www.researchgate.net/publication/317912710_Analysis_of_mixed_convection_in_the_Czochralski_model_in_a_wide_range_of_Prandtl_numbers [accessed Apr 03 2018].
Oleg Bessonov
Technological Aspects of the Hybrid Parallelization with OpenMP and MPI Proceedings Article
Dans: Malyshkin, Victor (Ed.): Parallel Computing Technologies, p. 101–113, Springer International Publishing, Cham, 2017, ISBN: 978-3-319-62932-2.
@inproceedings{10.1007/978-3-319-62932-2_9,
title = {Technological Aspects of the Hybrid Parallelization with OpenMP and MPI},
author = {Oleg Bessonov},
editor = {Victor Malyshkin},
doi = {10.1007/978-3-319-62932-2_9},
isbn = {978-3-319-62932-2},
year = {2017},
date = {2017-01-01},
booktitle = {Parallel Computing Technologies},
pages = {101--113},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {In this paper we present practical parallelization techniques for different explicit and implicit numerical algorithms. These algorithms are considered on the base of the analysis of characteristics of modern computer systems and the nature of modeled physical processes. Limits of applicability of methods and parallelization techniques are determined in terms of practical implementation. Finally, the unified parallelization approach for OpenMP and MPI for solving a CFD problem in a regular domain is presented and discussed.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Patrick Maget; Fabien Widmer; Olivier Février; Xavier Garbet; Hinrich Lütjens
Stabilization of a magnetic island by localized heating in a tokamak with stiff temperature profile Non publié
2017, (working paper or preprint).
@unpublished{maget:hal-01614656,
title = {Stabilization of a magnetic island by localized heating in a tokamak with stiff temperature profile},
author = {Patrick Maget and Fabien Widmer and Olivier Février and Xavier Garbet and Hinrich Lütjens},
url = {https://hal.archives-ouvertes.fr/hal-01614656},
year = {2017},
date = {2017-01-01},
abstract = {In tokamaks plasmas, turbulent transport is triggered above a threshold in the temperature gradient and leads to stiff profiles. This particularity, neglected so far in the problem of magnetic island stabilization by a localized heat source, is investigated analytically in the present paper. We show that the efficiency of the stabilization is larger than previously estimated due to the reduced turbulence level inside the island. },
note = {working paper or preprint},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
Benjamin Kadoch; Wouter Bos; Kai Schneider
Directional change of fluid particles in two-dimensional turbulence and of football players Article de journal
Dans: Physical Review Fluids, vol. 2, no. 6, p. 064604, 2017.
@article{kadoch:hal-01705321,
title = {Directional change of fluid particles in two-dimensional turbulence and of football players},
author = {Benjamin Kadoch and Wouter Bos and Kai Schneider},
url = {https://hal.archives-ouvertes.fr/hal-01705321},
doi = {10.1103/PhysRevFluids.2.064604},
year = {2017},
date = {2017-01-01},
journal = {Physical Review Fluids},
volume = {2},
number = {6},
pages = {064604},
publisher = {American Physical Society},
abstract = {Multiscale directional statistics are investigated in two-dimensional incompressible turbulence. It is shown that the short-time behavior of the mean angle of directional change of fluid particles is linearly dependent on the time lag and that no inertial range behavior is observed in the directional change associated with the enstrophy-cascade range. In simulations of the inverse-cascade range, the directional change shows a power law behavior at inertial range time scales. By comparing the directional change in space-periodic and wall-bounded flow, it is shown that the probability density function of the directional change at long times carries the signature of the confinement. The geometrical origin of this effect is validated by Monte Carlo simulations. The same effect is also observed in the directional statistics computed from the trajectories of football players (soccer players in American English).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
D Galassi; P Tamain; C Baudoin; H Bufferand; G Ciraolo; N Fedorczak; Ph. Ghendrih; N Nace; E Serre
Flux expansion effect on turbulent transport in 3D global simulations Article de journal
Dans: Nuclear Materials and Energy, vol. 12, p. 953 - 958, 2017, ISSN: 2352-1791, (Proceedings of the 22nd International Conference on Plasma Surface Interactions 2016, 22nd PSI).
@article{GALASSI2017953,
title = {Flux expansion effect on turbulent transport in 3D global simulations},
author = {D Galassi and P Tamain and C Baudoin and H Bufferand and G Ciraolo and N Fedorczak and Ph. Ghendrih and N Nace and E Serre},
url = {http://www.sciencedirect.com/science/article/pii/S2352179116302216},
doi = {https://doi.org/10.1016/j.nme.2017.01.008},
issn = {2352-1791},
year = {2017},
date = {2017-01-01},
journal = {Nuclear Materials and Energy},
volume = {12},
pages = {953 - 958},
abstract = {The flux expansion effect on the Scrape-Off Layer equilibrium is inspected through TOKAM3X 3D turbulence simulations. Three magnetic equilibria with analytically controlled flux expansion are built, representing respectively a positive, a null and a negative Shafranov shift. Turbulent E × B fluxes across flux surfaces show similar amplitudes and poloidal distributions in all cases. The ballooning nature of the interchange instability is recovered, with an enhancement of turbulence in the vicinity of the limiter, probably due to a Kelvin–Helmoltz instability. Interestingly, the poloidally averaged density decay length is found to be shorter almost by a factor 2 in the case of flux surfaces compressed at the low-field side midplane, with respect to the opposite case, indicating the presence of unfavorable conditions for the turbulent transport. The difference in the magnetic field line shape is pointed out as a mechanism which affects the turbulent transport across the flux surfaces. Indeed the unstable region has a larger parallel extension when flux expansion in the low-field side is larger. Moreover, the configuration with a lower magnetic shear at the low-field side midplane shows a more unstable behavior. The role of this parameter in turbulence stabilization is qualitatively evaluated. The difference in the distribution of transport along the parallel direction is shown to affect also the parallel flows, which are analyzed for the three proposed cases.},
note = {Proceedings of the 22nd International Conference on Plasma Surface Interactions 2016, 22nd PSI},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Umberto D'Ortona; Nathalie Thomas; Richard M Lueptow
Axial segregation in spherical and cylindrical rotating tumblers Article de journal
Dans: EPJ Web of Conferences, vol. 140, p. 03011, 2017.
@article{dortona:hal-01671207,
title = {Axial segregation in spherical and cylindrical rotating tumblers},
author = {Umberto D'Ortona and Nathalie Thomas and Richard M Lueptow},
url = {https://hal.archives-ouvertes.fr/hal-01671207},
doi = {10.1051/epjconf/201714003011},
year = {2017},
date = {2017-01-01},
journal = {EPJ Web of Conferences},
volume = {140},
pages = {03011},
publisher = {EDP Sciences},
series = {Powders and Grains 2017 -- 8th International Conference on Micromechanics on Granular Media},
abstract = {Monodisperse and bidisperse granular flows are studied in rotating tumblers using DEM. In spherical tumblers, flowing particles’ trajectories do not follow straight lines but are curved. At the same time particles near the surface drift toward the pole, inducing two global recirculation cells. Combined with radial segregation, drift and curvature compete to impose the axial segregation pattern: Small-Large-Small (SLS) or Large-Small-Large (LSL). Fill level, rotation speed and wall roughness influence drift and curvature, and modify the resulting segregation pattern. In cylindrical tumblers, equivalent recirculation cells occur next to the end walls. A second pair of recirculation cells with a weak drift in the opposite direction appears at the center for long enough tumblers. Unlike the sphere case, curvature and drift in the primary cells combine to push large particles toward the end walls, explaining why large particle bands appear at the end walls for axial segregation in cylinder.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ljiljana Stojanović; Saadullah G Aziz; Rifaat H Hilal; Felix Plasser; Thomas A Niehaus; Mario Barbatti
Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 13, no. 12, p. 5846-5860, 2017, (PMID: 29140693).
@article{doi:10.1021/acs.jctc.7b01000,
title = {Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping},
author = {Ljiljana Stojanović and Saadullah G Aziz and Rifaat H Hilal and Felix Plasser and Thomas A Niehaus and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jctc.7b01000},
doi = {10.1021/acs.jctc.7b01000},
year = {2017},
date = {2017-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
number = {12},
pages = {5846-5860},
abstract = {We implemented a version of the decoherence-corrected fewest switches surface hopping based on linear-response time-dependent density functional tight binding (TD-DFTB), enhanced by transition density analysis. The method has been tested for the gas-phase relaxation dynamics of two cycloparaphenylene molecules, [8]CPP and [10]CPP, explaining some important features of their nonadiabatic dynamics, such as the origin of their long fluorescence lifetimes (related to the slow radiative emission from the S1 state) and the trend of increasing the fluorescence rate with the molecular size (related to an increase in the S1–S0 energy gaps and oscillator strengths in the larger molecule). The quality of the TD-DFTB electronic structure information was assessed through four quantities: excitation energies; charge-transfer (CT) numbers, which estimate the charge transfer character of states; participation ratio (PR), which describes delocalization of electronic density; and participation ratio of natural transition orbitals (PRNTO), which describes the multiconfigurational character of states. These quantities were computed during dynamics and recomputed for the same geometries with the higher-level long-range-corrected TD-LC-DFTB and a lower-level single-determinant approximation for the excited states, SD-(LC)-DFTB. Taking TD-LC-DFTB as the standard, TD-DFTB underestimates the excitation energies by ∼0.5 eV and overestimates CT and PR. SD-DFTB underestimates excitation energies and overestimates CT to the same extent that TD-DFTB does, but it predicts reasonable PR distributions. SD-LC-DFTB leads to an extreme overestimation of the excitation energies by ∼3 eV, overestimates the charge transfer character of the state, but predicts the PR values very close to those obtained with TD-LC-DFTB.},
note = {PMID: 29140693},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
Spatial Factors for Triplet Fusion Reaction of Singlet Oxygen Photosensitization Article de journal
Dans: The Journal of Physical Chemistry Letters, vol. 8, no. 21, p. 5456-5460, 2017, (PMID: 29058918).
@article{doi:10.1021/acs.jpclett.7b02574,
title = {Spatial Factors for Triplet Fusion Reaction of Singlet Oxygen Photosensitization},
author = {Shuming Bai and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jpclett.7b02574},
doi = {10.1021/acs.jpclett.7b02574},
year = {2017},
date = {2017-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {8},
number = {21},
pages = {5456-5460},
abstract = {First-principles quantum-chemical description of photosensitized singlet oxygen generation kinetics is challenging because of the intrinsic complexity of the underlying triplet fusion process in a floppy molecular complex with open-shell character. With a quantum-chemical kinetic model specifically tailored to deal with this problem, the reaction rates are investigated as a function of intermolecular incidence direction, orientation, and distance between O2 and the photosensitizer. The adopted photosensitizer, 6-azo-2-thiothymine, combines practical interest and prototypical variability. The study quantitatively determined maximum singlet oxygen generation rates for 15 incidence/orientation directions, showing that they span 5 orders of magnitude between the largest and the smallest rate. Such information may provide a hands-on guideline for the experimental molecular design of new photosensitizers as well as further higher-level theoretical research.},
note = {PMID: 29058918},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
Divide-to-Conquer: A Kinetic Model for Singlet Oxygen Photosensitization Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 13, no. 11, p. 5528-5538, 2017, (PMID: 28953379).
@article{doi:10.1021/acs.jctc.7b00619,
title = {Divide-to-Conquer: A Kinetic Model for Singlet Oxygen Photosensitization},
author = {Shuming Bai and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jctc.7b00619},
doi = {10.1021/acs.jctc.7b00619},
year = {2017},
date = {2017-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
number = {11},
pages = {5528-5538},
abstract = {Photosensitized singlet oxygen generation occurring in a PS–O2 complex, where PS is a photosensitizer chromophore, is a weakly coupled intermolecular energy-transfer process, a still challenging problem for theoretical chemistry. To investigate the reaction rate directly from quantum-chemical calculations, we built a semiclassical kinetic model that minimizes the computational effort for the calculation of diabatic couplings, activation energies, and reorganization energies, which are the components of the rate. The model splits the system into sets of orthogonal coordinates, which are then explored to compute the reaction rate. This model offers an effective way to evaluate the reaction probability of singlet oxygen generation along different directions and intramolecular distances of the PS–O2 complex. The model can also be applied to other similar intermolecular energy-transfer problems, to connect the reaction kinetics and quantum-chemical calculations.},
note = {PMID: 28953379},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Daniele Fazzi; Mario Barbatti; Walter Thiel
Hot and Cold Charge-Transfer Mechanisms in Organic Photovoltaics: Insights into the Excited States of Donor/Acceptor Interfaces Article de journal
Dans: The Journal of Physical Chemistry Letters, vol. 8, no. 19, p. 4727-4734, 2017, (PMID: 28903560).
@article{doi:10.1021/acs.jpclett.7b02144,
title = {Hot and Cold Charge-Transfer Mechanisms in Organic Photovoltaics: Insights into the Excited States of Donor/Acceptor Interfaces},
author = {Daniele Fazzi and Mario Barbatti and Walter Thiel},
url = {https://doi.org/10.1021/acs.jpclett.7b02144},
doi = {10.1021/acs.jpclett.7b02144},
year = {2017},
date = {2017-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {8},
number = {19},
pages = {4727-4734},
abstract = {The evolution of the excited-state manifold in organic D/A aggregates (e.g., the prototypical P3HT/PCBM) is investigated through a bottom-up approach via first-principles calculations. We show how the excited-state energies, the charge transfer (CT) states, and the electron–hole density distributions are strongly influenced by the size, the orientation, and the position (i.e., on-top versus on-edge phases) of P3HT/PCBM domains. We discuss how the structural order influences the excited-state electronic structure, providing an atomistic interpretation of the photophysics of organic blends. We show how the simultaneous presence of on-top and on-edge phases does not alter the optical absorption spectrum of the blend but does affect the photophysics. Photovoltaic processes such as (i) the simultaneous charge generation obtained from hot and cold excitations, (ii) the instantaneous and delayed charge separation, and (iii) the pump–push–probe charge generation can be interpreted based on our study.},
note = {PMID: 28903560},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Josene M Toldo; Mario Barbatti; Paulo F B Goncalves
A three-state model for the photo-Fries rearrangement Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 19, p. 19103-19108, 2017.
@article{C7CP03777E,
title = {A three-state model for the photo-Fries rearrangement},
author = {Josene M Toldo and Mario Barbatti and Paulo F B Goncalves},
url = {http://dx.doi.org/10.1039/C7CP03777E},
doi = {10.1039/C7CP03777E},
year = {2017},
date = {2017-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {19},
pages = {19103-19108},
publisher = {The Royal Society of Chemistry},
abstract = {A three-state model for the photo-Fries rearrangement (PFR) is proposed based on multiconfigurational calculations. It provides a comprehensive mechanistic picture of all steps of the reaction, from the photoabsorption to the final tautomerization. The three states participating in the PFR are an aromatic 1[small pi][small pi]*, which absorbs the radiation; a pre-dissociative 1n[small pi]*, which transfers the energy to the dissociative region; and a 1[small pi][sigma]*, along which dissociation occurs. The transfer from 1[small pi][small pi]* to 1n[small pi]* involves pyramidalization of the carbonyl carbon, while transfer from 1n[small pi]* to 1[small pi][sigma]* takes place through CO stretching. Different products are available after a conical intersection with the ground state. Among them is a recombined radical intermediate, which can yield ortho-PFR products after an intramolecular 1,3-H tunneling. The three-state model is developed for phenyl acetate, the basic prototype for the PFR, and it reconciles the theory with a series of observations from time-resolved spectroscopy. It also delivers a rational way to optimize PFR yields, since, as shown for four different systems, diverse substituents can change the energetic order of the 1[small pi][small pi]* and 1n[small pi]* states, preventing or enhancing the PFR.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Claudia Climent; Mario Barbatti; Michael O Wolf; Christopher J Bardeen; David Casanova
The photophysics of naphthalene dimers controlled by sulfur bridge oxidation Article de journal
Dans: Chem. Sci., vol. 8, p. 4941-4950, 2017.
@article{C7SC01285C,
title = {The photophysics of naphthalene dimers controlled by sulfur bridge oxidation},
author = {Claudia Climent and Mario Barbatti and Michael O Wolf and Christopher J Bardeen and David Casanova},
url = {http://dx.doi.org/10.1039/C7SC01285C},
doi = {10.1039/C7SC01285C},
year = {2017},
date = {2017-01-01},
journal = {Chem. Sci.},
volume = {8},
pages = {4941-4950},
publisher = {The Royal Society of Chemistry},
abstract = {In this study we investigate in detail the photophysics of naphthalene dimers covalently linked by a sulfur atom. We explore and rationalize how the oxidation state of the sulfur-bridging atom directly influences the photoluminescence of the dimer by enhancing or depriving its radiative and non-radiative relaxation pathways. In particular, we discuss how oxidation controls the amount of electronic transfer between the naphthalene moieties and the participation of the SOn bridge in the low-lying electronic transitions. We identify the sulfur electron lone-pairs as crucial actors in the non-radiative decay of the excited sulfide and sulfoxide dimers, which are predicted to proceed via a conical intersection (CI). Concretely, two types of CI have been identified for these dimers, which are associated with the photo-induced pyramidal inversion and reverse fragmentation mechanisms found in aryl sulfoxide dimers. The obtained results and conclusions are general enough to be extrapolated to other sulfur-bridged conjugated dimers, therefore proportionating novel strategies in the design of strongly photoluminescent organic molecules with controlled charge transfer.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
On the decay of the triplet state of thionucleobases Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 19, p. 12674-12682, 2017.
@article{C7CP02050C,
title = {On the decay of the triplet state of thionucleobases},
author = {Shuming Bai and Mario Barbatti},
url = {http://dx.doi.org/10.1039/C7CP02050C},
doi = {10.1039/C7CP02050C},
year = {2017},
date = {2017-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {19},
pages = {12674-12682},
publisher = {The Royal Society of Chemistry},
abstract = {Singlet oxygen production upon photosensitization plays a critical role in drugs based on thionucleobases. While for immunosuppressants its yield must be near zero, for phototherapeutic drugs it should be near the unity. In this work, we apply high-level quantum chemical modelling to investigate the decay of the triplet state of thionucleobases, a main determinant of the singlet oxygen yield. Working on CASPT2 optimizations of two prototypical thiothymines (2-thiothymine and 6-aza-2-thiothymine), we showed that the T1 state is characterized by two [small pi][small pi]* minima and by the intersection of T1 with the singlet ground state. On the basis of this topography, we propose a two-step mechanistic model, which, depending on the energetic balance between the two minima, may have as a determining step either a slow transition between minima or a faster intersystem crossing to S0. Chemical kinetics modelling, as well as simulations of the transient absorption spectra, confirmed that the two-step model can explain the experimental results available for both molecules. Moreover, through additional investigations of 2-thiocytosine and 6-thioguanine, we show that such a T1 topography is a common theme for nucleobases. We also discuss how the triplet-state topography may be used to control the singlet oxygen yield, aiming at different medical applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Joanna Jankowska; Mario Barbatti; Joanna Sadlej; Andrzej L Sobolewski
Tailoring the Schiff base photoswitching - a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer Article de journal
Dans: Phys. Chem. Chem. Phys., vol. 19, p. 5318-5325, 2017.
@article{C6CP08545H,
title = {Tailoring the Schiff base photoswitching - a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer},
author = {Joanna Jankowska and Mario Barbatti and Joanna Sadlej and Andrzej L Sobolewski},
url = {http://dx.doi.org/10.1039/C6CP08545H},
doi = {10.1039/C6CP08545H},
year = {2017},
date = {2017-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {19},
pages = {5318-5325},
publisher = {The Royal Society of Chemistry},
abstract = {Small molecular systems exhibiting Excited State Intramolecular Proton Transfer (ESIPT) attract considerable attention due to their possible role as ultrafast, efficient, and photostable molecular photoswitches. Here, by means of static potential energy profile scan and on-the-fly non-adiabatic dynamics simulations we study the photodeactivation process of a minimal-chromophore aromatic Schiff base, salicylidene methylamine (SMA), and its two derivatives 6-cyano-salicylidene methylamine (6-CN-SMA) and 3-hydroxy-salicylidene methylamine (3-OH-SMA). We show that the dominant character of the lowest excited singlet state - [small pi][small pi]* vs. n[small pi]* - plays a crucial role in the system's photophysics and controls the ESIPT efficiency. We also show that the relative alignment of the [small pi][small pi]* and n[small pi]* states may be controlled through chemical substitutions made to the aromatic ring of the Schiff-base molecule. We believe that our findings will improve the rational-design strategies employed for the ESIPT systems, especially in the context of their possible photoswitching.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2016
S. A. Rodionov, E. Athanassoula; N. Peschken
Forming disk galaxies in major mergers II. Article de journal
Dans: A&A , vol. 600, 2016.
@article{Rodionov2016,
title = {Forming disk galaxies in major mergers II. },
author = {S. A. Rodionov, E. Athanassoula and N. Peschken},
url = {https://www.aanda.org/articles/aa/abs/2017/04/aa28319-16/aa28319-16.html},
doi = {10.1051/0004-6361/201628319 },
year = {2016},
date = {2016-12-28},
journal = {A&A },
volume = {600},
abstract = {Context. In a series of papers, we study the major merger of two disk galaxies in order to establish whether or not such a merger can produce a disk galaxy.
Aims. Our aim here is to describe in detail the technical aspects of our numerical experiments.
Methods. We discuss the initial conditions of our major merger, which consist of two protogalaxies on a collision orbit. We show that such merger simulations can produce a non-realistic central mass concentration, and we propose simple, parametric, active galactic nuclei (AGN)-like feedback as a solution to this problem. Our AGN-like feedback algorithm is very simple: at each time-step we take all particles whose local volume density is above a given threshold value and increase their temperature to a preset value. We also compare the GADGET3 and GIZMO codes, by applying both of them to the same initial conditions.
Results. We show that the evolution of isolated protogalaxies resembles the evolution of disk galaxies, thus arguing that our protogalaxies are well suited for our merger simulations. We demonstrate that the problem with the unphysical central mass concentration in our merger simulations is further aggravated when we increase the resolution. We show that our AGN-like feedback removes this non-physical central mass concentration, and thus allows the formation of realistic bars. Note that our AGN-like feedback mainly affects the central region of a model, without significantly modifying the rest of the galaxy. We demonstrate that, in the context of our kind of simulation, GADGET3 gives results which are very similar to those obtained with the PSPH (density independent SPH) flavor of GIZMO. Moreover, in the examples we tried, the differences between the results of the two flavors of GIZMO – namely PSPH, and MFM (mesh-less algorithm) – are similar to and, in some comparisons, larger than the differences between the results of GADGET3 and PSPH. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Aims. Our aim here is to describe in detail the technical aspects of our numerical experiments.
Methods. We discuss the initial conditions of our major merger, which consist of two protogalaxies on a collision orbit. We show that such merger simulations can produce a non-realistic central mass concentration, and we propose simple, parametric, active galactic nuclei (AGN)-like feedback as a solution to this problem. Our AGN-like feedback algorithm is very simple: at each time-step we take all particles whose local volume density is above a given threshold value and increase their temperature to a preset value. We also compare the GADGET3 and GIZMO codes, by applying both of them to the same initial conditions.
Results. We show that the evolution of isolated protogalaxies resembles the evolution of disk galaxies, thus arguing that our protogalaxies are well suited for our merger simulations. We demonstrate that the problem with the unphysical central mass concentration in our merger simulations is further aggravated when we increase the resolution. We show that our AGN-like feedback removes this non-physical central mass concentration, and thus allows the formation of realistic bars. Note that our AGN-like feedback mainly affects the central region of a model, without significantly modifying the rest of the galaxy. We demonstrate that, in the context of our kind of simulation, GADGET3 gives results which are very similar to those obtained with the PSPH (density independent SPH) flavor of GIZMO. Moreover, in the examples we tried, the differences between the results of the two flavors of GIZMO – namely PSPH, and MFM (mesh-less algorithm) – are similar to and, in some comparisons, larger than the differences between the results of GADGET3 and PSPH.
Meradji S., Accary G., Morvan D., Bessonov O., Fougére D.
Numerical Simulation of Grassland-Fires Behavior Using Firestar 3D Model Article de journal
Dans: In Proceedings Topical Problems of Fluid Mechanics , p. 129-140, 2016, ISBN: 978-80-87012-58-1.
@article{S.2016,
title = {Numerical Simulation of Grassland-Fires Behavior Using Firestar 3D Model },
author = {Meradji S., Accary G., Morvan D., Bessonov O., Fougére D.},
url = {http://dx.doi.org/10.14311/TPFM.2016.018 },
isbn = {978-80-87012-58-1},
year = {2016},
date = {2016-12-01},
journal = {In Proceedings Topical Problems of Fluid Mechanics },
pages = {129-140},
abstract = {This study reports 3D numerical simulations of the ignition and the propagation of grassland fires. The mathematical model consists in solving the conservation equations governing the behavior of the coupled system formed by the vegetation and the ambient atmosphere. Based on a finite volume discretization, the computation code is parallelized using OpenMP directives and had been the subject of numerous validations. The model was previously tested on small scale in case of homogeneous litter fires; in this study it is proposed to test it on larger scale in case of grassland fires. The results are in fairly good agreement with experimental data, with predictions of operational empirical-models developed in Australia (MK5) and in the USA (BEHAVE), as well as with and predictions of physical models (FIRETEC, WFDS, FireStar2D). The comparison with the literature is based on the estimation of the rate of fire spread (ROS) and the analysis of the fire-front shape.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jauzac, Eckert, et al.
The extraordinary amount of substructure in the Hubble Frontier Fields cluster Abell 2744 Article de journal
Dans: p. 3876-3893, 2016.
@article{Jauzac2016,
title = {The extraordinary amount of substructure in the Hubble Frontier Fields cluster Abell 2744 },
author = {Jauzac, Eckert, et al.},
url = { https://doi.org/10.1093/mnras/stw2251 },
year = {2016},
date = {2016-09-07},
pages = {3876-3893},
abstract = {We present a joint optical/X-ray analysis of the massive galaxy cluster Abell 2744 (z = 0.308). Our strong- and weak-lensing analysis within the central region of the cluster, i.e. at R < 1 Mpc from the brightest cluster galaxy, reveals eight substructures, including the main core. All of these dark matter haloes are detected with a significance of at least 5σ and feature masses ranging from 0.5 to 1.4 × 1014 M⊙ within R < 150 kpc. Merten et al. and Medezinski et al. substructures are also detected by us. We measure a slightly higher mass for the main core component than reported previously and attribute the discrepancy to the inclusion of our tightly constrained strong-lensing mass model built on Hubble Frontier Fields data. X-ray data obtained by XMM–Newton reveal four remnant cores, one of them a new detection, and three shocks. Unlike Merten et al., we find all cores to have both dark and luminous counterparts. A comparison with clusters of similar mass in the Millennium XXL simulations yields no objects with as many massive substructures as observed in Abell 2744, confirming that Abell 2744 is an extreme system. We stress that these properties still do not constitute a challenge to Λ cold dark matter, as caveats apply to both the simulation and the observations: for instance, the projected mass measurements from gravitational lensing and the limited resolution of the subhaloes finders. We discuss implications of Abell 2744 for the plausibility of different dark matter candidates and, finally, measure a new upper limit on the self-interaction cross-section of dark matter of σDM < 1.28 cm2 g−1 (68 per cent CL), in good agreement with previous results from Harvey et al.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
B. Kadoch, T. Reimann, K. Schneider, & M. Schäfer
Comparison of a spectral method With volume penalization and a finite volume method with body fitted grids for turbulent flows Article de journal
Dans: Computers & Fluids, vol. 133, p. 140-150, 2016.
@article{Kadoch2016,
title = {Comparison of a spectral method With volume penalization and a finite volume method with body fitted grids for turbulent flows},
author = {B. Kadoch, T. Reimann, K. Schneider, & M. Schäfer},
doi = {10.1016/j.compfluid.2016.04.028},
year = {2016},
date = {2016-04-01},
journal = {Computers & Fluids},
volume = {133},
pages = {140-150},
abstract = {We consider a turbulent flow past periodic hills at Reynolds number 1400 and compare two numerical methods: A Fourier pseudo–spectral scheme with volume penalization to model the no-slip boundary conditions and a finite volume method with body fitted grids. A detailed comparison of the results is presented for mean velocity profiles and Reynolds stress and confronted with those obtained by Breuer et al., [1]. In addition higher order statistics are performed and their scale-dependence is analyzed using orthogonal wavelets. Moreover, for the Fourier pseudo-spectral scheme, the influence of the Reynolds number is investigated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pivano A.; Dolocan V. O.
Chaotic dynamics of magnetic domain walls in nanowires Article de journal
Dans: Phys. Rev. B, vol. 93, p. 144410, 2016.
@article{PhysRevB.93.144410,
title = {Chaotic dynamics of magnetic domain walls in nanowires},
author = {Pivano A. and Dolocan V. O.},
url = {http://link.aps.org/doi/10.1103/PhysRevB.93.144410},
doi = {10.1103/PhysRevB.93.144410},
year = {2016},
date = {2016-04-01},
journal = {Phys. Rev. B},
volume = {93},
pages = {144410},
publisher = {American Physical Society},
abstract = {The strong east–west jet flows on the gas giants, Jupiter1 and Saturn2, have persisted for hundreds of years. Yet, experimental studies cannot reach the planetary regime and similarly strong and quasi-steady jets have been reproduced in numerical models only under simplifying assumptions and limitations. Two models have been proposed: a shallow model where jets are confined to the weather layer and a deep model where the jets extend into the planetary molecular envelope. Here we show that turbulent laboratory flows naturally generate multiple, alternating jets in a rapidly rotating cylindrical container. The observed properties of gas giants’ jets are only now reproduced in a laboratory experiment emulating the deep model. Our findings demonstrate that long-lived jets can persist at high latitudes even under conditions including viscous dissipation and friction and bear relevance to the shallow versus deep models debate in the context of the ongoing Juno mission.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
J. Gounley; G. Boedec; M. Jaeger; M. Leonetti
Influence of surface viscosity on droplets in shear flow Article de journal
Dans: Journal of Fluid Mechanics, vol. 791, p. 464-494, 2016.
@article{gounley2016,
title = {Influence of surface viscosity on droplets in shear flow},
author = {J. Gounley and G. Boedec and M. Jaeger and M. Leonetti},
url = {https://www.cambridge.org/core/article/div-class-title-influence-of-surface-viscosity-on-droplets-in-shear-flow-div/F6179DAA0126660CA250EAEF7890D1F8},
doi = {10.1017/jfm.2016.39},
year = {2016},
date = {2016-03-02},
journal = {Journal of Fluid Mechanics},
volume = {791},
pages = {464-494},
publisher = {Cambridge University Press},
address = {Cambridge, UK},
abstract = {The behaviour of a single droplet in an immiscible external fluid, submitted to shear flow is investigated using numerical simulations. The surface of the droplet is modelled by a Boussinesq–Scriven constitutive law involving the interfacial viscosities and a constant surface tension. A numerical method using Loop subdivision surfaces to represent droplet interface is introduced. This method couples boundary element method for fluid flows and finite element method to take into account the stresses due to the surface dilational and shear viscosities and surface tension. Validation of the numerical scheme with respect to previous analytic and computational work is provided, with particular attention to the viscosity contrast and the shear and dilational viscosities characterized both by a Boussinesq number $B_q$. Then, influence of equal surface viscosities on steady-state characteristics of a droplet in shear flow are studied, considering both small and large deformations and for a large range of bulk viscosity contrast. We find that small deformation analysis is surprisingly predictive at moderate and high surface viscosities. Equal surface viscosities decrease the Taylor deformation parameter and tank-treading angle and also strongly modify the dynamics of the droplet: when the Boussinesq number (surface viscosity) is large relative to the capillary number (surface tension), the droplet displays damped oscillations prior to steady-state tank-treading, reminiscent from the behaviour at large viscosity contrast. In the limit of infinite capillary number $Ca$, such oscillations are permanent. The influence of surface viscosities on breakup is also investigated, and results show that the critical capillary number is increased. A diagram $(B_q;Ca)$ of breakup is established with the same inner and outer bulk viscosities. Additionally, the separate roles of shear and dilational surface viscosity are also elucidated, extending results from small deformation analysis. Indeed, shear (dilational) surface viscosity increases (decreases) the stability of drops to breakup under shear flow. The steady-state deformation (Taylor parameter) varies nonlinearly with each Boussinesq number or a linear combination of both Boussinesq numbers. Finally, the study shows that for certain combinations of shear and dilational viscosities, drop deformation for a given capillary number is the same as in the case of a clean surface while the inclination angle varies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Camenen, Y.; Casson, F. J.; Manas, P.; Peeters, A. G.
Interplay between toroidal rotation and flow shear in turbulence stabilisation Article de journal
Dans: Physics of Plasmas, vol. 23, no. 2, 2016.
@article{:/content/aip/journal/pop/23/2/10.1063/1.4942422,
title = {Interplay between toroidal rotation and flow shear in turbulence stabilisation},
author = {Camenen, Y. and Casson, F. J. and Manas, P. and Peeters, A. G.},
url = {http://scitation.aip.org/content/aip/journal/pop/23/2/10.1063/1.4942422},
doi = {http://dx.doi.org/10.1063/1.4942422},
year = {2016},
date = {2016-01-01},
journal = {Physics of Plasmas},
volume = {23},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F Riva; C Colin; J Denis; L Easy; I Furno; J Madsen; F Militello; V Naulin; A H Nielsen; J M B Olsen; J T Omotani; J J Rasmussen; P Ricci; E Serre; P Tamain; C Theiler
Blob dynamics in the TORPEX experiment: a multi-code validation Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 58, no. 4, p. 044005, 2016.
@article{0741-3335-58-4-044005,
title = {Blob dynamics in the TORPEX experiment: a multi-code validation},
author = {F Riva and C Colin and J Denis and L Easy and I Furno and J Madsen and F Militello and V Naulin and A H Nielsen and J M B Olsen and J T Omotani and J J Rasmussen and P Ricci and E Serre and P Tamain and C Theiler},
url = {http://stacks.iop.org/0741-3335/58/i=4/a=044005},
year = {2016},
date = {2016-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {58},
number = {4},
pages = {044005},
abstract = {Three-dimensional and two-dimensional seeded blob simulations are performed with five different fluid models, all based on the drift-reduced Braginskii equations, and the numerical results are compared among themselves and validated against experimental measurements provided by the TORPEX device (Fasoli et al 2006 Phys. Plasmas 13 055902). The five models are implemented in four simulation codes, typically used to simulate the plasma dynamics in the tokamak scrape-off layer, namely BOUT++ (Dudson et al 2009 Comput. Phys. Commun . 180 1467), GBS (Ricci et al 2012 Plasma Phys. Control. Fusion 54 124047), HESEL (Nielsen et al 2015 Phys. Lett . A 379 3097), and TOKAM3X (Tamain et al 2014 Contrib. Plasma Phys . 54 555). Three blobs with different velocities and different stability properties are simulated. The differences observed among the simulation results and the different levels of agreement with experimental measurements are investigated, increasing our confidence in our simulation tools and shedding light on the blob dynamics. The comparisons demonstrate that the radial blob dynamics observed in the three-dimensional simulations is in good agreement with experimental measurements and that, in the present experimental scenario, the two-dimensional model derived under the assumption of ##IMG## [http://ej.iop.org/images/0741-3335/58/4/044005/ppcfaa0dc5ieqn001.gif] $k_parallel=0$ is able to recover the blob dynamics observed in the three-dimensional simulations. Moreover, it is found that an accurate measurement of the blob temperature is important to perform reliable seeded blob simulations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jauzac, M.; Richard, J.; Limousin, M.; Knowles, K.; Mahler, G.; Smith, G. P.; Kneib, J.-P.; Jullo, E.; Natarajan, P.; Ebeling, H.; Atek, H.; Clément, B.; Eckert, D.; Egami, E.; Massey, R.; Rexroth, M.
Hubble Frontier Fields: predictions for the return of SN Refsdal with the MUSE and GMOS spectrographs Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 457, no. 2, p. 2029-2042, 2016.
@article{Jauzac01042016,
title = {Hubble Frontier Fields: predictions for the return of SN Refsdal with the MUSE and GMOS spectrographs},
author = {Jauzac, M. and Richard, J. and Limousin, M. and Knowles, K. and Mahler, G. and Smith, G. P. and Kneib, J.-P. and Jullo, E. and Natarajan, P. and Ebeling, H. and Atek, H. and Clément, B. and Eckert, D. and Egami, E. and Massey, R. and Rexroth, M.},
url = {http://mnras.oxfordjournals.org/content/457/2/2029.abstract},
doi = {10.1093/mnras/stw069},
year = {2016},
date = {2016-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {457},
number = {2},
pages = {2029-2042},
abstract = {We present a high-precision mass model of the galaxy cluster MACS J1149.6+ 2223, based on a strong gravitational lensing analysis of Hubble Space Telescope Frontier Fields (HFF) imaging data and spectroscopic follow-up with Gemini/Gemini Multi-Object Spectrographs (GMOS) and Very Large Telescope (VLT)/Multi Unit Spectroscopic Explorer (MUSE). Our model includes 12 new multiply imaged galaxies, bringing the total to 22, composed of 65 individual lensed images. Unlike the first two HFF clusters, Abell 2744 and MACS J0416.1−2403, MACS J1149 does not reveal as many multiple images in the HFF data. Using the lenstool software package and the new sets of multiple images, we model the cluster with several cluster-scale dark matter haloes and additional galaxy-scale haloes for the cluster members. Consistent with previous analyses, we find the system to be complex, composed of five cluster-scale haloes. Their spatial distribution and lower mass, however, makes MACS J1149 a less powerful lens. Our best-fitting model predicts image positions with an rms of 0.91 arcsec. We measure the total projected mass inside a 200-kpc aperture as (1.840 ± 0.006) × 1014 M⊙, thus reaching again 1 per cent precision, following our previous HFF analyses of MACS J0416.1−2403 and Abell 2744. In light of the discovery of the first resolved quadruply lensed supernova, SN Refsdal, in one of the multiply imaged galaxies identified in MACS J1149, we use our revised mass model to investigate the time delays and predict the rise of the next image between 2015 November and 2016 January.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Miquel Huix-Rotllant; Irene Burghardt; Nicolas Ferré
Population of triplet states in acetophenone: A quantum dynamics perspective Article de journal
Dans: Comptes Rendus Chimie, p. -, 2016, ISSN: 1631-0748.
@article{HuixRotllant2016,
title = {Population of triplet states in acetophenone: A quantum dynamics perspective},
author = {Miquel Huix-Rotllant and Irene Burghardt and Nicolas Ferré},
url = {http://www.sciencedirect.com/science/article/pii/S1631074815002660},
doi = {http://dx.doi.org/10.1016/j.crci.2015.10.002},
issn = {1631-0748},
year = {2016},
date = {2016-01-01},
journal = {Comptes Rendus Chimie},
pages = {-},
abstract = {When initially excited to its first singlet excited state, acetophenone, a prototypical aromatic ketone, is characterized by a singlet to triplet conversion quantum yield close to 100%. In this work, the time evolution of photo-excited acetophenone is theoretically investigated using quantum dynamics simulations based on the Multi Configuration Time Dependent Hartree (MCTDH) method. A model Hamiltonian, comprising both electronic and vibronic terms, is defined and its parameters are fitted to available data obtained by high-level quantum chemical calculations. An exploratory MCTDH dynamics shows a sequential mechanism S1→T2→T1. The population in the triplet manifold is distributed evenly among the two states, explaining the origin of acetophenone rich photochemistry.
Initialement excité vers son premier état excité singulet, l’acétophénone, une cétone aromatique typique, est caractérisée par une conversion singulet vers triplet proche de 100%. Dans ce travail, l’évolution temporelle de l’acétophénone photo-excitée est étudiée de fa,on théorique par dynamique quantique basée sur la méthode Multi Configuration Time Dependent Hartree (MCTDH). Un Hamiltonien modèle, comprenant des termes électroniques et vibroniques, est défini et ses paramètres sont déterminés à partir de données obtenues par des calculs de chimie quantique de haut niveau. La dynamique MCTDH exploratoire montre un mécanisme séquentiel S1→T2→T1. La population est distribuée également dans les deux états triplet, expliquant l’origine de la photochimie riche de l’acétophénone.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Initialement excité vers son premier état excité singulet, l’acétophénone, une cétone aromatique typique, est caractérisée par une conversion singulet vers triplet proche de 100%. Dans ce travail, l’évolution temporelle de l’acétophénone photo-excitée est étudiée de fa,on théorique par dynamique quantique basée sur la méthode Multi Configuration Time Dependent Hartree (MCTDH). Un Hamiltonien modèle, comprenant des termes électroniques et vibroniques, est défini et ses paramètres sont déterminés à partir de données obtenues par des calculs de chimie quantique de haut niveau. La dynamique MCTDH exploratoire montre un mécanisme séquentiel S1→T2→T1. La population est distribuée également dans les deux états triplet, expliquant l’origine de la photochimie riche de l’acétophénone.
O Février; P Maget; H Lütjens; J F Luciani; J Decker; G Giruzzi; M Reich; P Beyer; E Lazzaro; S Nowak; the ASDEX Upgrade team
First principles fluid modelling of magnetic island stabilization by electron cyclotron current drive (ECCD) Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 58, no. 4, p. 045015, 2016.
@article{0741-3335-58-4-045015,
title = {First principles fluid modelling of magnetic island stabilization by electron cyclotron current drive (ECCD)},
author = {O Février and P Maget and H Lütjens and J F Luciani and J Decker and G Giruzzi and M Reich and P Beyer and E Lazzaro and S Nowak and the ASDEX Upgrade team},
url = {http://stacks.iop.org/0741-3335/58/i=4/a=045015},
year = {2016},
date = {2016-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {58},
number = {4},
pages = {045015},
abstract = {Tearing modes are MagnetoHydroDynamics (MHD) instabilities that reduce the performance of fusion devices. They can however be controlled and suppressed using electron cyclotron current drive (ECCD) as demonstrated in various tokamaks. In this work, simulations of island stabilization by ECCD-driven current have been carried out using the toroidal nonlinear 3D full MHD code xtor-2f , in which a current source term modeling the ECCD has been implemented. The efficiency parameter, ##IMG## [http://ej.iop.org/images/0741-3335/58/4/045015/ppcfaa1068ieqn001.gif] $eta_textRF$ , has been computed and its variations with respect to source width and location were also computed. The influence of parameters such as current intensity, source width and position with respect to the island was evaluated and compared to the modified Rutherford equation. We retrieved a good agreement between the simulations and the analytical predictions concerning the variations of control efficiency with source width and position. We also show that the 3D nature of the current source term can lead to the onset of an island if the source term is precisely applied on a rational surface. We report the observation of a flip phenomenon in which the O- and X-points of the island rapidly switch their position in order for the island to take advantage of the current drive to grow.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Engels, T.; Kolomenskiy, D.; Schneider, K.; Lehmann, F.-O.; Sesterhenn, J.
Bumblebee Flight in Heavy Turbulence Article de journal
Dans: Phys. Rev. Lett., vol. 116, p. 028103, 2016.
@article{PhysRevLett.116.028103,
title = {Bumblebee Flight in Heavy Turbulence},
author = {Engels, T. and Kolomenskiy, D. and Schneider, K. and Lehmann, F.-O. and Sesterhenn, J.},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.116.028103},
doi = {10.1103/PhysRevLett.116.028103},
year = {2016},
date = {2016-01-01},
journal = {Phys. Rev. Lett.},
volume = {116},
pages = {028103},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cartier-Michaud, T.; Ghendrih, P.; Sarazin, Y.; Abiteboul, J.; Bufferand, H.; Dif-Pradalier, G.; Garbet, X.; Grandgirard, V.; Latu, G.; Norscini, C.; Passeron, C.; Tamain, P.
Projection on Proper elements for code control: Verification, numerical convergence, and reduced models. Application to plasma turbulence simulations Article de journal
Dans: Physics of Plasmas, vol. 23, no. 2, 2016.
@article{:/content/aip/journal/pop/23/2/10.1063/1.4941974,
title = {Projection on Proper elements for code control: Verification, numerical convergence, and reduced models. Application to plasma turbulence simulations},
author = {Cartier-Michaud, T. and Ghendrih, P. and Sarazin, Y. and Abiteboul, J. and Bufferand, H. and Dif-Pradalier, G. and Garbet, X. and Grandgirard, V. and Latu, G. and Norscini, C. and Passeron, C. and Tamain, P.},
url = {http://scitation.aip.org/content/aip/journal/pop/23/2/10.1063/1.4941974},
doi = {http://dx.doi.org/10.1063/1.4941974},
year = {2016},
date = {2016-01-01},
journal = {Physics of Plasmas},
volume = {23},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
S Pamela; T Eich; L Frassinetti; B Sieglin; S Saarelma; G Huijsmans; M Hoelzl; M Becoulet; F Orain; S Devaux; I Chapman; I Lupelli; E Solano; JET Contributors
Non-linear MHD simulations of ELMs in JET and quantitative comparisons to experiments Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 58, no. 1, p. 014026, 2016.
@article{0741-3335-58-1-014026,
title = {Non-linear MHD simulations of ELMs in JET and quantitative comparisons to experiments},
author = {S Pamela and T Eich and L Frassinetti and B Sieglin and S Saarelma and G Huijsmans and M Hoelzl and M Becoulet and F Orain and S Devaux and I Chapman and I Lupelli and E Solano and JET Contributors},
url = {http://stacks.iop.org/0741-3335/58/i=1/a=014026},
year = {2016},
date = {2016-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {58},
number = {1},
pages = {014026},
abstract = {A subset of JET ITER-like wall (ILW) discharges, combining electron density and temperature as well as divertor heat flux measurements, has been collected for the validation of non-linear magnetohydrodynamic (MHD) simulations of edge-localised-modes (ELMs). This permits a quantitative comparison of simulation results against experiments, which is required for the validation of predicted ELM energy losses and divertor heat fluxes in future tokamaks like ITER. This paper presents the first results of such a quantitative comparison, and gives a perspective of what will be necessary to achieve full validation of non-linear codes like JOREK. In particular, the present study highlights the importance of pre-ELM equilibria and parallel energy transport models in MHD simulations, which form the underlying basis of ELM physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
R. Aganetti; A. Lamorlette; E. Guilbert; D. Morvan; G.R. Thorpe
Advection and the self-heating of organic porous media Article de journal
Dans: International Journal of Heat and Mass Transfer, vol. 93, p. 1150 - 1158, 2016, ISSN: 0017-9310.
@article{Aganetti20161150,
title = {Advection and the self-heating of organic porous media},
author = {R. Aganetti and A. Lamorlette and E. Guilbert and D. Morvan and G.R. Thorpe},
url = {http://www.sciencedirect.com/science/article/pii/S0017931015307122},
doi = {http://dx.doi.org/10.1016/j.ijheatmasstransfer.2015.11.023},
issn = {0017-9310},
year = {2016},
date = {2016-01-01},
journal = {International Journal of Heat and Mass Transfer},
volume = {93},
pages = {1150 - 1158},
abstract = {Abstract Self-heating is commonly observed when organic materials such as biosolids, coal, food grains and compost are stockpiled. A convection–diffusion model is presented that accounts for the roles of advection and the transport of oxygen in the self-heating process, as well as the development of an empirical correlation between dimensionless Darcy number, Frank–Kamenetskii parameter and pile aspect ratio, to predict the critical permeability above which thermal runaway can be avoided. It is apparent that the permeability of the stockpile determines the likelihood of the thermal runaway. However, the solids that form a stockpile are poly-disperse and it is essential to determine an effective permeability. This has been achieved using experimental data on biosolids obtained from a wastewater treatment plant in Australia. With this method the model is used to demonstrate how the permeability of a stockpile might be adjusted to reduce the incidence of thermal runaway.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M. El Houssami; J.C. Thomas; A. Lamorlette; D. Morvan; M. Chaos; R. Hadden; A. Simeoni
Experimental and numerical studies characterizing the burning dynamics of wildland fuels Article de journal
Dans: Combustion and Flame, vol. 168, p. 113 - 126, 2016, ISSN: 0010-2180.
@article{Houssami2016113,
title = {Experimental and numerical studies characterizing the burning dynamics of wildland fuels},
author = {M. El Houssami and J.C. Thomas and A. Lamorlette and D. Morvan and M. Chaos and R. Hadden and A. Simeoni},
url = {http://www.sciencedirect.com/science/article/pii/S0010218016300517},
doi = {http://dx.doi.org/10.1016/j.combustflame.2016.04.004},
issn = {0010-2180},
year = {2016},
date = {2016-01-01},
journal = {Combustion and Flame},
volume = {168},
pages = {113 - 126},
abstract = {Abstract A method to accurately understand the processes controlling the burning behavior of porous wildland fuels is presented using numerical simulations and laboratory experiments. A multiphase approach has been implemented in OpenFOAM, which is based on the FireFOAM solver for large eddy simulations (LES). Conservation equations are averaged in a control volume containing a gas and a solid phase. Drying, pyrolysis, and char oxidation are described by interaction between the two phases. Numerical simulations are compared to laboratory experiments carried out with porous pine needle beds in the FM Global Fire Propagation Apparatus (FPA). These experiments are used to support the use and the development of submodels that represent heat transfer, pyrolysis, gas-phase combustion, and smoldering processes. The model is tested for different bulk densities, two distinct species and two different radiative heat fluxes used to heat up the samples. It has been possible to reproduce mass loss rates, heat release rates, and temperatures that agree with experimental observations, and to highlight the current limitations of the model.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wilmer Arbelo-González; Rachel Crespo-Otero; Mario Barbatti
Steady and time-resolved photoelectron spectra based on nuclear ensembles Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 0, no. ja, p. null, 2016, (PMID: 27588827).
@article{doi:10.1021/acs.jctc.6b00704,
title = {Steady and time-resolved photoelectron spectra based on nuclear ensembles},
author = {Wilmer Arbelo-González and Rachel Crespo-Otero and Mario Barbatti},
url = {http://dx.doi.org/10.1021/acs.jctc.6b00704},
doi = {10.1021/acs.jctc.6b00704},
year = {2016},
date = {2016-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {0},
number = {ja},
pages = {null},
abstract = {Semiclassical methods to simulate both steady and time-resolved photoelectron spectra are presented. These approaches provide spectra with absolute band shapes and vibrational broadening beyond the Condon approximation, using ensemble of nuclear configurations built either via distribution samplings or nonadiabatic dynamics simulations. Two models to account for the electron kinetic energy modulation due to vibrational overlaps between initial and final states are discussed. As illustrative examples, the steady photoelectron spectra of imidazole and adenine and the time- and kinetic-energy-resolved photoelectron spectrum of imidazole were simulated within the frame of time-dependent density functional theory. While for steady spectra only electrons ejected with maximum allowed kinetic energy need to be considered, it is shown that to properly describe time-resolved spectra, electrons ejected with low kinetic energies must be considered in the simulations as well. The results also show that simulations based either on full computation of photoelectron cross section or on simple Dyson orbital norms provide results of similar quality.},
note = {PMID: 27588827},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ivana Antol; Zoran Glasovac; Davor Margetić; Rachel Crespo-Otero; Mario Barbatti
Insights on the Auxochromic Properties of the Guanidinium Group Article de journal
Dans: The Journal of Physical Chemistry A, vol. 0, no. 0, p. null, 2016, (PMID: 27556411).
@article{doi:10.1021/acs.jpca.6b05180,
title = {Insights on the Auxochromic Properties of the Guanidinium Group},
author = {Ivana Antol and Zoran Glasovac and Davor Margetić and Rachel Crespo-Otero and Mario Barbatti},
url = {http://dx.doi.org/10.1021/acs.jpca.6b05180},
doi = {10.1021/acs.jpca.6b05180},
year = {2016},
date = {2016-01-01},
journal = {The Journal of Physical Chemistry A},
volume = {0},
number = {0},
pages = {null},
abstract = {UV/vis spectra of phenylguanidine (PHGU) in the gas phase and in acetonitrile have been simulated by TD-DFT calculations. Several DFT hybrid and long-range corrected functionals were tested with respect to CASPT2 gas phase calculations. Solvent effects were considered using polarizable continuum model (PCM) and compared with the measured data in acetonitrile. Comparison with isoelectronic phenylurea and related phenyltiourea was done as well. The PBE0 and long-range corrected CAM-B3LYP functionals were selected to investigate the effect of protonation on the excitation energies and absorption intensities of PHGU and several guanidine derivatives with different aromatic chromophoric groups (naphthyl, anthracenyl, quinolinyl, anthraquinonyl, and coumarinyl). Also, the effect of complexation and specific interactions through hydrogen bonds with different anions was examined. It was shown that the protonation of the guanidine subunit shifts the low energy absorption bands toward higher energies (hypsochromic shift). The shift is reduced upon complexation with anions. In phenylguanidine salts, λmax values are correlated to the anion basicity and strength of H-bonding. The observed changes diminish upon increase of chromophoric size (naphthyl, anthracenyl). Theoretical predictions of UV/vis spectra correlate well with experimentally measured spectra of selected guanidine derivatives and their salts.},
note = {PMID: 27556411},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shuming Bai; Mario Barbatti
Why Replacing Different Oxygens of Thymine with Sulfur Causes Distinct Absorption and Intersystem Crossing Article de journal
Dans: The Journal of Physical Chemistry A, vol. 120, no. 32, p. 6342-6350, 2016, (PMID: 27454198).
@article{doi:10.1021/acs.jpca.6b05110,
title = {Why Replacing Different Oxygens of Thymine with Sulfur Causes Distinct Absorption and Intersystem Crossing},
author = {Shuming Bai and Mario Barbatti},
url = {http://dx.doi.org/10.1021/acs.jpca.6b05110},
doi = {10.1021/acs.jpca.6b05110},
year = {2016},
date = {2016-01-01},
journal = {The Journal of Physical Chemistry A},
volume = {120},
number = {32},
pages = {6342-6350},
abstract = {Recent experiments replacing oxygen atoms by sulfur in thymine have revealed that absorption and intersystem crossing properties of these derivatives are strongly dependent on the position and number of the substitutions, affecting their potential performance for photodynamical therapy. Using multireference quantum chemical methods (CASPT2 and DFT/MRCI), we calculated absorption spectra and spin–orbit coupling matrix elements for thymine (Thy), 2-thiothymine (2tThy), 4-thiothymine (4tThy), and 2,4-dithiothymine (2,4dtThy), to investigate this relation between structure and photophysics. The simulations showed that a simple 4-electrons/4-orbital minimum model can explain the main experimentally observed spectral features. Moreover, the computational estimate of intersystem crossing lifetimes in this sequence of molecules revealed that the experimental value attributed to thymine in water might be underestimated by a factor 20, most probably due to an overlap of singlet/triplet absorption signals in the transient absorption spectrum. The difference between the absorptivity of 2tThy and 2tThd was also investigated, but no conclusive explanation could be found.},
note = {PMID: 27454198},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Daniele Fazzi; Mario Barbatti; Walter Thiel
Unveiling the Role of Hot Charge-Transfer States in Molecular Aggregates via Nonadiabatic Dynamics Article de journal
Dans: Journal of the American Chemical Society, vol. 138, no. 13, p. 4502-4511, 2016, (PMID: 26967020).
@article{doi:10.1021/jacs.5b13210,
title = {Unveiling the Role of Hot Charge-Transfer States in Molecular Aggregates via Nonadiabatic Dynamics},
author = {Daniele Fazzi and Mario Barbatti and Walter Thiel},
url = {http://dx.doi.org/10.1021/jacs.5b13210},
doi = {10.1021/jacs.5b13210},
year = {2016},
date = {2016-01-01},
journal = {Journal of the American Chemical Society},
volume = {138},
number = {13},
pages = {4502-4511},
abstract = {Exciton dynamics governs energy transfer and charge generation in organic functional materials. We investigate high-energy nonadiabatic excited-state dynamics for a bithiophene dimer to describe time-dependent excitonic effects in molecular aggregates. We show that the lowest excited states are populated on the subpicosecond time scale. These states are localized and unproductive in terms of charge separation. Productive high-energy charge-transfer (CT) states are populated within 50 fs during exciton deactivation, but they are short-lived (∼100 fs) and quickly transfer their population to lower states. Our simulations offer molecular-level insights into ultrafast photoinduced charge separation potentially triggered by hot CT states in solid-state organic materials. Design rules are suggested to increase hot exciton lifetimes, favoring the population of CT states as gateways for direct charge generation. These rules may boost the CT quantum yield by depleting unproductive recombination channels.},
note = {PMID: 26967020},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Xie Zhinan; Matzen René; Cristini Paul; Komatitsch Dimitri; Martin Roland
A perfectly matched layer for fluid-solid problems: Application to ocean-acoustics simulations with solid ocean bottoms Article de journal
Dans: The Journal of the Acoustical Society of America, vol. 140, no. 1, 2016.
@article{:/content/asa/journal/jasa/140/1/10.1121/1.4954736,
title = {A perfectly matched layer for fluid-solid problems: Application to ocean-acoustics simulations with solid ocean bottoms},
author = {Xie Zhinan and Matzen René and Cristini Paul and Komatitsch Dimitri and Martin Roland},
url = {165-175},
doi = {http://scitation.aip.org/content/asa/journal/jasa/140/1/10.1121/1.4954736},
year = {2016},
date = {2016-01-01},
journal = {The Journal of the Acoustical Society of America},
volume = {140},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P. Tamain; H. Bufferand; G. Ciraolo; C. Colin; D. Galassi; Ph. Ghendrih; F. Schwander; E. Serre
The TOKAM3X code for edge turbulence fluid simulations of tokamak plasmas in versatile magnetic geometries Article de journal
Dans: Journal of Computational Physics, vol. 321, p. 606 - 623, 2016, ISSN: 0021-9991.
@article{Tamain2016606,
title = {The TOKAM3X code for edge turbulence fluid simulations of tokamak plasmas in versatile magnetic geometries},
author = {P. Tamain and H. Bufferand and G. Ciraolo and C. Colin and D. Galassi and Ph. Ghendrih and F. Schwander and E. Serre},
url = {http://www.sciencedirect.com/science/article/pii/S0021999116301838},
doi = {http://dx.doi.org/10.1016/j.jcp.2016.05.038},
issn = {0021-9991},
year = {2016},
date = {2016-01-01},
journal = {Journal of Computational Physics},
volume = {321},
pages = {606 - 623},
abstract = {Abstract The new code TOKAM3X simulates plasma turbulence in full torus geometry including the open field lines of the Scrape-off Layer (SOL) and the edge closed field lines region in the vicinity of the separatrix. Based on drift-reduced Braginskii equations, TOKAM3X is able to simulate both limited and diverted plasmas. Turbulence is flux driven by incoming particles from the core plasma and no scale separation between the equilibrium and the fluctuations is assumed so that interactions between large scale flows and turbulence are consistently treated. Based on a domain decomposition, specific numerical schemes are proposed using conservative finite-differences associated to a semi-implicit time advancement. The process computation is multi-threaded and based on MPI and OpenMP libraries. In this paper, fluid model equations are presented together with the proposed numerical methods. The code is verified using the manufactured solution technique and validated through documented simple experiments. Finally, first simulations of edge plasma turbulence in X-point geometry are also introduced in a JET geometry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Futtersack, R.; Colin, C.; Tamain, P.; Ciraolo, G.; Ghendrih, Ph.; Marandet, Y.; Schwander, F.; Serre, E.
First Principle Modelling of Interplay between Langmuir Probes and Plasma Turbulence Article de journal
Dans: Contributions to Plasma Physics, vol. 56, no. 6-8, p. 575–580, 2016, ISSN: 1521-3986.
@article{CTPP:CTPP201610038,
title = {First Principle Modelling of Interplay between Langmuir Probes and Plasma Turbulence},
author = {Futtersack, R. and Colin, C. and Tamain, P. and Ciraolo, G. and Ghendrih, Ph. and Marandet, Y. and Schwander, F. and Serre, E.},
url = {http://dx.doi.org/10.1002/ctpp.201610038},
doi = {10.1002/ctpp.201610038},
issn = {1521-3986},
year = {2016},
date = {2016-01-01},
journal = {Contributions to Plasma Physics},
volume = {56},
number = {6-8},
pages = {575--580},
publisher = {WILEY-VCH Verlag},
abstract = {The interplay between Langmuir probes (LP) and Scrape-Off-Layer plasma turbulence is numerically investigated with the TOKAM2D and TOKAM3X fluid codes. The LP is modelled by biasing a part of the target plates surface; we then study its impact on the turbulent transport 1) in presence of electron temperature fluctuations and 2) with a complete description of the parallel dynamics. We find that a biased probe can disturb local plasma parameters as well as turbulent transport in its vicinity, by polarizing the connected flux tube and thus driving a strong ExB vortex. Moreover, electron temperature fluctuations are found to account significantly those of floating potential, but with a limited impact on flux measurements depending on the probe's exact geometry. The 3D study of the problem shows the attenuation, but the persistency, of these perturbations induced by the presence of the LP. (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tamain, P.; Bufferand, H.; Carbajal, L.; Marandet, Y.; Baudoin, C.; Ciraolo, G.; Colin, C.; Futtersack, R.; Galassi, D.; Ghendrih, P.; Nace, N.; Schwander, F.; Serre, E.
Interplay between Plasma Turbulence and Particle Injection in 3D Global Simulations Article de journal
Dans: Contributions to Plasma Physics, vol. 56, no. 6-8, p. 569–574, 2016, ISSN: 1521-3986.
@article{CTPP:CTPP201610063,
title = {Interplay between Plasma Turbulence and Particle Injection in 3D Global Simulations},
author = {Tamain, P. and Bufferand, H. and Carbajal, L. and Marandet, Y. and Baudoin, C. and Ciraolo, G. and Colin, C. and Futtersack, R. and Galassi, D. and Ghendrih, P. and Nace, N. and Schwander, F. and Serre, E.},
url = {http://dx.doi.org/10.1002/ctpp.201610063},
doi = {10.1002/ctpp.201610063},
issn = {1521-3986},
year = {2016},
date = {2016-01-01},
journal = {Contributions to Plasma Physics},
volume = {56},
number = {6-8},
pages = {569--574},
publisher = {WILEY-VCH Verlag},
abstract = {The impact of a 3D localized particle source on the edge plasma in 3D global turbulence simulations is investigated using the TOKAM3X fluid code. Results apply to advanced fueling methods such as Supersonic Molecular Beam Injection (SMBI) or pellets injection. The fueling source is imposed as a volumetric particle source in the simulations so that the physics leading to the ionization of particles and its localization are not taken into account. As already observed in experiments, the localized particle source strongly perturbs both turbulence and the large scale organization of the edge plasma. The localized increase of the pressure generated by the source drives sonic parallel flows in the plasma, leading to a poloidal redistribution of the particles on the time scale of the source duration. However, the particle deposition also drives localized transverse pressure gradients which impacts the stability of the plasma with respect to interchange processes. The resulting radial transport occurs on a sufficiently fast time scale to compete with the parallel redistribution of particles, leading to immediate radial losses of a significant proportion of the injected particles. Low Field Side (LFS) and High Field Side (HFS) injections exhibit different dynamics due to their interaction with curvature. In particular, HFS particle deposition drives an inward flux leading to differences in the particle deposition efficiency (higher for HFS than LFS). These results demonstrate the importance of taking into account plasma transport in a self-consistent manner when investigating fueling methods. (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Florian Carle; Sergey Semenov; Marc Medale; David Brutin
Contribution of convective transport to evaporation of sessile droplets: Empirical model Article de journal
Dans: International Journal of Thermal Sciences, vol. 101, p. 35 - 47, 2016, ISSN: 1290-0729.
@article{Carle201635,
title = {Contribution of convective transport to evaporation of sessile droplets: Empirical model},
author = {Florian Carle and Sergey Semenov and Marc Medale and David Brutin},
url = {http://www.sciencedirect.com/science/article/pii/S1290072915003130},
doi = {http://dx.doi.org/10.1016/j.ijthermalsci.2015.10.012},
issn = {1290-0729},
year = {2016},
date = {2016-01-01},
journal = {International Journal of Thermal Sciences},
volume = {101},
pages = {35 - 47},
abstract = {Abstract Despite the fact that sessile droplets evaporation dynamics has been studied for more than half a century, the scientific community struggles with the creation of an accurate quantitative description of the rate of evaporation. The classically used description considers evaporation as a quasi-steady process controlled by the diffusion of vapour into the air and the whole system is assumed to be isothermal at the ambient temperature. However, when two types of fluids (alcohols and alkanes) are let to evaporate on heated substrates, their evaporation rates tend to be underestimated by this model, mostly due to convection. This experimental study aims to understand how atmospheric convective transport in the vapour phase influences evaporation in order to develop an empirical model that accurately describes the evaporation rate. The Rayleigh number is used to analyse the contribution of natural convection and an empirical model is developed combining diffusive and convective transport for each type of fluid. The influence of the molecular chain length (and the increasing number of carbon atoms) is also being discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Omar Madani Fouatih; Marc Medale; Omar Imine; Bachir Imine
Design optimization of the aerodynamic passive flow control on NACA 4415 airfoil using vortex generators Article de journal
Dans: European Journal of Mechanics - B/Fluids, vol. 56, p. 82 - 96, 2016, ISSN: 0997-7546.
@article{Fouatih201682,
title = {Design optimization of the aerodynamic passive flow control on NACA 4415 airfoil using vortex generators},
author = {Omar Madani Fouatih and Marc Medale and Omar Imine and Bachir Imine},
url = {http://www.sciencedirect.com/science/article/pii/S0997754615001181},
doi = {http://dx.doi.org/10.1016/j.euromechflu.2015.11.006},
issn = {0997-7546},
year = {2016},
date = {2016-01-01},
journal = {European Journal of Mechanics - B/Fluids},
volume = {56},
pages = {82 - 96},
abstract = {Abstract The present paper provides an experimental optimization of a NACA 4415 airfoil equipped with vortex generators (VGs) to control its flow separation. To build this optimal configuration an experimental parametric study was conducted on five geometrical parameters: thickness and height of vortex generators, position, orientation angle with respect to the mean flow direction, spacing in the spanwise direction. Moreover, a new configuration that includes micro generators behind the conventional ones was also investigated as a potentially interesting solution. For all these cases wind tunnel tests were performed and compared for different angles of attack and various Reynolds numbers up to 2 10 5 . These experiments enabled us to highlight the main trends to get an optimal design, for which quantitative improvement can be achieved by passive means in terms of aerodynamic performances on NACA4415 airfoil. The results reveal that triangular shape vortex generators are best suited to control boundary layer separation. An optimum angle of VGs is obtained for 12°with a 3 mm distance between vortex generators located at 50% of the chord. It was found that micro vortex generators are very effective in controlling the flow with less parasite drag. The maximum lift coefficient for an airfoil with coupled vortex generators increases by 21% and a flow separation is delayed by 17°. However, this very good performance is counterbalanced by the appearance of parasitic drag. Indeed, it creates a counter-rotating array of vortices with the second raw of micro-vortex generators that reinforce the vortexes strength without any increase in device height.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bessonov, O. A.
Effect of crystal and crubicle rotation on the flow stability in the Czochralski model at low Prandtl numbers Article de journal
Dans: Fluid Dynamics, vol. 51, no. 4, p. 469–477, 2016, ISSN: 1573-8507.
@article{Bessonov2016,
title = {Effect of crystal and crubicle rotation on the flow stability in the Czochralski model at low Prandtl numbers},
author = {Bessonov, O. A.},
url = {http://dx.doi.org/10.1134/S0015462816040050},
doi = {10.1134/S0015462816040050},
issn = {1573-8507},
year = {2016},
date = {2016-01-01},
journal = {Fluid Dynamics},
volume = {51},
number = {4},
pages = {469--477},
abstract = {The results of a numerical investigation of the joint effect of crystal and crubicle rotation on the flow stability at low Prandtl numbers (Pr=0.01 to 0.07) are presented. The regimes with an elevated stability threshold are determined for various combinations of crystal and crubicle rotations and the heat flux distributions over the growing crystal endface are obtained. The mechanisms of the loss of stability, as the critical values of the Grashof number and the rotation velocities are exceeded, are considered and a new regime of stable nonaxisymmetric flow is established.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Maget; O Février; H Lütjens; J-F Luciani; X Garbet
Bifurcation of magnetic island saturation controlled by plasma viscosity Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 58, no. 5, p. 055003, 2016.
@article{0741-3335-58-5-055003,
title = {Bifurcation of magnetic island saturation controlled by plasma viscosity},
author = {P Maget and O Février and H Lütjens and J-F Luciani and X Garbet},
url = {http://stacks.iop.org/0741-3335/58/i=5/a=055003},
year = {2016},
date = {2016-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {58},
number = {5},
pages = {055003},
abstract = {Two nonlinear regimes, depending on the magnetic Prandtl number Prm, are identified for the magnetic islands described by resistive MHD equations. The frontier between these two regimes is sharp, and has the characteristics of a phase transition controlled by plasma viscosity. In the low Prm regime, a new form of the so-called flip instability, consisting of a sudden change in the island phase, is identified. Already known in the context of the forcing by external magnetic perturbations and localized current drive, it occurs spontaneously at low Prm. The main characteristics of this new structural instability are described. The low Prm regime is well described by the slab visco-resistive model in the linear phase, and is characterized by both a large saturation of the island and strong nonlinearly driven zonal flows (that do not significantly impact the island dynamics, however), while curvature physics strongly impacts the viscous regime.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Patrick Maget; Olivier Février; Xavier Garbet; Hinrich Lütjens; Jean-Francois Luciani; Alain Marx
Extended magneto-hydro-dynamic model for neoclassical tearing mode computations Article de journal
Dans: Nuclear Fusion, vol. 56, no. 8, p. 086004, 2016.
@article{0029-5515-56-8-086004,
title = {Extended magneto-hydro-dynamic model for neoclassical tearing mode computations},
author = {Patrick Maget and Olivier Février and Xavier Garbet and Hinrich Lütjens and Jean-Francois Luciani and Alain Marx},
url = {http://stacks.iop.org/0029-5515/56/i=8/a=086004},
year = {2016},
date = {2016-01-01},
journal = {Nuclear Fusion},
volume = {56},
number = {8},
pages = {086004},
abstract = {A self-consistent fluid model for describing neoclassical tearing modes in global magneto-hydro-dynamic simulations is presented. It is illustrated by its application to a simple toroidal configuration unstable to the (2, 1) tearing mode. The island saturation is verified to increase with the bootstrap current fraction. New features that are specific to this model are evidenced, like the unsteady saturated state of the island, and its deformation to a droplet shape, when the magnetic Prandtl number is not too high. Synthetic diagnostics demonstrate that diamagnetic and neoclassical effects should have in this case a measurable impact on the signature of magnetic islands.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jae-H Ahn; X Garbet; H Lütjens; R Guirlet
Dynamics of heavy impurities in non-linear MHD simulations of sawtoothing tokamak plasmas Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 58, no. 12, p. 125009, 2016.
@article{0741-3335-58-12-125009,
title = {Dynamics of heavy impurities in non-linear MHD simulations of sawtoothing tokamak plasmas},
author = {Jae-H Ahn and X Garbet and H Lütjens and R Guirlet},
url = {http://stacks.iop.org/0741-3335/58/i=12/a=125009},
year = {2016},
date = {2016-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {58},
number = {12},
pages = {125009},
abstract = {The effect of sawteeth on impurity dynamics is studied with the XTOR-2F code. Non-linear full 3D MHD simulations including appropriate fluid equations for impurities in the high collisional regime show that the presence of regular sawtooth crashes affects the impurity behaviour. A spatial non-uniformity of ##IMG## [http://ej.iop.org/images/0741-3335/58/12/125009/ppcfaa40d8ieqn001.gif] $5 % $ in post-crash impurity density profiles persists due to 2D structures of impurity density which appear during sawtooth crashes. They are shown to be mainly driven by the ##IMG## [http://ej.iop.org/images/0741-3335/58/12/125009/ppcfaa40d8ieqn002.gif] $mathbfEtimes mathbfB$ velocity, and are responsible for the sudden impurity transport in the core plasmas.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
J Denis; B Pégourié; J Bucalossi; H Bufferand; G Ciraolo; J-L Gardarein; J Gaspar; C Grisolia; E Hodille; M Missirlian; E Serre; P Tamain
Wall surface temperature calculation in the SolEdge2D-EIRENE transport code Article de journal
Dans: Physica Scripta, vol. 2016, no. T167, p. 014073, 2016.
@article{1402-4896-2016-T167-014073,
title = {Wall surface temperature calculation in the SolEdge2D-EIRENE transport code},
author = {J Denis and B Pégourié and J Bucalossi and H Bufferand and G Ciraolo and J-L Gardarein and J Gaspar and C Grisolia and E Hodille and M
Missirlian and E Serre and P Tamain},
url = {http://stacks.iop.org/1402-4896/2016/i=T167/a=014073},
year = {2016},
date = {2016-01-01},
journal = {Physica Scripta},
volume = {2016},
number = {T167},
pages = {014073},
abstract = {A thermal wall model is developed for the SolEdge2D-EIRENE edge transport code for calculating the surface temperature of the actively-cooled vessel components in interaction with the plasma. This is a first step towards a self-consistent evaluation of the recycling of particles, which depends on the wall surface temperature. The proposed thermal model is built to match both steady-state temperature and time constant of actively-cooled plasma facing components. A benchmark between this model and the Finite Element Modelling code CAST3M is performed in the case of an ITER–like monoblock. An example of application is presented for a SolEdge2D-EIRENE simulation of a medium-power discharge in the WEST tokamak, showing the steady-state wall temperature distribution and the temperature cycling due to an imposed Edge Localised Mode-like event.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Athanassoula, E.
Boxy/Peanut/X Bulges, Barlenses and the Thick Part of Galactic Bars: What Are They and How Did They Form? Chapitre d'ouvrage
Dans: Laurikainen, Eija; Peletier, Reynier; Gadotti, Dimitri (Ed.): Galactic Bulges, p. 391–412, Springer International Publishing, Cham, 2016, ISBN: 978-3-319-19378-6.
@inbook{Athanassoula2016,
title = {Boxy/Peanut/X Bulges, Barlenses and the Thick Part of Galactic Bars: What Are They and How Did They Form?},
author = {Athanassoula, E.},
editor = {Laurikainen, Eija
and Peletier, Reynier
and Gadotti, Dimitri},
url = {http://dx.doi.org/10.1007/978-3-319-19378-6_14},
doi = {10.1007/978-3-319-19378-6_14},
isbn = {978-3-319-19378-6},
year = {2016},
date = {2016-01-01},
booktitle = {Galactic Bulges},
pages = {391--412},
publisher = {Springer International Publishing},
address = {Cham},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Kim, Taehyun; Gadotti, Dimitri A.; Athanassoula, E.; Bosma, Albert; Sheth, Kartik; Lee, Myung Gyoon
Evidence of bar-induced secular evolution in the inner regions of stellar discs in galaxies: what shapes disc galaxies? Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 462, no. 4, p. 3430, 2016.
@article{doi:10.1093/mnras/stw1899,
title = {Evidence of bar-induced secular evolution in the inner regions of stellar discs in galaxies: what shapes disc galaxies?},
author = {Kim, Taehyun and Gadotti, Dimitri A. and Athanassoula, E. and Bosma, Albert and Sheth, Kartik and Lee, Myung Gyoon},
url = {+ http://dx.doi.org/10.1093/mnras/stw1899},
doi = {10.1093/mnras/stw1899},
year = {2016},
date = {2016-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {462},
number = {4},
pages = {3430},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M. Ness; G. Zasowski; J. A. Johnson; E. Athanassoula; S. R. Majewski; A. E. García Pérez; J. Bird; D. Nidever; Donald P. Schneider; J. Sobeck; P. Frinchaboy; Kaike Pan; Dmitry Bizyaev; Daniel Oravetz; Audrey Simmons
APOGEE Kinematics. I. Overview of the Kinematics of the Galactic Bulge as Mapped By APOGEE Article de journal
Dans: The Astrophysical Journal, vol. 819, no. 1, p. 2, 2016.
@article{0004-637X-819-1-2,
title = {APOGEE Kinematics. I. Overview of the Kinematics of the Galactic Bulge as Mapped By APOGEE},
author = {M. Ness and G. Zasowski and J. A. Johnson and E. Athanassoula and S. R. Majewski and A. E. García Pérez and J. Bird and D.
Nidever and Donald P. Schneider and J. Sobeck and P. Frinchaboy and Kaike Pan and Dmitry Bizyaev and Daniel Oravetz and Audrey
Simmons},
url = {http://stacks.iop.org/0004-637X/819/i=1/a=2},
year = {2016},
date = {2016-01-01},
journal = {The Astrophysical Journal},
volume = {819},
number = {1},
pages = {2},
abstract = {We present the stellar kinematics across the Galactic bulge and into the disk at positive longitudes from the SDSS-III APOGEE spectroscopic survey of the Milky Way. APOGEE includes extensive coverage of the stellar populations of the bulge along the midplane and near-plane regions. From these data, we have produced kinematic maps of 10,000 stars across longitudes of 0° < l < 65°, and primarily across latitudes of ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn1.gif] $| b| $ < 5° in the bulge region. The APOGEE data reveal that the bulge is cylindrically rotating across all latitudes and is kinematically hottest at the very center of the bulge, with the smallest gradients in both kinematic and chemical space inside the innermost region ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn2.gif] $(| l,b| )$ < (5°, 5°). The results from APOGEE show good agreement with data from other surveys at higher latitudes and a remarkable similarity to the rotation and dispersion maps of barred galaxies viewed edge-on. The thin bar that is reported to be present in the inner disk within a narrow latitude range of ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn3.gif] $| b| $ < 2° appears to have a corresponding signature in ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn4.gif] $[mathrmFe/rmĦ]$ and ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn5.gif] $[alpha /mathrmFe]$ . Stars with ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn6.gif] $[mathrmFe/rmĦ]$ > −0.5 have dispersion and rotation profiles that are similar to that of N -body models of boxy/peanut bulges. There is a smooth kinematic transition from the thin bar and boxy bulge ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn7.gif] $(l,| b| )$ < (15°, 12°) out to the disk for stars with ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn8.gif] $[mathrmFe/rmĦ]$ > −1.0, and the chemodynamics across ( l , b ) suggests that the stars in the inner Galaxy with ##IMG## [http://ej.iop.org/images/0004-637X/819/1/2/apj522289ieqn9.gif] $[mathrmFe/rmĦ]$ > −1.0 originate in the disk.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wang, Yougang; Athanassoula, E.; Mao, Shude
Orbital classification in an N-body bar Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 463, no. 4, p. 3499, 2016.
@article{doi:10.1093/mnras/stw2301,
title = {Orbital classification in an N-body bar},
author = {Wang, Yougang and Athanassoula, E. and Mao, Shude},
url = {+ http://dx.doi.org/10.1093/mnras/stw2301},
doi = {10.1093/mnras/stw2301},
year = {2016},
date = {2016-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {463},
number = {4},
pages = {3499},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
E. Athanassoula; S. A. Rodionov; N. Peschken; J. C. Lambert
Forming Disk Galaxies in Wet Major Mergers. I. Three Fiducial Examples Article de journal
Dans: The Astrophysical Journal, vol. 821, no. 2, p. 90, 2016.
@article{0004-637X-821-2-90,
title = {Forming Disk Galaxies in Wet Major Mergers. I. Three Fiducial Examples},
author = {E. Athanassoula and S. A. Rodionov and N. Peschken and J. C. Lambert},
url = {http://stacks.iop.org/0004-637X/821/i=2/a=90},
year = {2016},
date = {2016-01-01},
journal = {The Astrophysical Journal},
volume = {821},
number = {2},
pages = {90},
abstract = {Using three fiducial N -body+SPH simulations, we follow the merging of two disk galaxies that each have a hot gaseous halo component, and examine whether the merger remnant can be a spiral galaxy. The stellar progenitor disks are destroyed by violent relaxation during the merging and most of their stars form a classical bulge, while the remaining stars, as well as stars born during the merging times, form a thick disk and its bar. A new stellar disk forms subsequently and gradually in the remnant from the gas accreted mainly from the halo. It is vertically thin and well extended in its equatorial plane. A bar starts forming before the disk is fully in place, which is contrary to what is assumed in idealized simulations of isolated bar-forming galaxies, and has morphological features such as ansae and boxy/peanut bulges. Stars of different ages populate different parts of the box/peanut. A disky pseudobulge also forms, so that by the end of the simulation all three types of bulges coexist. The oldest stars are found in the classical bulge, followed by those of the thick disk, then by those in the thin disk. The youngest stars are in the spiral arms and the disky pseudobulge. The disk surface density profiles are of type II (exponential with downbending); the circular velocity curves are flat and show that the disks are submaximum in these examples: two clearly so and one near-borderline between maximum and submaximum. On average, only roughly between 10% and 20% of the stellar mass is in the classical bulge of the final models, i.e., much less than in previous simulations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huix-Rotllant Miquel; Ferré Nicolas
An Effective Procedure for Analyzing Molecular Vibrations in Terms of Local Fragment Modes Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 12, no. 10, p. 4768-4777, 2016, (PMID: 27642675).
@article{doi:10.1021/acs.jctc.6b00514,
title = {An Effective Procedure for Analyzing Molecular Vibrations in Terms of Local Fragment Modes},
author = {Huix-Rotllant Miquel and Ferré Nicolas},
url = {http://dx.doi.org/10.1021/acs.jctc.6b00514},
doi = {10.1021/acs.jctc.6b00514},
year = {2016},
date = {2016-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {12},
number = {10},
pages = {4768-4777},
abstract = {Normal mode analysis is nowadays routinely performed in most quantum chemistry codes as a valuable tool for studying molecular motions. In systems formed by several molecular units, such as noncovalently bound donor–acceptor systems, normal modes are frequently delocalized over the whole structure, leading to a complicated interpretation of vibrations. Here, we propose a simple procedure to localize normal modes, based on the definition of fragment Hessian submatrices that lead to legitimate local fragment modes. These fragment modes can be defined for any arbitrary number of atoms and fragments and form in general a complete basis that can be used to expand the total normal modes. We use this fragment basis to explore the molecular origin of the normal modes of benzene, and several peaks in the infrared spectrum of tetraalanine. Additionally, we propose a criteria to define breathing modes in noncovalently bound systems, based on the fact that motions of the center of mass of fragments are not translational and rotational invariant with respect to the total center of mass of the system. By using the Sayvetz-Eckart conditions of fragments, we can quantify the contribution of rotation and translation of the fragments center of mass on the normal modes of the total system.},
note = {PMID: 27642675},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stojanović Ljiljana; Bai Shuming; Nagesh Jayashree; Izmaylov Artur F.; Crespo-Otero Rachel; Lischka Hans; Barbatti Mario
New Insights into the State Trapping of UV-Excited Thymine Article de journal
Dans: Molecules, vol. 21, no. 11, ARTICLE NUMBER = 1603, 2016, ISSN: 1420-3049.
@article{molecules21111603,
title = {New Insights into the State Trapping of UV-Excited Thymine},
author = {Stojanović Ljiljana and Bai Shuming and Nagesh Jayashree and Izmaylov Artur F. and Crespo-Otero Rachel and Lischka Hans and Barbatti Mario},
url = {http://www.mdpi.com/1420-3049/21/11/1603},
doi = {10.3390/molecules21111603},
issn = {1420-3049},
year = {2016},
date = {2016-01-01},
journal = {Molecules},
volume = {21},
number = {11, ARTICLE NUMBER = 1603},
abstract = {After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S1) or in the second (S2) excited states. In the present study, a nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S2 is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO π bond in S2.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ljiljana Stojanović; Abdulrahman O. Alyoubi; Saadullah G. Aziz; Rifaat H. Hilal; Mario Barbatti
UV excitations of halons Article de journal
Dans: The Journal of Chemical Physics, vol. 145, no. 18, p. 184306, 2016.
@article{doi:10.1063/1.4967170,
title = {UV excitations of halons},
author = {Ljiljana Stojanović and Abdulrahman O. Alyoubi and Saadullah G. Aziz and Rifaat H. Hilal and Mario Barbatti},
url = {http://dx.doi.org/10.1063/1.4967170},
doi = {10.1063/1.4967170},
year = {2016},
date = {2016-01-01},
journal = {The Journal of Chemical Physics},
volume = {145},
number = {18},
pages = {184306},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Achim Guckenberger; Marcel P. Schraml; Paul G. Chen; Marc Leonetti; Stephan Gekle
On the bending algorithms for soft objects in flows Article de journal
Dans: Computer Physics Communications, vol. 207, p. 1 - 23, 2016, ISSN: 0010-4655.
@article{Guckenberger20161,
title = {On the bending algorithms for soft objects in flows},
author = {Achim Guckenberger and Marcel P. Schraml and Paul G. Chen and Marc Leonetti and Stephan Gekle},
url = {http://www.sciencedirect.com/science/article/pii/S0010465516301072},
doi = {http://dx.doi.org/10.1016/j.cpc.2016.04.018},
issn = {0010-4655},
year = {2016},
date = {2016-01-01},
journal = {Computer Physics Communications},
volume = {207},
pages = {1 - 23},
abstract = {Abstract One of the most challenging aspects in the accurate simulation of three-dimensional soft objects such as vesicles or biological cells is the computation of membrane bending forces. The origin of this difficulty stems from the need to numerically evaluate a fourth order derivative on the discretized surface geometry. Here we investigate six different algorithms to compute membrane bending forces, including regularly used methods as well as novel ones. All are based on the same physical model (due to Canham and Helfrich) and start from a surface discretization with flat triangles. At the same time, they differ substantially in their numerical approach. We start by comparing the numerically obtained mean curvature, the Laplace–Beltrami operator of the mean curvature and finally the surface force density to analytical results for the discocyte resting shape of a red blood cell. We find that none of the considered algorithms converges to zero error at all nodes and that for some algorithms the error even diverges. There is furthermore a pronounced influence of the mesh structure: Discretizations with more irregular triangles and node connectivity present serious difficulties for most investigated methods. To assess the behavior of the algorithms in a realistic physical application, we investigate the deformation of an initially spherical capsule in a linear shear flow at small Reynolds numbers. To exclude any influence of the flow solver, two conceptually very different solvers are employed: the Lattice–Boltzmann and the Boundary Integral Method. Despite the largely different quality of the bending algorithms when applied to the static red blood cell, we find that in the actual flow situation most algorithms give consistent results for both hydrodynamic solvers. Even so, a short review of earlier works reveals a wide scattering of reported results for, e.g., the Taylor deformation parameter. Besides the presented application to biofluidic systems, the investigated algorithms are also of high relevance to the computer graphics and numerical mathematics communities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alexis Bottero; Paul Cristini; Dimitri Komatitsch; Mark Asch
An axisymmetric time-domain spectral-element method for full-wave simulations: Application to ocean acoustics Article de journal
Dans: The Journal of the Acoustical Society of America, vol. 140, no. 5, p. 3520-3530, 2016.
@article{doi:10.1121/1.4965964,
title = {An axisymmetric time-domain spectral-element method for full-wave simulations: Application to ocean acoustics},
author = {Alexis Bottero and Paul Cristini and Dimitri Komatitsch and Mark Asch},
url = {http://dx.doi.org/10.1121/1.4965964},
doi = {10.1121/1.4965964},
year = {2016},
date = {2016-01-01},
journal = {The Journal of the Acoustical Society of America},
volume = {140},
number = {5},
pages = {3520-3530},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
D Galassi; Patrick Tamain; Hugo Bufferand; G Ciraolo; Philippe Ghendrih; C Baudoin; C Colin; Nicolas Fedorczak; N Nace; E Serre
2016, (working paper or preprint).
@unpublished{galassi:hal-01398227b,
title = {Drive of parallel flows by turbulence and large-scale E x B transverse transport in divertor geometry},
author = { D Galassi and Patrick Tamain and Hugo Bufferand and G Ciraolo and Philippe Ghendrih and C Baudoin and C Colin and Nicolas Fedorczak and N Nace and E Serre},
url = {https://hal.archives-ouvertes.fr/hal-01398227},
year = {2016},
date = {2016-01-01},
abstract = {Poloidal asymmetries of parallel flows in edge plasmas are investigated by the 3D fluid turbulence code TOKAM3X. A diverted COMPASS-like magnetic equilibrium is used for simulations. Measurements and simulations of parallel Mach numbers are compared and exhibit good qualitative agreement. Small-scale turbulent transport is observed to dominate near the Low Field Side midplane, even though co-existing with significant large-scale cross-field fluxes. Despite the turbulent nature of the plasma in the divertor region, simulations show a low effectiveness of turbulence for the cross-field transport towards the Private Flux region. Nevertheless, a complex pattern of fluxes associated to the average field components, are found to cross the separatrix in the divertor region. Large-scale and small-scale turbulent E × B transport, along with the grad(B) drift, drive the asymmetries in parallel flows. A semi-analytical model based on mass and parallel momentum balances allows one to evaluate the poloidal drifts effects on the asymmetry pattern. As in experiments, a reversed B_T simulation provides one a way to separate self-consistently the effects of turbulent transport and the large-scale flows, that must reverse for a reversed field. The large-scale contribution is found to be responsible for typically the 50% of the effect on the Mach number, evaluated at the top of the machine. The presented picture shows a complex interplay between drifts and turbulence, underlining the necessity of a global approach in the edge plasma modelling including the self-consistent turbulence description. },
note = {working paper or preprint},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
2015
Dominique Eckert, Mathilde Jauzac, HuanYuan Shan, Jean-Paul Kneib, Thomas Erben, Holger Israel, Eric Jullo, Matthias Klein, Richard Massey, Johan Richard & Céline Tchernin
Warm–hot baryons comprise 5–10 per cent of filaments in the cosmic web Article de journal
Dans: Nature, no. 528, p. 105–107, 2015.
@article{Eckert2015,
title = {Warm–hot baryons comprise 5–10 per cent of filaments in the cosmic web},
author = { Dominique Eckert, Mathilde Jauzac, HuanYuan Shan, Jean-Paul Kneib, Thomas Erben, Holger Israel, Eric Jullo, Matthias Klein, Richard Massey, Johan Richard & Céline Tchernin},
url = {http://www.nature.com/nature/journal/v528/n7580/full/nature16058.html#access},
doi = {doi:10.1038/nature16058},
year = {2015},
date = {2015-12-03},
journal = {Nature},
number = {528},
pages = { 105–107},
abstract = {Observations of the cosmic microwave background indicate that baryons account for 5 per cent of the Universe’s total energy content1. In the local Universe, the census of all observed baryons falls short of this estimate by a factor of two2, 3. Cosmological simulations indicate that the missing baryons have not condensed into virialized haloes, but reside throughout the filaments of the cosmic web (where matter density is larger than average) as a low-density plasma at temperatures of 105−107 kelvin, known as the warm–hot intergalactic medium3, 4, 5, 6. There have been previous claims of the detection of warm–hot baryons along the line of sight to distant blazars7, 8, 9, 10 and of hot gas between interacting clusters11, 12, 13, 14. These observations were, however, unable to trace the large-scale filamentary structure, or to estimate the total amount of warm–hot baryons in a representative volume of the Universe. Here we report X-ray observations of filamentary structures of gas at 107 kelvin associated with the galaxy cluster Abell 2744. Previous observations of this cluster15 were unable to resolve and remove coincidental X-ray point sources. After subtracting these, we find hot gas structures that are coherent over scales of 8 megaparsecs. The filaments coincide with over-densities of galaxies and dark matter, with 5–10 per cent of their mass in baryonic gas. This gas has been heated up by the cluster’s gravitational pull and is now feeding its core. Our findings strengthen evidence for a picture of the Universe in which a large fraction of the missing baryons reside in the filaments of the cosmic web.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O. Bessonov
Highly Parallel Multigrid Solvers for Multicore and Manycore Processors. Article de journal
Dans: 2015.
@article{Bessonov2015b,
title = {Highly Parallel Multigrid Solvers for Multicore and Manycore Processors.},
author = {O. Bessonov},
url = {href="http://link.springer.com/chapter/10.1007/978-3-319-21909-7_2},
doi = {10.1007/978-3-319-21909-7_2},
year = {2015},
date = {2015-07-25},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ferraro, D.; Rech, J.; Jonckheere, T.; Martin, T.
Single quasiparticle and electron emitter in the fractional quantum Hall regime Article de journal
Dans: Phys. Rev. B, vol. 91, p. 205409, 2015.
@article{PhysRevB.91.205409,
title = {Single quasiparticle and electron emitter in the fractional quantum Hall regime},
author = {Ferraro, D. and Rech, J. and Jonckheere, T. and Martin, T.},
url = {http://link.aps.org/doi/10.1103/PhysRevB.91.205409},
doi = {10.1103/PhysRevB.91.205409},
year = {2015},
date = {2015-05-01},
journal = {Phys. Rev. B},
volume = {91},
pages = {205409},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A. Pivano; Voicu O. Dolocan
3D versus 2D domain wall interaction in ideal and rough nanowires Article de journal
Dans: Journal of Magnetism and Magnetic Materials, vol. 393, p. 334 - 340, 2015, ISSN: 0304-8853.
@article{Pivano2015334,
title = {3D versus 2D domain wall interaction in ideal and rough nanowires},
author = {A. Pivano and Voicu O. Dolocan},
url = {http://www.sciencedirect.com/science/article/pii/S0304885315302018},
doi = {http://dx.doi.org/10.1016/j.jmmm.2015.05.083},
issn = {0304-8853},
year = {2015},
date = {2015-01-01},
journal = {Journal of Magnetism and Magnetic Materials},
volume = {393},
pages = {334 - 340},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bessonov, O. A.
Convective interactions and flow stability in the czochralskimodel in the case of crystal rotation Article de journal
Dans: Fluid Dynamics, vol. 50, no. 3, p. 351–360, 2015, ISSN: 1573-8507.
@article{Bessonov2015,
title = {Convective interactions and flow stability in the czochralskimodel in the case of crystal rotation},
author = {Bessonov, O. A.},
url = {http://dx.doi.org/10.1134/S0015462815030059},
doi = {10.1134/S0015462815030059},
issn = {1573-8507},
year = {2015},
date = {2015-01-01},
journal = {Fluid Dynamics},
volume = {50},
number = {3},
pages = {351--360},
abstract = {The results of a numerical investigation of the crystal rotation effect on the flow stability are presented on a wide Prandtl number (Pr) range. For low Pr the regimes with an elevated stability threshold are determined and the mechanisms of the loss of stability, as the critical values of the Grashof number (Gr) and the rotation velocity are exceeded, are considered. For medium and high Pr the tables of flow regimes are given, the special features of stable nonaxisymmetric helical flows are considered, and the zones of partial flow stabilization are established.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jung, J.; Yi, X.; Huang, G.; Calvez, G.; Daiguebonne, C.; Guillou, O.; Cador, O.; Caneschi, A.; Roisnel, T.; Le Guennic, B.; Bernot, K.
Analysis of the electrostatics in DyIII single-molecule magnets: the case study of Dy(Murex)3 Article de journal
Dans: Dalton Trans., vol. 44, p. 18270-18275, 2015.
@article{C5DT03345D,
title = {Analysis of the electrostatics in DyIII single-molecule magnets: the case study of Dy(Murex)3},
author = {Jung, J. and Yi, X. and Huang, G. and Calvez, G. and Daiguebonne, C. and Guillou, O. and Cador, O. and Caneschi, A. and Roisnel, T. and Le Guennic, B. and Bernot, K.},
url = {http://dx.doi.org/10.1039/C5DT03345D},
doi = {10.1039/C5DT03345D},
year = {2015},
date = {2015-01-01},
journal = {Dalton Trans.},
volume = {44},
pages = {18270-18275},
publisher = {The Royal Society of Chemistry},
abstract = {A DyIII-based single-molecule magnet is reported. Ab initio calculations highlight that molecular symmetry plays a predominant role over site symmetry in determining the shape and orientation of DyIII magnetic anisotropy. Moreover the dipolar component of the electrostatic potential created by the surrounding ligands is shown to be the driving force of its magnetic behaviour.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Manas, P.; Camenen, Y.; Benkadda, S.; Hornsby, W. A.; Peeters, A. G.
Enhanced stabilisation of trapped electron modes by collisional energy scattering in tokamaks Article de journal
Dans: Physics of Plasmas, vol. 22, no. 6, 2015.
@article{:/content/aip/journal/pop/22/6/10.1063/1.4922754,
title = {Enhanced stabilisation of trapped electron modes by collisional energy scattering in tokamaks},
author = {Manas, P. and Camenen, Y. and Benkadda, S. and Hornsby, W. A. and Peeters, A. G.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/6/10.1063/1.4922754},
doi = {http://dx.doi.org/10.1063/1.4922754},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Poyé, A.; Agullo, O.; Muraglia, M.; Garbet, X.; Benkadda, S.; Sen, A.; Dubuit, N.
Generation of a magnetic island by edge turbulence in tokamak plasmas Article de journal
Dans: Physics of Plasmas, vol. 22, no. 3, 2015.
@article{:/content/aip/journal/pop/22/3/10.1063/1.4916580,
title = {Generation of a magnetic island by edge turbulence in tokamak plasmas},
author = {Poyé, A. and Agullo, O. and Muraglia, M. and Garbet, X. and Benkadda, S. and Sen, A. and Dubuit, N.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/3/10.1063/1.4916580},
doi = {http://dx.doi.org/10.1063/1.4916580},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thomas Engels; Dmitry Kolomenskiy; Kai Schneider; Jörn Sesterhenn
Numerical simulation of fluid–structure interaction with the volume penalization method Article de journal
Dans: Journal of Computational Physics, vol. 281, p. 96 - 115, 2015, ISSN: 0021-9991.
@article{Engels201596,
title = {Numerical simulation of fluid–structure interaction with the volume penalization method},
author = {Thomas Engels and Dmitry Kolomenskiy and Kai Schneider and Jörn Sesterhenn},
url = {http://www.sciencedirect.com/science/article/pii/S0021999114006792},
doi = {http://dx.doi.org/10.1016/j.jcp.2014.10.005},
issn = {0021-9991},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computational Physics},
volume = {281},
pages = {96 - 115},
abstract = {Abstract We present a novel scheme for the numerical simulation of fluid–structure interaction problems. It extends the volume penalization method, a member of the family of immersed boundary methods, to take into account flexible obstacles. We show how the introduction of a smoothing layer, physically interpreted as surface roughness, allows for arbitrary motion of the deformable obstacle. The approach is carefully validated and good agreement with various results in the literature is found. A simple one-dimensional solid model is derived, capable of modeling arbitrarily large deformations and imposed motion at the leading edge, as it is required for the simulation of simplified models for insect flight. The model error is shown to be small, while the one-dimensional character of the model features a reasonably easy implementation. The coupled fluid–solid interaction solver is shown not to introduce artificial energy in the numerical coupling, and validated using a widely used benchmark. We conclude with the application of our method to models for insect flight and study the propulsive efficiency of one and two wing sections.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicolas Foos; Corinne Maurel-Zaffran; María Jesús Maté; Renaud Vincentelli; Matthieu Hainaut; Hélène Berenger; Jacques Pradel; Andrew J. Saurin; Miguel Ortiz-Lombardía; Yacine Graba
A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/PBC Interaction Mode Article de journal
Dans: Structure, vol. 23, no. 2, p. 270 - 279, 2015, ISSN: 0969-2126.
@article{Foos2015270,
title = {A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/PBC Interaction Mode},
author = {Nicolas Foos and Corinne Maurel-Zaffran and María Jesús Maté and Renaud Vincentelli and Matthieu Hainaut and Hélène Berenger and Jacques Pradel and Andrew J. Saurin and Miguel Ortiz-Lombardía and Yacine Graba},
url = {http://www.sciencedirect.com/science/article/pii/S0969212614004201},
doi = {http://dx.doi.org/10.1016/j.str.2014.12.011},
issn = {0969-2126},
year = {2015},
date = {2015-01-01},
journal = {Structure},
volume = {23},
number = {2},
pages = {270 - 279},
abstract = {Summary The patterning function of Hox proteins relies on assembling protein complexes with PBC proteins, which often involves a protein motif found in most Hox proteins, the so-called Hexapeptide (HX). Hox/PBC complexes likely gained functional diversity by acquiring additional modes of interaction. Here, we structurally characterize the first HX alternative interaction mode based on the paralogue-specific UbdA motif and further functionally validate structure-based predictions. The UbdA motif folds as a flexible extension of the homeodomain recognition helix and defines Hox/PBC contacts that occur, compared with those mediated by the HX motif, on the opposing side of the DNA double helix. This provides a new molecular facet to Hox/PBC complex assembly and suggests possible mechanisms for the diversification of Hox protein function.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F. Golay; M. Ersoy; L. Yushchenko; D. Sous
Block-based adaptive mesh refinement scheme using numerical density of entropy production for three-dimensional two-fluid flows Article de journal
Dans: International Journal of Computational Fluid Dynamics, vol. 29, no. 1, p. 67-81, 2015.
@article{doi:10.1080/10618562.2015.1012161,
title = {Block-based adaptive mesh refinement scheme using numerical density of entropy production for three-dimensional two-fluid flows},
author = {F. Golay and M. Ersoy and L. Yushchenko and D. Sous},
url = {http://dx.doi.org/10.1080/10618562.2015.1012161},
doi = {10.1080/10618562.2015.1012161},
year = {2015},
date = {2015-01-01},
journal = {International Journal of Computational Fluid Dynamics},
volume = {29},
number = {1},
pages = {67-81},
abstract = {In this work, we present a fast and parallel finite volume scheme on unstructured meshes applied to complex fluid flow. The mathematical model is based on a three-dimensional compressible low Mach two-phase flows model, combined with a linearised ‘artificial pressure’ law. This hyperbolic system of conservation laws allows an explicit scheme, improved by a block-based adaptive mesh refinement scheme. Following a previous one-dimensional work, the useful numerical density of entropy production is used as mesh refinement criterion. Moreover, the computational time is preserved using a local time-stepping method. Finally, we show through several test cases the efficiency of the present scheme on two- and three-dimensional dam-break problems over an obstacle.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Favier, B.; Grannan, A. M.; Le Bars, M.; Aurnou, J. M.
Generation and maintenance of bulk turbulence by libration-driven elliptical instability Article de journal
Dans: Physics of Fluids, vol. 27, no. 6, 2015.
@article{:/content/aip/journal/pof2/27/6/10.1063/1.4922085,
title = {Generation and maintenance of bulk turbulence by libration-driven elliptical instability},
author = {Favier, B. and Grannan, A. M. and Le Bars, M. and Aurnou, J. M.},
url = {http://scitation.aip.org/content/aip/journal/pof2/27/6/10.1063/1.4922085},
doi = {http://dx.doi.org/10.1063/1.4922085},
year = {2015},
date = {2015-01-01},
journal = {Physics of Fluids},
volume = {27},
number = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
de Loubens,C.; Deschamps,J.; Boedec,G.; Leonetti,M.
Stretching of capsules in an elongation flow, a route to constitutive law Article de journal
Dans: Journal of Fluid Mechanics, vol. 767, p. R3 (11 pages) doi = 10.1017/jfm.2015.69, 2015, ISSN: 1469-7645.
@article{FLM:9568478,
title = {Stretching of capsules in an elongation flow, a route to constitutive law},
author = {de Loubens,C. and Deschamps,J. and Boedec,G. and Leonetti,M.},
url = {http://journals.cambridge.org/article_S0022112015000695},
issn = {1469-7645},
year = {2015},
date = {2015-01-01},
journal = {Journal of Fluid Mechanics},
volume = {767},
pages = {R3 (11 pages) doi = 10.1017/jfm.2015.69},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mollitor, Pol; Nezri, Emmanuel; Teyssier, Romain
Baryonic and dark matter distribution in cosmological simulations of spiral galaxies Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 447, no. 2, p. 1353-1369, 2015.
@article{Mollitor21022015,
title = {Baryonic and dark matter distribution in cosmological simulations of spiral galaxies},
author = {Mollitor, Pol and Nezri, Emmanuel and Teyssier, Romain},
url = {http://mnras.oxfordjournals.org/content/447/2/1353.abstract},
doi = {10.1093/mnras/stu2466},
year = {2015},
date = {2015-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {447},
number = {2},
pages = {1353-1369},
abstract = {We study three cosmological hydrodynamical simulations of Milky Way(MW)-sized haloes including a comparison with the dark matter(DM)-only counterparts. We find one of our simulated galaxies with interesting MW-like features. Thanks to a consistently tuned star formation rate and supernovae feedback we obtain an extended disc and a flat rotation curve with a satisfying circular velocity and a reasonable DM density in the solar neighbourhood. Mimicking observational methods, we re-derive the stellar mass and obtain stellar-to-halo mass ratios reduced by more than 50uc0u8201 peru8201 cent. We show the interaction between the baryons and the DM which is first contracted by star formation and then cored by feedback processes. Indeed, we report an unprecedentedly observed effect in the DM density profile consisting of a central core combined with an adiabatic contraction at larger galactic radii. The cores obtained are typically u8764 5u8201 kpc large. Moreover, this also impacts the DM density at the solar radius. In our simulation resembling most to the MW, the density is raised from 0.23 GeV'a0cmu8722 3 in the DM only run to 0.36 GeV'a0cmu8722 3 (spherical shell) or 0.54 GeV'a0cmu8722 3 (circular ring) in the hydrodynamical run. Studying the subhaloes, the DM within luminous satellites is also affected by baryonic processes and exhibits cored profiles whereas dark satellites are cuspy. We find a shift in mass compared to DM-only simulations and obtain, for haloes in the lower MW mass range, a distribution of luminous satellites comparable to the MW spheroidal dwarf galaxies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Y. Marandet; H. Bufferand; J. Bucalossi; G. Ciraolo; S.W. Lisgo; E. Tsitrone
Assessment of tungsten sources in the edge plasma of WEST Article de journal
Dans: Journal of Nuclear Materials, vol. 463, p. 629 - 633, 2015, ISSN: 0022-3115, (PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014).
@article{Marandet2015629,
title = {Assessment of tungsten sources in the edge plasma of WEST},
author = {Y. Marandet and H. Bufferand and J. Bucalossi and G. Ciraolo and S.W. Lisgo and E. Tsitrone},
url = {http://www.sciencedirect.com/science/article/pii/S0022311514008216},
doi = {http://dx.doi.org/10.1016/j.jnucmat.2014.11.030},
issn = {0022-3115},
year = {2015},
date = {2015-01-01},
journal = {Journal of Nuclear Materials},
volume = {463},
pages = {629 - 633},
abstract = {Abstract The WEST project, an on-going upgrade of Tore Supra, aims at providing the capability to test ITER relevant tungsten (W) divertor components under realistic tokamak plasma conditions. This work provides an assessment of tungsten sources in the edge plasma of WEST. The focus is on the contribution of the W coated pumping baffle. The modelling is performed with the Soledge2D-EIRENE transport code, which can include structures like the baffle explicitly in the computational grid. Gross erosion sources and prompt redeposition are then discussed in the light of recent new results.},
note = {PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
H. Bufferand; J. Bucalossi; G. Ciraolo; N. Fedorczak; P. Genesio; Ph. Ghendrih; J. Gunn; Y. Marandet; C. Martin; N. Mellet; E. Serre; P. Tamain
Comparison on heat flux deposition between carbon and tungsten wall – Investigations on energy recycling Article de journal
Dans: Journal of Nuclear Materials, vol. 463, p. 420 - 423, 2015, ISSN: 0022-3115, (PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014).
@article{Bufferand2015420,
title = {Comparison on heat flux deposition between carbon and tungsten wall – Investigations on energy recycling},
author = {H. Bufferand and J. Bucalossi and G. Ciraolo and N. Fedorczak and P. Genesio and Ph. Ghendrih and J. Gunn and Y. Marandet and C. Martin and N. Mellet and E. Serre and P. Tamain},
url = {http://www.sciencedirect.com/science/article/pii/S0022311514006515},
doi = {http://dx.doi.org/10.1016/j.jnucmat.2014.09.061},
issn = {0022-3115},
year = {2015},
date = {2015-01-01},
journal = {Journal of Nuclear Materials},
volume = {463},
pages = {420 - 423},
abstract = {Abstract The influence of the plasma facing components material on the scrape-off layer plasma is investigated. In particular, the energy recycling is found to be more pronounced for tungsten wall compared with carbon wall. Edge plasma simulations performed with the transport code SOLEDGE2D-EIRENE show that this enhanced energy recycling in the tungsten case leads to an increase of the scrape-off layer temperature. Moreover, the energy recycling depends on the ion angle of incidence with the wall. A PIC code has been used to model the ion acceleration in the magnetic pre-sheath and determine the later angle of incidence. These simulations show that ions mostly impact the wall with rather shallow incident angles leading to a further increase of the energy recycling.},
note = {PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Colin, Clothilde; Tamain, Patrick; Schwander, Frederic; Serre, Eric; Bufferand, Hugo; Ciraolo, Guido; Fedorczak, Nicolas; Ghendrih, Philippe
Impact of the plasma-wall contact position on edge turbulent transport and poloidal asymmetries in 3D global turbulence simulations Article de journal
Dans: Journal of Nuclear Materials, vol. 463, p. 654-658, 2015.
@article{colin:hal-01225200,
title = {Impact of the plasma-wall contact position on edge turbulent transport and poloidal asymmetries in 3D global turbulence simulations},
author = {Colin, Clothilde and Tamain, Patrick and Schwander, Frederic and Serre, Eric and Bufferand, Hugo and Ciraolo, Guido and Fedorczak, Nicolas and Ghendrih, Philippe},
url = {https://hal.archives-ouvertes.fr/hal-01225200},
doi = {10.1016/j.jnucmat.2015.01.019},
year = {2015},
date = {2015-01-01},
journal = {Journal of Nuclear Materials},
volume = {463},
pages = {654-658},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
P Tamain; Ph Ghendrih; H Bufferand; G Ciraolo; C Colin; N Fedorczak; N Nace; F Schwander; E Serre
Multi-scale self-organisation of edge plasma turbulent transport in 3D global simulations Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 57, no. 5, p. 054014, 2015.
@article{0741-3335-57-5-054014,
title = {Multi-scale self-organisation of edge plasma turbulent transport in 3D global simulations},
author = {P Tamain and Ph Ghendrih and H Bufferand and G Ciraolo and C Colin and N Fedorczak and N Nace and F Schwander and E Serre},
url = {http://stacks.iop.org/0741-3335/57/i=5/a=054014},
year = {2015},
date = {2015-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {57},
number = {5},
pages = {054014},
abstract = {The 3D global edge turbulence code TOKAM3X is used to study the properties of edge particle turbulent transport in circular limited plasmas, including both closed and open flux surfaces. Turbulence is driven by an incoming particle flux from the core plasma and no scale separation between the equilibrium and the fluctuations is assumed. Simulations show the existence of a complex self-organization of turbulence transport coupling scales ranging from a few Larmor radii up to the machine scale. Particle transport is largely dominated by small scale turbulence with fluctuations forming quasi field-aligned filaments. Radial particle transport is intermittent and associated with the propagation of coherent structures on long distances via avalanches. Long range correlations are also found in the poloidal and toroidal direction. The statistical properties of fluctuations vary with the radial and poloidal directions, with larger fluctuation levels and intermittency found in the outboard scrape-off layer (SOL). Radial turbulent transport is strongly ballooned, with 90% of the flux at the separatrix flowing through the low-field side. One of the main consequences is the existence of quasi-sonic asymmetric parallel flows driving a net rotation of the plasma. Simulations also show the spontaneous onset of an intermittent E × B rotation characterized by a larger shear at the separatrix. Strong correlation is found between the turbulent particle flux and the E × B flow shear in a phenomenology reminiscent of H-mode physics. The poloidal position of the limiter is a key player in the observed dynamics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Juan Magaña; V. Motta; Vi´ctor H. Cárdenas; T. Verdugo; Eric Jullo
A Magnified Glance into the Dark Sector: Probing Cosmological Models with Strong Lensing in A1689 Article de journal
Dans: The Astrophysical Journal, vol. 813, no. 1, p. 69, 2015.
@article{0004-637X-813-1-69,
title = {A Magnified Glance into the Dark Sector: Probing Cosmological Models with Strong Lensing in A1689},
author = {Juan Magaña and V. Motta and Vi´ctor H. Cárdenas and T. Verdugo and Eric Jullo},
url = {http://stacks.iop.org/0004-637X/813/i=1/a=69},
year = {2015},
date = {2015-01-01},
journal = {The Astrophysical Journal},
volume = {813},
number = {1},
pages = {69},
abstract = {In this paper we constrain four alternative models to the late cosmic acceleration in the universe: Chevallier–Polarski–Linder (CPL), interacting dark energy (IDE), Ricci holographic dark energy (HDE), and modified polytropic Cardassian (MPC). Strong lensing (SL) images of background galaxies produced by the galaxy cluster Abell 1689 are used to test these models. To perform this analysis we modify the LENSTOOL lens modeling code. The value added by this probe is compared with other complementary probes: Type Ia supernovae (SN Ia), baryon acoustic oscillations (BAO), and cosmic microwave background (CMB). We found that the CPL constraints obtained for the SL data are consistent with those estimated using the other probes. The IDE constraints are consistent with the complementary bounds only if large errors in the SL measurements are considered. The Ricci HDE and MPC constraints are weak, but they are similar to the BAO, SN Ia, and CMB estimations. We also compute the figure of merit as a tool to quantify the goodness of fit of the data. Our results suggest that the SL method provides statistically significant constraints on the CPL parameters but is weak for those of the other models. Finally, we show that the use of the SL measurements in galaxy clusters is a promising and powerful technique to constrain cosmological models. The advantage of this method is that cosmological parameters are estimated by modeling the SL features for each underlying cosmology. These estimations could be further improved by SL constraints coming from other galaxy clusters.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jauzac, M.,; Richard, J.,; Jullo, E.,; Cl'ement, B.,; Limousin, M.,; Kneib, J.-P.,; Ebeling, H.,; Natarajan, P.,; Rodney, S.,; Atek, H.,; Massey, R.,; Eckert, D.,; Egami, E.,; Rexroth, M.,
Hubble Frontier Fields: a high-precision strong-lensing analysis of the massive galaxy cluster Abell 2744 using ˜180 multiple images Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 452, p. 1437 - 1446, 2015.
@article{jauzac:hal-01183914,
title = {Hubble Frontier Fields: a high-precision strong-lensing analysis of the massive galaxy cluster Abell 2744 using ˜180 multiple images},
author = {Jauzac, M., and Richard, J., and Jullo, E., and Cl'ement, B., and Limousin, M., and Kneib, J.-P., and Ebeling, H., and Natarajan, P., and Rodney, S., and Atek, H., and Massey, R., and Eckert, D., and Egami, E., and Rexroth, M.,},
url = {https://hal.archives-ouvertes.fr/hal-01183914},
year = {2015},
date = {2015-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {452},
pages = {1437 - 1446},
publisher = {Oxford University Press (OUP)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jauzac, Mathilde; Jullo, Eric; Eckert, Dominique; Ebeling, Harald; Richard, Johan; Limousin, Marceau; Atek, Hakim; Kneib, Jean-Paul; Clément, Benjamin; Egami, Eiichi; Harvey, David; Knowles, Kenda; Massey, Richard; Natarajan, Priyamvada; Neichel, Benoît; Rexroth, M.
Hubble Frontier Fields: the geometry and dynamics of the massive galaxy cluster merger MACSJ0416.1−2403 Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 446, no. 4, p. 4132-4147, 2015.
@article{Jauzac01022015,
title = {Hubble Frontier Fields: the geometry and dynamics of the massive galaxy cluster merger MACSJ0416.1−2403},
author = {Jauzac, Mathilde and Jullo, Eric and Eckert, Dominique and Ebeling, Harald and Richard, Johan and Limousin, Marceau and Atek, Hakim and Kneib, Jean-Paul and Clément, Benjamin and Egami, Eiichi and Harvey, David and Knowles, Kenda and Massey, Richard and Natarajan, Priyamvada and Neichel, Benoît and Rexroth, M.},
url = {http://mnras.oxfordjournals.org/content/446/4/4132.abstract},
doi = {10.1093/mnras/stu2425},
year = {2015},
date = {2015-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {446},
number = {4},
pages = {4132-4147},
abstract = {We use a joint optical/X-ray analysis to constrain the geometry and history of the ongoing merging event in the massive galaxy cluster MACSJ0416.1−2403 (z = 0.397). Our investigation of cluster substructure rests primarily on a combined strong- and weak-lensing mass reconstruction based on the deep, high-resolution images obtained for the Hubble Frontier Fields initiative. To reveal the system's dynamics, we complement this lensing analysis with a study of the intracluster gas using shallow Chandra data, and a three-dimensional model of the distribution and motions of cluster galaxies derived from over 100 spectroscopic redshifts. The multiscale grid model obtained from our combined lensing analysis extends the high-precision strong-lensing mass reconstruction recently performed to cluster-centric distances of almost 1 Mpc. Our analysis detects the two well-known mass concentrations in the cluster core. A pronounced offset between collisional and collisionless matter is only observed for the SW cluster component, while excellent alignment is found for the NE cluster. Both the lensing analysis and the distribution of cluster light strongly suggest the presence of a third massive structure, almost 2 arcmin SW of the cluster centre. Since no X-ray emission is detected in this region, we conclude that this structure is non-virialized and speculate that it might be part of a large-scale filament almost aligned with our line of sight. Combining all evidence from the distribution of dark and luminous matter, we propose two alternative scenarios for the trajectories of the components of MACSJ0416.1−2403. Upcoming deep X-ray observations that allow the detection of shock fronts, cold cores, and sloshing gas (all key diagnostics for studies of cluster collisions) will allow us to test, and distinguish between these two scenarios.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Marc Medale; Bruno Cochelin
High performance computations of steady-state bifurcations in 3D incompressible fluid flows by Asymptotic Numerical Method Article de journal
Dans: Journal of Computational Physics, vol. 299, p. 581 - 596, 2015, ISSN: 0021-9991.
@article{Medale2015581,
title = {High performance computations of steady-state bifurcations in 3D incompressible fluid flows by Asymptotic Numerical Method},
author = {Marc Medale and Bruno Cochelin},
url = {http://www.sciencedirect.com/science/article/pii/S0021999115004660},
doi = {http://dx.doi.org/10.1016/j.jcp.2015.07.021},
issn = {0021-9991},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computational Physics},
volume = {299},
pages = {581 - 596},
abstract = {Abstract This paper presents a powerful numerical model that implements the Asymptotic Numerical Method to compute 3D steady-state incompressible fluid flow solutions. This continuation algorithm enables to explore branches of steady-state solutions, stable or unstable, to accurately determine any simple steady-state bifurcation points and their emanating bifurcated branches. The powerfulness of the model stands on an optimal step length continuation thanks to the combination of power series analysis in the framework of ANM along with an efficient parallel implementation of the resulting algorithm on high performance computers. The outcome of this approach is demonstrated throughout 3D incompressible fluid flows inside a sudden expansion channel (expansion ratio E = 3 , cross-section aspect ratio 10 ≤ B ≤ 20 ). We have computed for the first time up to four steady symmetry breaking (pitchfork) bifurcations together with their associated bifurcated branches. The main characteristic of this 3D symmetric expansion configuration is that for a given cross-section aspect ratio the first bifurcation mode induces a top–bottom asymmetry, as in the 2D case, whereas the subsequent ones modulate the former in the span-wise direction with increasing wave numbers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Medale, M.; Cerisier, P.
Influence of container shape and size on surface-tension-driven Bénard convection Article de journal
Dans: The European Physical Journal Special Topics, vol. 224, no. 2, p. 217-227, 2015.
@article{Medale2015,
title = {Influence of container shape and size on surface-tension-driven Bénard convection},
author = {Medale, M. and Cerisier, P.},
doi = {10.1140/epjst/e2015-02354-6},
year = {2015},
date = {2015-01-01},
journal = {The European Physical Journal Special Topics},
volume = {224},
number = {2},
pages = {217-227},
abstract = {The aim of this study is to investigate the influence of the container size and shape on the main fluid flow characteristics of Surface-Tension-Driven Bénard Convection. Computations have been performed for high Prandtl number fluids and realistic boundary conditions in various configurations either at steady state when it exists or unsteady one for Ma c ≤ Ma ≤ 2.5 Ma c . The threshold value, its associated pattern and secondary bifurcation one are presented for each configuration. For very small aspect ratios, it turns out that the threshold value is determined by the friction coefficient whereas for medium size aspect ratios both size and shape enters the game in a more subtle way. Some containers have been found to induce a quasi-perfect hexagonal pattern in their core region provided they satisfy shape and size compatibility conditions. Otherwise, dynamical regimes may appear even close to the threshold so their peculiar characteristics have been reported and analyzed as they seem to be intrinsic to small aspect ratio configurations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huix-Rotllant, Miquel; Dumont, Elise; Ferré, Nicolas; Monari, Antonio
Photophysics of Acetophenone Interacting with DNA: Why the Road to Photosensitization is Open Article de journal
Dans: Photochemistry and Photobiology, vol. 91, no. 2, p. 323–330, 2015, ISSN: 1751-1097.
@article{PHP:PHP12395,
title = {Photophysics of Acetophenone Interacting with DNA: Why the Road to Photosensitization is Open},
author = {Huix-Rotllant, Miquel and Dumont, Elise and Ferré, Nicolas and Monari, Antonio},
url = {http://dx.doi.org/10.1111/php.12395},
doi = {10.1111/php.12395},
issn = {1751-1097},
year = {2015},
date = {2015-01-01},
journal = {Photochemistry and Photobiology},
volume = {91},
number = {2},
pages = {323--330},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Engels, T.; Kolomenskiy, D.; Schneider, K.; Sesterhenn, J.
FluSI: A novel parallel simulation tool for flapping insect flight using a Fourier method with volume penalization Article de journal
Dans: ArXiv e-prints, 2015.
@article{2015arXiv150606513E,
title = {FluSI: A novel parallel simulation tool for flapping insect flight using a Fourier method with volume penalization},
author = {Engels, T. and Kolomenskiy, D. and Schneider, K. and Sesterhenn, J.},
year = {2015},
date = {2015-01-01},
journal = {ArXiv e-prints},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Drouot, T.; Gravier, E.; Reveille, T.; Sarrat, M.; Collard, M.; Bertrand, P.; Cartier-Michaud, T.; Ghendrih, P.; Sarazin, Y.; Garbet, X.
Global gyrokinetic simulations of trapped-electron mode and trapped-ion mode microturbulence Article de journal
Dans: Physics of Plasmas, vol. 22, no. 8, 2015.
@article{:/content/aip/journal/pop/22/8/10.1063/1.4927920,
title = {Global gyrokinetic simulations of trapped-electron mode and trapped-ion mode microturbulence},
author = {Drouot, T. and Gravier, E. and Reveille, T. and Sarrat, M. and Collard, M. and Bertrand, P. and Cartier-Michaud, T. and Ghendrih, P. and Sarazin, Y. and Garbet, X.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/8/10.1063/1.4927920},
doi = {http://dx.doi.org/10.1063/1.4927920},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Drouot, T.; Gravier, E.; Reveille, T.; Collard, M.
Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities Article de journal
Dans: Physics of Plasmas, vol. 22, no. 10, 2015.
@article{:/content/aip/journal/pop/22/10/10.1063/1.4933358,
title = {Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities},
author = {Drouot, T. and Gravier, E. and Reveille, T. and Collard, M.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/10/10.1063/1.4933358},
doi = {http://dx.doi.org/10.1063/1.4933358},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Palermo, F.; Garbet, X.; Ghizzo, A.; Cartier-Michaud, T.; Ghendrih, P.; Grandgirard, V.; Sarazin, Y.
Shear flow instabilities induced by trapped ion modes in collisionless temperature gradient turbulence Article de journal
Dans: Physics of Plasmas, vol. 22, no. 4, 2015.
@article{:/content/aip/journal/pop/22/4/10.1063/1.4916770,
title = {Shear flow instabilities induced by trapped ion modes in collisionless temperature gradient turbulence},
author = {Palermo, F. and Garbet, X. and Ghizzo, A. and Cartier-Michaud, T. and Ghendrih, P. and Grandgirard, V. and Sarazin, Y.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/4/10.1063/1.4916770},
doi = {http://dx.doi.org/10.1063/1.4916770},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ghizzo, A.; Palermo, F.
Shear-flow trapped-ion-mode interaction revisited. I. Influence of low-frequency zonal flow on ion-temperature-gradient driven turbulence Article de journal
Dans: Physics of Plasmas, vol. 22, no. 8, 2015.
@article{:/content/aip/journal/pop/22/8/10.1063/1.4928102,
title = {Shear-flow trapped-ion-mode interaction revisited. I. Influence of low-frequency zonal flow on ion-temperature-gradient driven turbulence},
author = {Ghizzo, A. and Palermo, F.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/8/10.1063/1.4928102},
doi = {http://dx.doi.org/10.1063/1.4928102},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ghizzo, A.; Palermo, F.
Shear-flow trapped-ion-mode interaction revisited. II. Intermittent transport associated with low-frequency zonal flow dynamics Article de journal
Dans: Physics of Plasmas, vol. 22, no. 8, 2015.
@article{:/content/aip/journal/pop/22/8/10.1063/1.4928103,
title = {Shear-flow trapped-ion-mode interaction revisited. II. Intermittent transport associated with low-frequency zonal flow dynamics},
author = {Ghizzo, A. and Palermo, F.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/8/10.1063/1.4928103},
doi = {http://dx.doi.org/10.1063/1.4928103},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Richard MARCER et Kevin PONS et Camille JOURNEAU et Fr'e9d'e9ric GOLAY
SHORT NOTE: Validation of CFD models for tsunami simulation. TANDEM Project Article de journal
Dans: Revue Paralia, vol. 8, no. 0, 2015, ISSN: 1760-8716.
@article{RPrevue-paralia.2015.n04,
title = {SHORT NOTE: Validation of CFD models for tsunami simulation. TANDEM Project},
author = {Richard MARCER et Kevin PONS et Camille JOURNEAU et Fr'e9d'e9ric GOLAY},
url = {http://www.paralia.fr/editions/index.php/revue/article/view/revue-paralia.2015.n04},
issn = {1760-8716},
year = {2015},
date = {2015-01-01},
journal = {Revue Paralia},
volume = {8},
number = {0},
abstract = {Into the frame of the TANDEM project (Tsunamis in the Atlantic and the English ChaNnel: Definition of the Effects through numerical Modeling) a first step of the study aims for Principia to qualify different 3D CFD (Computational Fluid Dynamics) models for the simulation of tsunamis. The EOLE code solves a 3D bi-fluid flow on multi-structures meshes coupled with a free surface tracking VOF model, whereas the EOLENS code is based on an interface capturing method using unstructured meshes. This paper presents some simulations / measurements comparisons for academic test cases of wave propagation and run-up. On the whole, the results are satisfactory showing the high potential of both codes to simulate tsunamis impact.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Romain Oguic; Stéphane Viazzo; Sébastien Poncet
A parallelized multidomain compact solver for incompressible turbulent flows in cylindrical geometries Article de journal
Dans: Journal of Computational Physics, vol. 300, p. 710 - 731, 2015, ISSN: 0021-9991.
@article{Oguic2015710,
title = {A parallelized multidomain compact solver for incompressible turbulent flows in cylindrical geometries},
author = {Romain Oguic and Stéphane Viazzo and Sébastien Poncet},
url = {http://www.sciencedirect.com/science/article/pii/S0021999115005203},
doi = {http://dx.doi.org/10.1016/j.jcp.2015.08.003},
issn = {0021-9991},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computational Physics},
volume = {300},
pages = {710 - 731},
abstract = {Abstract We present an efficient parallelized multidomain algorithm for solving the 3D Navier–Stokes equations in cylindrical geometries. The numerical method is based on fourth-order compact schemes in the two non-homogeneous directions and Fourier series expansion in the azimuthal direction. The temporal scheme is a second-order semi-implicit projection scheme leading to the solution of five Helmholtz/Poisson equations. To handle the singularity appearing at the axis in cylindrical coordinates, while being able to have a thinner or conversely a coarser mesh in this zone, parity conditions are imposed at r = 0 for each flow variable and azimuthal Fourier mode. To simulate flows in irregularly shaped cylindrical geometries and benefit from a hybrid OpenMP/MPI parallelization, an accurate perfectly free-divergence multidomain method based on the influence matrix technique is proposed. First, the accuracy of the present solver is checked by comparison with analytical solutions and the scalability is then evaluated. Simulations using the present code are then compared to reliable experimental and numerical results of the literature showing good quantitative agreements in the cases of the axisymmetric and 3D unsteady vortex breakdowns in a cylinder and turbulent pipe flow. Finally to show the capability of the algorithm to deal with more complex flows relevant of turbomachineries, the turbulent flow inside a simplified stage of High-Pressure compressor is considered.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F. Liu; G.T.A. Huijsmans; A. Loarte; A.M. Garofalo; W.M. Solomon; P.B. Snyder; M. Hoelzl; L. Zeng
Nonlinear MHD simulations of Quiescent H-mode plasmas in DIII-D Article de journal
Dans: Nuclear Fusion, vol. 55, no. 11, p. 113002, 2015.
@article{0029-5515-55-11-113002,
title = {Nonlinear MHD simulations of Quiescent H-mode plasmas in DIII-D},
author = {F. Liu and G.T.A. Huijsmans and A. Loarte and A.M. Garofalo and W.M. Solomon and P.B. Snyder and M. Hoelzl and L. Zeng},
url = {http://stacks.iop.org/0029-5515/55/i=11/a=113002},
year = {2015},
date = {2015-01-01},
journal = {Nuclear Fusion},
volume = {55},
number = {11},
pages = {113002},
abstract = {In the Quiescent H-mode (QH-mode) regime, the edge harmonic oscillation (EHO), thought to be a saturated kink-peeling mode (KPM) driven unstable by current and rotation, is found in experiment to provide sufficient stationary edge particle transport to avoid the periodic expulsion of particles and energy by edge localized modes (ELMs). In this paper, both linear and nonlinear MHD modelling of QH-mode plasmas from the DIII-D tokamak have been investigated to understand the mechanism leading to the appearance of the EHO in QH-mode plasmas. For the first time nonlinear MHD simulations with low-n modes both with ideal wall and resistive wall boundary conditions have been carried out with the 3D non-linear MHD code JOREK. The results show, in agreement with the original conjectures, that in the non-linear phase, kink peeling modes are the main unstable modes in QH-mode plasmas of DIII-D and that the kink-peeling modes saturate non-linearly leading to a 3D stationary state. The characteristics of the kink-peeling modes, in terms of mode structure and associated decrease of the edge plasma density associated with them, are in good agreement with experimental measurements of the EHO in DIII-D. The effect of plasma resistivity, the role of plasma parallel rotation as well as the effect of the conductivity of the vacuum vessel wall on the destabilization and saturation of kink-peeling modes have been evaluated for experimental QH-mode plasma conditions in DIII-D.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A. Loarte; F. Liu; G.T.A. Huijsmans; A.S. Kukushkin; R.A. Pitts
MHD stability of the ITER pedestal and SOL plasma and its influence on the heat flux width Article de journal
Dans: Journal of Nuclear Materials, vol. 463, p. 401 - 405, 2015, ISSN: 0022-3115, (PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014).
@article{Loarte2015401,
title = {MHD stability of the ITER pedestal and SOL plasma and its influence on the heat flux width},
author = {A. Loarte and F. Liu and G.T.A. Huijsmans and A.S. Kukushkin and R.A. Pitts},
url = {http://www.sciencedirect.com/science/article/pii/S0022311514009295},
doi = {http://dx.doi.org/10.1016/j.jnucmat.2014.11.122},
issn = {0022-3115},
year = {2015},
date = {2015-01-01},
journal = {Journal of Nuclear Materials},
volume = {463},
pages = {401 - 405},
abstract = {Abstract MHD stability of ITER plasmas has been analyzed for QDT = 10 edge and SOL plasma conditions, showing that the SOL plasma is MHD stable down to pressure gradient scale lengths of λp ∼ 1 mm, but that MHD pedestal plasma stability can limit λp to values of 5–8 mm just inside the separatrix. Modelling of the corresponding plasma conditions with the SOLPS code shows that heat flux widths λq ∼ 1.2–1.5 mm can be obtained which are compatible with λp ∼ 5–8 mm. This is due to the fact that the ITER divertor plasma enters the high recycling regime at low values of separatrix densities (∼4.0 × 1018 m−3), which leads to the appearance of a region with reversed flow near the separatrix, modifying plasma transport and leading to high SOL density gradient scale lengths and divertor plasma pressures near the separatrix.},
note = {PLASMA-SURFACE INTERACTIONS 21Proceedings of the 21st International Conference on Plasma-Surface Interactions in Controlled Fusion Devices Kanazawa, Japan May 26-30, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fil, A.; Nardon, E.; Hoelzl, M.; Huijsmans, G. T. A; Orain, F.; Becoulet, M.; Beyer, P.; Dif-Pradalier, G.; Guirlet, R.; Koslowski, H. R.; Lehnen, M.; Morales, J.; Pamela, S.; Passeron, C.; Reux, C.; Saint-Laurent, F.; JET Contributors
Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET Article de journal
Dans: Physics of Plasmas, vol. 22, no. 6, 2015.
@article{:/content/aip/journal/pop/22/6/10.1063/1.4922846,
title = {Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET},
author = {Fil, A. and Nardon, E. and Hoelzl, M. and Huijsmans, G. T. A and Orain, F. and Becoulet, M. and Beyer, P. and Dif-Pradalier, G. and Guirlet, R. and Koslowski, H. R. and Lehnen, M. and Morales, J. and Pamela, S. and Passeron, C. and Reux, C. and Saint-Laurent, F. and JET Contributors},
url = {http://scitation.aip.org/content/aip/journal/pop/22/6/10.1063/1.4922846},
doi = {http://dx.doi.org/10.1063/1.4922846},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huijsmans, G. T. A.; Chang, C. S.; Ferraro, N.; Sugiyama, L.; Waelbroeck, F.; Xu, X. Q.; Loarte, A.; Futatani, S.
Modelling of edge localised modes and edge localised mode control Article de journal
Dans: Physics of Plasmas, vol. 22, no. 2, 2015.
@article{:/content/aip/journal/pop/22/2/10.1063/1.4905231,
title = {Modelling of edge localised modes and edge localised mode control},
author = {Huijsmans, G. T. A. and Chang, C. S. and Ferraro, N. and Sugiyama, L. and Waelbroeck, F. and Xu, X. Q. and Loarte, A. and Futatani, S.},
url = {http://scitation.aip.org/content/aip/journal/pop/22/2/10.1063/1.4905231},
doi = {http://dx.doi.org/10.1063/1.4905231},
year = {2015},
date = {2015-01-01},
journal = {Physics of Plasmas},
volume = {22},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
François Orain; M Bécoulet; J Morales; G T A Huijsmans; G Dif-Pradalier; M Hoelzl; X Garbet; S Pamela; E Nardon; C Passeron; G Latu; A Fil; P Cahyna
Non-linear MHD modeling of edge localized mode cycles and mitigation by resonant magnetic perturbations Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 57, no. 1, p. 014020, 2015.
@article{0741-3335-57-1-014020,
title = {Non-linear MHD modeling of edge localized mode cycles and mitigation by resonant magnetic perturbations},
author = {François Orain and M Bécoulet and J Morales and G T A Huijsmans and G Dif-Pradalier and M Hoelzl and X Garbet and S Pamela and E Nardon and C Passeron and G Latu and A Fil and P Cahyna},
url = {http://stacks.iop.org/0741-3335/57/i=1/a=014020},
year = {2015},
date = {2015-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {57},
number = {1},
pages = {014020},
abstract = {The dynamics of a multi-edge localized mode (ELM) cycle as well as the ELM mitigation by resonant magnetic perturbations (RMPs) are modeled in realistic tokamak X-point geometry with the non-linear reduced MHD code JOREK. The diamagnetic rotation is found to be a key parameter enabling us to reproduce the cyclical dynamics of the plasma relaxations and to model the near-symmetric ELM power deposition on the inner and outer divertor target plates consistently with experimental measurements. Moreover, the non-linear coupling of the RMPs with unstable modes are found to modify the edge magnetic topology and induce a continuous MHD activity in place of a large ELM crash, resulting in the mitigation of the ELMs. At larger diamagnetic rotation, a bifurcation from unmitigated ELMs—at low RMP current—towards fully suppressed ELMs—at large RMP current—is obtained.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morvan, Dominique
Numerical study of the behaviour of a surface fire propagating through a firebreak built in a Mediterranean shrub layer Article de journal
Dans: Fire Safety Journal, vol. 71, no. 7, p. 34–48, 2015.
@article{morvan:hal-01297711,
title = {Numerical study of the behaviour of a surface fire propagating through a firebreak built in a Mediterranean shrub layer},
author = {Morvan, Dominique},
url = {https://hal.archives-ouvertes.fr/hal-01297711},
doi = {10.1016/j.firesaf.2014.11.012},
year = {2015},
date = {2015-01-01},
journal = {Fire Safety Journal},
volume = {71},
number = {7},
pages = {34--48},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lamorlette, Aymeric; El Houssami, Mohamad; Thomas, Jan C.; Simeoni, Albert; Morvan, Dominique
A dimensional analysis of forest fuel layer ignition model: Application to the ignition of pine needle litters Article de journal
Dans: Journal of Fire Sciences, p. NC, 2015.
@article{lamorlette:hal-01157866,
title = {A dimensional analysis of forest fuel layer ignition model: Application to the ignition of pine needle litters},
author = {Lamorlette, Aymeric and El Houssami, Mohamad and Thomas, Jan C. and Simeoni, Albert and Morvan, Dominique},
url = {https://hal.archives-ouvertes.fr/hal-01157866},
doi = {10.1177/ToBeAssigned},
year = {2015},
date = {2015-01-01},
journal = {Journal of Fire Sciences},
pages = {NC},
publisher = {SAGE Publications},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
R. Trozzo; G. Boedec; M. Leonetti; M. Jaeger
Axisymmetric Boundary Element Method for vesicles in a capillary Article de journal
Dans: Journal of Computational Physics, vol. 289, p. 62 - 82, 2015, ISSN: 0021-9991.
@article{Trozzo201562,
title = {Axisymmetric Boundary Element Method for vesicles in a capillary},
author = {R. Trozzo and G. Boedec and M. Leonetti and M. Jaeger},
url = {http://www.sciencedirect.com/science/article/pii/S0021999115000923},
doi = {http://dx.doi.org/10.1016/j.jcp.2015.02.022},
issn = {0021-9991},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computational Physics},
volume = {289},
pages = {62 - 82},
abstract = {Abstract The problem of a vesicle transported by a fluid flow can present a large range of length scales. One example is the case of a vesicle producing a tether, and eventually pearls, in an elongational flow. Another case occurs when a lubrication film is formed, such as during the short range interaction between two vesicles. Such problems are still challenging for 3D simulations. On the other hand, a good understanding could be obtained by first considering the axisymmetric regime when such a regime exists. An axisymmetric model could then be used, without the criticisms that can be made of a 2D approach. We propose such a model, primarily interested in flows through narrow cylindrical capillaries. Two options are compared, with and without explicit representation of the capillary boundaries by a mesh. The numerical effort is characterized as a function of the vesicle's initial shape, the flow magnitude and the confinement. The model is able to treat typical configurations of red blood cells flowing through very narrow pores with extremely thin lubrication films.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2014
Thomas Cartier-Michaud, Philippe Ghendrih, Virginie Grandgirard; Guillaume Latu
Optimizing the parallel scheme of the Poisson solver for the reduced kinetic code TERESA Article de journal
Dans: 2014.
@article{Cartier-Michaud2014,
title = {Optimizing the parallel scheme of the Poisson solver for the reduced kinetic code TERESA},
author = {Thomas Cartier-Michaud, Philippe Ghendrih, Virginie Grandgirard and Guillaume Latu},
url = {http://dx.doi.org/10.1051/proc/201343017 },
doi = {10.1051/proc/201343017 },
year = {2014},
date = {2014-01-10},
abstract = {The parallelization performance of the TERESA Code for Trapped Element REduction in Semi lagrangian Approach is analyzed. TERESA is a kinetic code in four dimensions (4D), two in "real" space and two "energy" coordinates. It addresses the turbulent evolution of the distribution of ions governed by uctuations of the electric potential. The numerical scheme is split into four steps: the 4D advection of the distribution function with the Vlasov equation, the computation of the charge density, the calculation of the electric potential using the quasineutrality asymptotic limit of the Poisson equation and finally, the two high frequency averages of the electric potential in order to compute the advection field. Starting from an initial standard parallelization scheme we find that the Poisson solver accounts for most of the execution time of TERESA (up to 90% at aimed meshes) and that its scaling performance is poor. Two improvements of the Poisson solver have been implemented and tested. These show that performance levelling are due to interference phenomena when addressing computation resources as well as communication overheads when the loading of the CPUs with MPI processes / OpenMP threads is not optimized. Tests on two computers, Rheticus et Helios, with very similar architecture, allows one to better diagnose the interference phenomena. These developments lead to reduction by up to a factor 100 of the execution time and extends the scalability properties up to 1024 cores for large meshes cases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Miquel Huix-Rotllant; Nicolas Ferré
Theoretical Study of the Photochemical Initiation in Nitroxide-Mediated Photopolymerization Article de journal
Dans: The Journal of Physical Chemistry A, vol. 118, no. 25, p. 4464-4470, 2014, (PMID: 24922558).
@article{doi:10.1021/jp501773n,
title = {Theoretical Study of the Photochemical Initiation in Nitroxide-Mediated Photopolymerization},
author = {Miquel Huix-Rotllant and Nicolas Ferré},
url = {http://dx.doi.org/10.1021/jp501773n},
doi = {10.1021/jp501773n},
year = {2014},
date = {2014-01-01},
journal = {The Journal of Physical Chemistry A},
volume = {118},
number = {25},
pages = {4464-4470},
abstract = {Nitroxide-mediated photopolymerization (NMP2) is a promising novel route to initiate radical polymerization. In NMP2, alkoxyamines bounded to a monomer are attached to a chromophore. Upon light absorption, the excitation energy is transferred from the chromophore to the alkoxyamine moiety, inducing the cleavage of the oxygen–carbon bond and thus initiating the polymerization. The NMP2 mechanism depends strongly on several factors like the type of chromophore, the monomer, the connectivity pattern, etc. This complexity makes it difficult to design new NMP2 initiators with increased polymerization efficiency and selectivity. In the present article, we characterize by means of quantum mechanical calculations the main steps of the NMP2 initiation for alkoxyamines attached to aromatic ketones. We show how the excitation energy can be transferred from the chromophore to the alkoxyamine moiety, and present two easily computed parameters which can account for the selectivity of the O–C bond photocleaveage. Finally, using results obtained for a series of isomers, we give some rules that may help the design of more efficient NMP2 initiators.},
note = {PMID: 24922558},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Malcolm Roberts; Matthieu Leroy; Jorge Morales; Wouter Bos; Kai Schneider
Self-organization of helically forced MHD flow in confined cylindrical geometries Article de journal
Dans: Fluid Dynamics Research, vol. 46, no. 6, p. 061422, 2014.
@article{1873-7005-46-6-061422,
title = {Self-organization of helically forced MHD flow in confined cylindrical geometries},
author = {Malcolm Roberts and Matthieu Leroy and Jorge Morales and Wouter Bos and Kai Schneider},
url = {http://stacks.iop.org/1873-7005/46/i=6/a=061422},
year = {2014},
date = {2014-01-01},
journal = {Fluid Dynamics Research},
volume = {46},
number = {6},
pages = {061422},
abstract = {The dynamics of a magnetically forced conducting fluid in confined geometries is studied. A pseudospectral method with volume penalisation is used to solve the resistive magnetohydrodynamic equations. A helical magnetic field is imposed via boundary conditions, which generates a response in the velocity field for large enough magnitudes. Different helical structures are observed in the flow depending on the magnitude and direction of the forcing and the cross-sectional geometry of the fluid domain. A computational technique for finding a solenoidal vector field which can be used in complex geometries is also proposed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huix-Rotllant, Miquel; Ferré, Nicolas
Triplet state photochemistry and the three-state crossing of acetophenone within time-dependent density-functional theory Article de journal
Dans: The Journal of Chemical Physics, vol. 140, no. 13, 2014.
@article{:/content/aip/journal/jcp/140/13/10.1063/1.4869802,
title = {Triplet state photochemistry and the three-state crossing of acetophenone within time-dependent density-functional theory},
author = {Huix-Rotllant, Miquel and Ferré, Nicolas},
url = {http://scitation.aip.org/content/aip/journal/jcp/140/13/10.1063/1.4869802},
doi = {http://dx.doi.org/10.1063/1.4869802},
year = {2014},
date = {2014-01-01},
journal = {The Journal of Chemical Physics},
volume = {140},
number = {13},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Samer Gozem; Federico Melaccio; Alessio Valentini; Michael Filatov; Miquel Huix-Rotllant; Nicolas Ferré; Luis Manuel Frutos; Celestino Angeli; Anna I. Krylov; Alexander A. Granovsky; Roland Lindh; Massimo Olivucci
Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection Article de journal
Dans: Journal of Chemical Theory and Computation, vol. 10, no. 8, p. 3074-3084, 2014, (PMID: 26588278).
@article{doi:10.1021/ct500154k,
title = {Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection},
author = {Samer Gozem and Federico Melaccio and Alessio Valentini and Michael Filatov and Miquel Huix-Rotllant and Nicolas Ferré and Luis Manuel Frutos and Celestino Angeli and Anna I. Krylov and Alexander A. Granovsky and Roland Lindh and Massimo Olivucci},
url = {http://dx.doi.org/10.1021/ct500154k},
doi = {10.1021/ct500154k},
year = {2014},
date = {2014-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {10},
number = {8},
pages = {3074-3084},
abstract = {We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (CI) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-cluster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.},
note = {PMID: 26588278},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Drouot, Thomas; Gravier, Etienne; Reveille, Thierry; Ghizzo, Alain; Bertrand, Pierre; Garbet, Xavier; Sarazin, Yanick; Cartier-Michaud, Thomas
A gyro-kinetic model for trapped electron and ion modes* Article de journal
Dans: Eur. Phys. J. D, vol. 68, no. 10, p. 280, 2014.
@article{refId0,
title = {A gyro-kinetic model for trapped electron and ion modes*},
author = {Drouot, Thomas and Gravier, Etienne and Reveille, Thierry and Ghizzo, Alain and Bertrand, Pierre and Garbet, Xavier and Sarazin, Yanick and Cartier-Michaud, Thomas},
url = {http://dx.doi.org/10.1140/epjd/e2014-50151-2},
doi = {10.1140/epjd/e2014-50151-2},
year = {2014},
date = {2014-01-01},
journal = {Eur. Phys. J. D},
volume = {68},
number = {10},
pages = {280},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
T Cartier-Michaud; P Ghendrih; Y Sarazin; G Dif-Pradalier; T Drouot; D Estève; X Garbet; V Grandgirard; G Latu; C Norscini; C Passeron
Staircase temperature profiles and plasma transport self-organisation in a minimum kinetic model of turbulence based on the trapped ion mode instability Article de journal
Dans: Journal of Physics: Conference Series, vol. 561, no. 1, p. 012003, 2014.
@article{1742-6596-561-1-012003,
title = {Staircase temperature profiles and plasma transport self-organisation in a minimum kinetic model of turbulence based on the trapped ion mode instability},
author = {T Cartier-Michaud and P Ghendrih and Y Sarazin and G Dif-Pradalier and T Drouot and D Estève and X Garbet and V Grandgirard and G Latu and C Norscini and C Passeron},
url = {http://stacks.iop.org/1742-6596/561/i=1/a=012003},
year = {2014},
date = {2014-01-01},
journal = {Journal of Physics: Conference Series},
volume = {561},
number = {1},
pages = {012003},
abstract = {A minimum model of plasma turbulence in a kinetic framework is presented. It is based on trapped ion turbulence, gyro and bounce averaged, and implemented in the versatile and efficient code TERESA. Zonal flow - streamer interplay are readily shown to be key players that govern the confinement properties of the model. The parameter space of the model is explored with brute force numerics. A generic result is either a streamer dominated pattern with large transport, or a staircase temperature profile with very marked corrugations and quenched transport. A case with off-axis heating is found to exhibit quasiperiodic relaxation events relevant to investigate dynamical turbulence self-organisation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Julien Chauchat; Marc Médale
A three-dimensional numerical model for dense granular flows based on the rheology Article de journal
Dans: Journal of Computational Physics, vol. 256, p. 696 - 712, 2014, ISSN: 0021-9991.
@article{Chauchat2014696,
title = {A three-dimensional numerical model for dense granular flows based on the rheology},
author = {Julien Chauchat and Marc Médale},
url = {http://www.sciencedirect.com/science/article/pii/S0021999113006098},
doi = {http://dx.doi.org/10.1016/j.jcp.2013.09.004},
issn = {0021-9991},
year = {2014},
date = {2014-01-01},
journal = {Journal of Computational Physics},
volume = {256},
pages = {696 - 712},
abstract = {Abstract This paper presents a three-dimensional implementation of the so-called μ ( I ) rheology to accurately and efficiently compute steady-state dense granular flows. The tricky pressure dependent visco-plastic behaviour within an incompressible flow solver has been overcome using a regularisation technique along with a complete derivation of the incremental formulation associated with the Newton–Raphson algorithm. The computational accuracy and efficiency of the proposed numerical model have been assessed on two representative problems that have an analytical solution. Then, two application examples dealing with actual lab experiments have also been considered: the first one concerns a granular flow on a heap and the second one deals with the granular flow around a cylinder. In both configurations the obtained computational results are in good agreement with available experimental data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Berrahil, Farid; Benissaad, Smail; Ch'e9rifa, Abid; M'e9dale, Marc
Natural convection with volumetric heat generation and external magnetic field in differentially heated enclosure Article de journal
Dans: Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science, 2014.
@article{Berrahil07022014,
title = {Natural convection with volumetric heat generation and external magnetic field in differentially heated enclosure},
author = {Berrahil, Farid and Benissaad, Smail and Ch'e9rifa, Abid and M'e9dale, Marc},
url = {http://pic.sagepub.com/content/early/2014/02/03/0954406214521792.abstract},
doi = {10.1177/0954406214521792},
year = {2014},
date = {2014-01-01},
journal = {Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science},
abstract = {This work presents a numerical study of natural convection in a laterally heated cavity filled with an electrically conductive fluid (Pr = 0.0321) in the presence of an external magnetic field and an internal heat source. The finite volume method with the SIMPLER algorithm is used to solve the system of equations governing the magnetohydrodynamics flow. The influence of volumetric heating SQ on the flow structure and on the heat transfer within the cavity for Gruc0u8201 =u8201 104, 105, and 106 was examined. The effects of aspect ratio (Au8201 =u8201 1, 0.5, and 2), Prandtl number (low Prandtl number fluids), and magnetic field (Ha = 0 to 100) were determined in the steady state with internal heat generation. Two orientations of the magnetic field were considered in order to have better control of the flow. The strongest stabilization of the flow field with internal heat generation is found when the magnetic field is oriented horizontally.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Boedec,G.; Jaeger,M.; Leonetti,M.
Pearling instability of a cylindrical vesicle Article de journal
Dans: Journal of Fluid Mechanics, vol. 743, p. 262–279, 2014, ISSN: 1469-7645.
@article{FLM:9188570,
title = {Pearling instability of a cylindrical vesicle},
author = {Boedec,G. and Jaeger,M. and Leonetti,M.},
url = {http://journals.cambridge.org/article_S0022112014000342},
doi = {10.1017/jfm.2014.34},
issn = {1469-7645},
year = {2014},
date = {2014-01-01},
journal = {Journal of Fluid Mechanics},
volume = {743},
pages = {262--279},
abstract = {ABSTRACT A cylindrical vesicle under tension can undergo a pearling instability, characterized by the growth of a sinusoidal perturbation which evolves towards a collection of quasi-spherical bulbs connected by thin tethers, like pearls on a necklace. This is reminiscent of the well-known Rayleigh–Plateau instability, where surface tension drives the amplification of sinusoidal perturbations of a cylinder of fluid. We calculate the growth rate of perturbations for a cylindrical vesicle under tension, considering the effect of both inner and outer fluids, with different viscosities. We show that this situation differs strongly from the classical Rayleigh–Plateau case in the sense that, first, the tension must be above a critical value for the instability to develop and, second, even in the strong tension limit, the surface preservation constraint imposed by the presence of the membrane leads to a different asymptotic behaviour. The results differ from previous studies on pearling due to the consideration of variations of tension, which are shown to enhance the pearling instability growth rate, and lower the wavenumber of the fastest growing mode.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ciraolo, G.; Bufferand, H.; Ghendrih, Ph.; Tamain, P.; Bucalossi, J.; Marandet, Y.; Serre, E.
Investigation of Edge and SOL Particle Flux Patterns in High Density Regimes using SOLEDGE2D-EIRENE Code Article de journal
Dans: Contributions to Plasma Physics, vol. 54, no. 4-6, p. 432–436, 2014, ISSN: 1521-3986.
@article{CTPP:CTPP201410018,
title = {Investigation of Edge and SOL Particle Flux Patterns in High Density Regimes using SOLEDGE2D-EIRENE Code},
author = {Ciraolo, G. and Bufferand, H. and Ghendrih, Ph. and Tamain, P. and Bucalossi, J. and Marandet, Y. and Serre, E.},
url = {http://dx.doi.org/10.1002/ctpp.201410018},
doi = {10.1002/ctpp.201410018},
issn = {1521-3986},
year = {2014},
date = {2014-01-01},
journal = {Contributions to Plasma Physics},
volume = {54},
number = {4-6},
pages = {432--436},
publisher = {WILEY-VCH Verlag},
abstract = {We present numerical simulations of plasma transport obtained with the SOLEDGE2D code coupled to the EIRENE Montecarlo code for neutrals. We consider a double null magnetic configuration in a WEST geometry. Density and temperatures parallel profiles in the SOL domain are presented as well as Mach profile. We detail how using the penalization technique we are able to model plasma transport up to the first wall having access to energy and particle fluxes on the entire chamber wall. Moreover, we present the computed 2D contour map of the plasma mach number and of the magnitude of the ionisation source term in the whole poloidal section, emphasizing how complex and realistic geometries can be handled thanks to the penalization technique. (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
H Bufferand; G Ciraolo; G Dif-Pradalier; P Ghendrih; Ph Tamain; Y Marandet; E Serre
Magnetic geometry and particle source drive of supersonic divertor regimes Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 56, no. 12, p. 122001, 2014.
@article{0741-3335-56-12-122001,
title = {Magnetic geometry and particle source drive of supersonic divertor regimes},
author = {H Bufferand and G Ciraolo and G Dif-Pradalier and P Ghendrih and Ph Tamain and Y Marandet and E Serre},
url = {http://stacks.iop.org/0741-3335/56/i=12/a=122001},
year = {2014},
date = {2014-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {56},
number = {12},
pages = {122001},
abstract = {We present a comprehensive picture of the mechanisms driving the transition from subsonic to supersonic flows in tokamak plasmas. We demonstrate that supersonic parallel flows into the divertor volume are ubiquitous at low density and governed by the divertor magnetic geometry. As the density is increased, subsonic divertor plasmas are recovered. On detachment, we show the change in particle source can also drive the transition to a supersonic regime. The comprehensive theoretical analysis is completed by simulations in ITER geometry. Such results are essential in assessing the divertor performance and when interpreting measurements and experimental evidence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Agullo, O.; Muraglia, M.; Poyé, A.; Benkadda, S.; Yagi, M.; Garbet, X.; Sen, A.
A signature for turbulence driven magnetic islands Article de journal
Dans: Physics of Plasmas, vol. 21, no. 9, 2014.
@article{:/content/aip/journal/pop/21/9/10.1063/1.4894699,
title = {A signature for turbulence driven magnetic islands},
author = {Agullo, O. and Muraglia, M. and Poyé, A. and Benkadda, S. and Yagi, M. and Garbet, X. and Sen, A.},
url = {http://scitation.aip.org/content/aip/journal/pop/21/9/10.1063/1.4894699},
doi = {http://dx.doi.org/10.1063/1.4894699},
year = {2014},
date = {2014-01-01},
journal = {Physics of Plasmas},
volume = {21},
number = {9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bufferand, H.; Bucalossi, J.; Ciraolo, G.; Fedorczak, N.; Ghendrih, P.; Leybros, R.; Marandet, Y.; Serre, E.; Tamain, P.
Density Regimes and Heat Flux Deposition in the WEST Shallow Divertor Configuration Article de journal
Dans: Contributions to Plasma Physics, vol. 54, no. 4-6, p. 378–382, 2014, ISSN: 1521-3986.
@article{CTPP:CTPP201410026,
title = {Density Regimes and Heat Flux Deposition in the WEST Shallow Divertor Configuration},
author = {Bufferand, H. and Bucalossi, J. and Ciraolo, G. and Fedorczak, N. and Ghendrih, P. and Leybros, R. and Marandet, Y. and Serre, E. and Tamain, P.},
url = {http://dx.doi.org/10.1002/ctpp.201410026},
doi = {10.1002/ctpp.201410026},
issn = {1521-3986},
year = {2014},
date = {2014-01-01},
journal = {Contributions to Plasma Physics},
volume = {54},
number = {4-6},
pages = {378--382},
publisher = {WILEY-VCH Verlag},
abstract = {To support ITER divertor design, the WEST project on Tore Supra aims at studying high heat fluxes on tungsten monoblock during long pulses. In that persective, a particular attention is paid to simulate the edge plasma interaction with complex PFCs using the transport code SOLEDGE2D-EIRENE. The plasma response to a heating and puffing scenario is described as well as the so-called divertor density regimes, characterizing the operational domain of the WEST divertor. These results are compared for two different magnetic configurations: a semi-open double null divertor with the X-point away from the target plates and a shallow divertor configuration with the X-point close to the targets. (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Poncet, Sébastien; Viazzo, Stéphane; Oguic, Romain
Large eddy simulations of Taylor-Couette-Poiseuille flows in a narrow-gap system Article de journal
Dans: Physics of Fluids, vol. 26, no. 10, 2014.
@article{:/content/aip/journal/pof2/26/10/10.1063/1.4899196,
title = {Large eddy simulations of Taylor-Couette-Poiseuille flows in a narrow-gap system},
author = {Poncet, Sébastien and Viazzo, Stéphane and Oguic, Romain},
url = {http://scitation.aip.org/content/aip/journal/pof2/26/10/10.1063/1.4899196},
doi = {http://dx.doi.org/10.1063/1.4899196},
year = {2014},
date = {2014-01-01},
journal = {Physics of Fluids},
volume = {26},
number = {10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stéphane Viazzo; Sébastien Poncet
Numerical simulation of the flow stability in a high aspect ratio Taylor–Couette system submitted to a radial temperature gradient Article de journal
Dans: Computers & Fluids, vol. 101, p. 15 - 26, 2014, ISSN: 0045-7930.
@article{Viazzo201415,
title = {Numerical simulation of the flow stability in a high aspect ratio Taylor–Couette system submitted to a radial temperature gradient},
author = {Stéphane Viazzo and Sébastien Poncet},
url = {http://www.sciencedirect.com/science/article/pii/S0045793014002230},
doi = {http://dx.doi.org/10.1016/j.compfluid.2014.05.025},
issn = {0045-7930},
year = {2014},
date = {2014-01-01},
journal = {Computers & Fluids},
volume = {101},
pages = {15 - 26},
abstract = {Abstract From 28 high-order DNS computations, one investigates the formation of instabilities due to the strong competition between an azimuthal flow induced by rotation and an axial flow due to convection in a tall Taylor–Couette apparatus ( Γ = 80 , η = 0.8 ) submitted to a radial temperature gradient. One explores the richness of the transition diagram that reports seven different flow patterns appearing either as spiral rolls, wavy vortices or a combination of both depending on the Taylor and Rayleigh numbers. The partial spiral regime observed experimentally by Guillerm [1] is not recovered at very low Rayleigh numbers. The spatio-temporal properties of the different spirals close to the threshold of the primary instability are fairly predicted and a new insight on the flow and thermal structures of the instabilities is gained from this study. Finally, the distributions of the Nusselt number against the Taylor number are established for various Rayleigh numbers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maget, Patrick; Lütjens, Hinrich; Luciani, Jean-François; Garbet, Xavier; Février, Olivier; Ségui, Jean-Luc
Bi-fluid and neoclassical effect on a Double-Tearing mode in Tore Supra Article de journal
Dans: Physics of Plasmas, vol. 21, no. 6, 2014.
@article{:/content/aip/journal/pop/21/6/10.1063/1.4882259,
title = {Bi-fluid and neoclassical effect on a Double-Tearing mode in Tore Supra},
author = {Maget, Patrick and Lütjens, Hinrich and Luciani, Jean-François and Garbet, Xavier and Février, Olivier and Ségui, Jean-Luc},
url = {http://scitation.aip.org/content/aip/journal/pop/21/6/10.1063/1.4882259},
doi = {http://dx.doi.org/10.1063/1.4882259},
year = {2014},
date = {2014-01-01},
journal = {Physics of Plasmas},
volume = {21},
number = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Poyé, A.; Agullo, O.; Smolyakov, A.; Benkadda, S.; Garbet, X.
Dynamics of magnetic islands in large Δ′ regimes Article de journal
Dans: Physics of Plasmas, vol. 21, no. 2, 2014.
@article{:/content/aip/journal/pop/21/2/10.1063/1.4867065,
title = {Dynamics of magnetic islands in large Δ′ regimes},
author = {Poyé, A. and Agullo, O. and Smolyakov, A. and Benkadda, S. and Garbet, X.},
url = {http://scitation.aip.org/content/aip/journal/pop/21/2/10.1063/1.4867065},
doi = {http://dx.doi.org/10.1063/1.4867065},
year = {2014},
date = {2014-01-01},
journal = {Physics of Plasmas},
volume = {21},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A I Smolyakov; A Poyé; O Agullo; S Benkadda; X Garbet
Saturation of magnetic islands in equilibria with a finite current gradient. Part I: asymptotic theory Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 56, no. 12, p. 125004, 2014.
@article{0741-3335-56-12-125004,
title = {Saturation of magnetic islands in equilibria with a finite current gradient. Part I: asymptotic theory},
author = {A I Smolyakov and A Poyé and O Agullo and S Benkadda and X Garbet},
url = {http://stacks.iop.org/0741-3335/56/i=12/a=125004},
year = {2014},
date = {2014-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {56},
number = {12},
pages = {125004},
abstract = {The problem of saturation of magnetic islands for the case of a finite current gradient at the rational surface has been revisited. The asymptotic procedure is presented giving the explicit expressions for the perturbed magnetic flux function at saturation. The resulting nonlinear equation for the island width has been obtained in the form similar to the previous work but with fully analytical expressions for the asymptotic series.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A Poyé; A I Smolyakov; O Agullo; S Benkadda; X Garbet
Saturation of magnetic islands in equilibria with a finite current gradient. Part II: numerical simulations Article de journal
Dans: Plasma Physics and Controlled Fusion, vol. 56, no. 12, p. 125005, 2014.
@article{0741-3335-56-12-125005,
title = {Saturation of magnetic islands in equilibria with a finite current gradient. Part II: numerical simulations},
author = {A Poyé and A I Smolyakov and O Agullo and S Benkadda and X Garbet},
url = {http://stacks.iop.org/0741-3335/56/i=12/a=125005},
year = {2014},
date = {2014-01-01},
journal = {Plasma Physics and Controlled Fusion},
volume = {56},
number = {12},
pages = {125005},
abstract = {The saturation of magnetic islands is studied numerically for the current profiles with a finite gradient at the rational surface. It is shown that the results of such simulations are in good agreement with analytical theory presented in part I. The effects of plasma viscosity is studied and shown not to affect the final state of the magnetic islands.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
I. Graur; M.T. Ho
Rarefied gas flow through a long rectangular channel of variable cross section Article de journal
Dans: Vacuum, vol. 101, p. 328 - 332, 2014, ISSN: 0042-207X, (Including rapid communications, original articles and a special section: Measurement Characteristics and Use of Quadrupole Mass Spectrometers for Vacuum Applications).
@article{Graur2014328,
title = {Rarefied gas flow through a long rectangular channel of variable cross section},
author = {I. Graur and M.T. Ho},
url = {http://www.sciencedirect.com/science/article/pii/S0042207X1300331X},
doi = {http://dx.doi.org/10.1016/j.vacuum.2013.07.047},
issn = {0042-207X},
year = {2014},
date = {2014-01-01},
journal = {Vacuum},
volume = {101},
pages = {328 - 332},
abstract = {Abstract The method, proposed previously by other authors, is applied here to calculate a mass flow rate of rarefied gas through a long rectangular channel of variable cross-section aspect ratio. The gas flow through this channel is generated by the pressure and/or temperature gradient. The method is based on the results obtained previously on the basis of the kinetic equation and it requires very modest computational efforts. As a demonstration of its application some examples of the mass flow rate calculations for the isothermal and non-isothermal flows through the channels with variable rectangular cross sections are given. The analytical expressions in the case of the hydrodynamic and free molecular flow regimes are proposed.},
note = {Including rapid communications, original articles and a special section: Measurement Characteristics and Use of Quadrupole Mass Spectrometers for Vacuum Applications},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
M.T. Ho; I. Graur
Numerical study of unsteady rarefied gas flow through an orifice Article de journal
Dans: Vacuum, vol. 109, p. 253 - 265, 2014, ISSN: 0042-207X.
@article{Ho2014253,
title = {Numerical study of unsteady rarefied gas flow through an orifice},
author = {M.T. Ho and I. Graur},
url = {http://www.sciencedirect.com/science/article/pii/S0042207X14001638},
doi = {http://dx.doi.org/10.1016/j.vacuum.2014.05.004},
issn = {0042-207X},
year = {2014},
date = {2014-01-01},
journal = {Vacuum},
volume = {109},
pages = {253 - 265},
abstract = {Abstract Transient flow of rarefied gas through an orifice caused by various pressure ratios between the reservoirs is investigated for a wide range of the gas rarefaction, varying from the free molecular to continuum regime. The problem is studied on the basis of the numerical solution of unsteady S-model kinetic equation. It is found that the mass flow rate takes from 2.35 to 30.37 characteristic times, which is defined by orifice radius over the most probable molecular speed, to reach its steady state value. The time of steady flow establishment and the steady state distribution of the flow parameters are compared with previously reported data obtained by the Direct Simulation Monte Carlo (DSMC) method. A simple fitting expression is proposed for the approximation of the mass flow rate evolution in time.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicolas, T.; Lütjens, H.; Luciani, J.-F.; Garbet, X.; Sabot, R.
Impurity behavior during sawtooth activity in tokamak plasmas Article de journal
Dans: Physics of Plasmas, vol. 21, no. 1, 2014.
@article{:/content/aip/journal/pop/21/1/10.1063/1.4861859,
title = {Impurity behavior during sawtooth activity in tokamak plasmas},
author = {Nicolas, T. and Lütjens, H. and Luciani, J.-F. and Garbet, X. and Sabot, R.},
url = {http://scitation.aip.org/content/aip/journal/pop/21/1/10.1063/1.4861859},
doi = {http://dx.doi.org/10.1063/1.4861859},
year = {2014},
date = {2014-01-01},
journal = {Physics of Plasmas},
volume = {21},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wahl, Claire; Rech, J'er^ome; Jonckheere, Thibaut; Martin, Thierry
Interactions and Charge Fractionalization in an Electronic Hong-Ou-Mandel Interferometer Article de journal
Dans: Phys. Rev. Lett., vol. 112, p. 046802, 2014.
@article{PhysRevLett.112.046802,
title = {Interactions and Charge Fractionalization in an Electronic Hong-Ou-Mandel Interferometer},
author = {Wahl, Claire and Rech, J'er^ome and Jonckheere, Thibaut and Martin, Thierry},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.112.046802},
doi = {10.1103/PhysRevLett.112.046802},
year = {2014},
date = {2014-01-01},
journal = {Phys. Rev. Lett.},
volume = {112},
pages = {046802},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
I. Graur, T. Veltzke , J. G. Méolans, M. T. Ho, J. Thöming
The gas flow diode effect: theoretical and experimental analysis of moderately rarefied gas flows through a microchannel with varying cross section Article de journal
Dans: 2014.
@article{Graur2014,
title = {The gas flow diode effect: theoretical and experimental analysis of moderately rarefied gas flows through a microchannel with varying cross section},
author = {I. Graur, T. Veltzke , J. G. Méolans, M. T. Ho, J. Thöming},
url = {http://link.springer.com/article/10.1007/s10404-014-1445-4/fulltext.html},
doi = {10.1007/s10404-014-1445-4},
year = {2014},
date = {2014-01-01},
abstract = {Moderately rarefied gas flows are clearly distinguished from viscous flow in the continuum regime and from free molecular flow at high rarefaction. Being of relevance for various technical applications, the understanding of such flow processes is crucial for considerable enhancement in micro electromechanical systems (MEMS) and vacuum techniques. In this work, we focus on the isothermal rarefied gas flow through long channels with longitudinally varying cross section. We apply two approaches, an analytical one and a numerical one that is based on the solution of the linearized S-model, both allowing us to predict the mass flow rate in diverging and converging flow directions for arbitrary pressure gradients. Both approaches are validated by CO2, N2 and Ar permeation experiments on tapered microchannels manufactured by means of micromilling. The local Knudsen numbers ranged from 0.0471 to 0.2263. All the numerical and analytical results are in good agreement to the experimental data and show that the mass flow rate is significantly higher when the duct is perfused in converging direction. The understanding of the physical phenomenon of this gas flow diode effect might pave the way for novel components in MEMS such as static one-way valves.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Richard, Johan; Jauzac, Mathilde; Limousin, Marceau; Jullo, Eric; Clément, Benjamin; Ebeling, Harald; Kneib, Jean-Paul; Atek, Hakim; Natarajan, Priya; Egami, Eiichi; Livermore, Rachael; Bower, Richard
Mass and magnification maps for the Hubble Space Telescope Frontier Fields clusters: implications for high-redshift studies Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 444, no. 1, p. 268-289, 2014.
@article{Richard11102014,
title = {Mass and magnification maps for the Hubble Space Telescope Frontier Fields clusters: implications for high-redshift studies},
author = {Richard, Johan and Jauzac, Mathilde and Limousin, Marceau and Jullo, Eric and Clément, Benjamin and Ebeling, Harald and Kneib, Jean-Paul and Atek, Hakim and Natarajan, Priya and Egami, Eiichi and Livermore, Rachael and Bower, Richard},
url = {http://mnras.oxfordjournals.org/content/444/1/268.abstract},
doi = {10.1093/mnras/stu1395},
year = {2014},
date = {2014-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {444},
number = {1},
pages = {268-289},
abstract = {Extending over three Hubble Space Telescope (HST) cycles, the Hubble Frontier Fields (HFF) initiative constitutes the largest commitment ever of HST time to the exploration of the distant Universe via gravitational lensing by massive galaxy clusters. Here, we present models of the mass distribution in the six HFF cluster lenses, derived from a joint strong- and weak-lensing analysis anchored by a total of 88 multiple-image systems identified in existing HST data. The resulting maps of the projected mass distribution and of the gravitational magnification effectively calibrate the HFF clusters as gravitational telescopes. Allowing the computation of search areas in the source plane, these maps are provided to the community to facilitate the exploitation of forthcoming HFF data for quantitative studies of the gravitationally lensed population of background galaxies. Our models of the gravitational magnification afforded by the HFF clusters allow us to quantify the lensing-induced boost in sensitivity over blank-field observations and predict that galaxies at z > 10 and as faint as m(AB) = 32 will be detectable, up to 2 mag fainter than the limit of the Hubble Ultra Deep Field.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jauzac, M.; Clément, B.; Limousin, M.; Richard, J.; Jullo, E.; Ebeling, H.; Atek, H.; Kneib, J.-P.; Knowles, K.; Natarajan, P.; Eckert, D.; Egami, E.; Massey, R.; Rexroth, M.
Hubble Frontier Fields: a high-precision strong-lensing analysis of galaxy cluster MACSJ0416.1-2403 using ∼200 multiple images Article de journal
Dans: Monthly Notices of the Royal Astronomical Society, vol. 443, no. 2, p. 1549-1554, 2014.
@article{Jauzac11092014,
title = {Hubble Frontier Fields: a high-precision strong-lensing analysis of galaxy cluster MACSJ0416.1-2403 using ∼200 multiple images},
author = {Jauzac, M. and Clément, B. and Limousin, M. and Richard, J. and Jullo, E. and Ebeling, H. and Atek, H. and Kneib, J.-P. and Knowles, K. and Natarajan, P. and Eckert, D. and Egami, E. and Massey, R. and Rexroth, M.},
url = {http://mnras.oxfordjournals.org/content/443/2/1549.abstract},
doi = {10.1093/mnras/stu1355},
year = {2014},
date = {2014-01-01},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {443},
number = {2},
pages = {1549-1554},
abstract = {We present a high-precision mass model of the galaxy cluster MACSJ0416.1-2403, based on a strong-gravitational-lensing analysis of the recently acquired Hubble Space Telescope Frontier Fields (HFF) imaging data. Taking advantage of the unprecedented depth provided by HST/Advanced Camera for Survey observations in three passbands, we identify 51 new multiply imaged galaxies, quadrupling the previous census and bringing the grand total to 68, comprising 194 individual lensed images. Having selected a subset of the 57 most securely identified multiply imaged galaxies, we use the lenstool software package to constrain a lens model comprised of two cluster-scale dark-matter haloes and 98 galaxy-scale haloes. Our best-fitting model predicts image positions with an rms error of 0.68 arcsec, which constitutes an improvement of almost a factor of 2 over previous, pre-HFF models of this cluster. We find the total projected mass inside a 200 kpc aperture to be (1.60 ± 0.01) × 1014 M⊙, a measurement that offers a three-fold improvement in precision, reaching the per cent level for the first time in any cluster. Finally, we quantify the increase in precision of the derived gravitational magnification of high-redshift galaxies and find an improvement by a factor of ∼2.5 in the statistical uncertainty. Our findings impressively confirm that HFF imaging has indeed opened the domain of high-precision mass measurements for massive clusters of galaxies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morvan, Dominique
Wind effects, unsteady behaviors, and regimes of propagation of surface fires in open field Article de journal
Dans: Combustion Science and Technology, vol. 186, no. 7, p. 869-888, 2014.
@article{morvan:hal-01049769,
title = {Wind effects, unsteady behaviors, and regimes of propagation of surface fires in open field},
author = {Morvan, Dominique},
url = {https://hal.archives-ouvertes.fr/hal-01049769},
doi = {10.1080/00102202.2014.885961},
year = {2014},
date = {2014-01-01},
journal = {Combustion Science and Technology},
volume = {186},
number = {7},
pages = {869-888},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dolocan, Voicu O.
Metastable domain wall dynamics in magnetic nanowires Article de journal
Dans: The European Physical Journal B, vol. 87, no. 8, p. 188, 2014, ISSN: 1434-6036.
@article{Dolocan2014,
title = {Metastable domain wall dynamics in magnetic nanowires},
author = {Dolocan, Voicu O.},
url = {http://dx.doi.org/10.1140/epjb/e2014-41059-8},
doi = {10.1140/epjb/e2014-41059-8},
issn = {1434-6036},
year = {2014},
date = {2014-01-01},
journal = {The European Physical Journal B},
volume = {87},
number = {8},
pages = {188},
abstract = {We study the formation and control of metastable states of pairs of domain walls in cylindrical nanowires of small diameter where the transverse walls are the lower energy state. We show that these pairs form bound states under certain conditions, with a lifetime as long as 200 ns, and are stabilized by the influence of a spin polarized current. Their stability is analyzed with a model based on the magnetostatic interaction and by 3D micromagnetic simulations. The apparition of bound states could hinder the operation of devices.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Voicu O. Dolocan
Domain wall pinning and interaction in rough cylindrical nanowires Article de journal
Dans: Applied Physics Letters, vol. 105, no. 16, p. 162401, 2014.
@article{doi:10.1063/1.4899128,
title = {Domain wall pinning and interaction in rough cylindrical nanowires},
author = {Voicu O. Dolocan},
url = {http://dx.doi.org/10.1063/1.4899128},
doi = {10.1063/1.4899128},
year = {2014},
date = {2014-01-01},
journal = {Applied Physics Letters},
volume = {105},
number = {16},
pages = {162401},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Voicu O Dolocan
Metastable domain wall dynamics in magnetic nanowires Article de journal
Dans: Eur. Phys. J. B, vol. 87, no. 8, p. 188, 2014.
@article{refId0b,
title = {Metastable domain wall dynamics in magnetic nanowires},
author = {Voicu O } {Dolocan},
url = {https://doi.org/10.1140/epjb/e2014-41059-8},
doi = {10.1140/epjb/e2014-41059-8},
year = {2014},
date = {2014-01-01},
journal = {Eur. Phys. J. B},
volume = {87},
number = {8},
pages = {188},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2013
Graur, Irina; Ho, Minh Tuan; Wuest, Martin
Simulation of the transient heat transfer between two coaxial cylinders Article de journal
Dans: Journal of Vacuum Science & Technology A, vol. 31, no. 6, 2013.
@article{:/content/avs/journal/jvsta/31/6/10.1116/1.4818870,
title = {Simulation of the transient heat transfer between two coaxial cylinders},
author = {Graur, Irina and Ho, Minh Tuan and Wuest, Martin},
url = {http://scitation.aip.org/content/avs/journal/jvsta/31/6/10.1116/1.4818870},
doi = {http://dx.doi.org/10.1116/1.4818870},
year = {2013},
date = {2013-01-01},
journal = {Journal of Vacuum Science & Technology A},
volume = {31},
number = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bocquillon, E.; Freulon, V.; Berroir, J.-M; Degiovanni, P.; Plac cais, B.; Cavanna, A.; Jin, Y.; F`eve, G.
Coherence and Indistinguishability of Single Electrons Emitted by Independent Sources Article de journal
Dans: Science, vol. 339, no. 6123, p. 1054–1057, 2013, ISSN: 0036-8075.
@article{Bocquillon1054,
title = {Coherence and Indistinguishability of Single Electrons Emitted by Independent Sources},
author = {Bocquillon, E. and Freulon, V. and Berroir, J.-M and Degiovanni, P. and Plac cais, B. and Cavanna, A. and Jin, Y. and F`eve, G.},
url = {http://science.sciencemag.org/content/339/6123/1054},
doi = {10.1126/science.1232572},
issn = {0036-8075},
year = {2013},
date = {2013-01-01},
journal = {Science},
volume = {339},
number = {6123},
pages = {1054--1057},
publisher = {American Association for the Advancement of Science},
abstract = {Quantum information processing requires the generation of indistinguishable and coherent particles. While these have been demonstrated for photons, carrying it over for electrons and the possibility of quantum electronic implementations has been challenging. Using two independent single-electron sources patterned into a two-dimensional electron gas, Bocquillon et al. (p. 1054, published online 24 January; see the Perspective by Sch"onenberger) performed single-electron interference experiments. The results demonstrate that the generated electrons can possess the desired properties for potential quantum applications. The on-demand emission of coherent and indistinguishable electrons by independent synchronized sources is a challenging task of quantum electronics, in particular regarding its application for quantum information processing. Using two independent on-demand electron sources, we triggered the emission of two single-electron wave packets at different inputs of an electronic beam splitter. Whereas classical particles would be randomly partitioned by the splitter, we observed two-particle interference resulting from quantum exchange. Both electrons, emitted in indistinguishable wave packets with synchronized arrival time on the splitter, exited in different outputs as recorded by the low-frequency current noise. The demonstration of two-electron interference provides the possibility of manipulating coherent and indistinguishable single-electron wave packets in quantum conductors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ersoy, Mehmet; Golay, Frederic; Yushchenko, Lyudmyla
Adaptive multi scale scheme based on numerical density of entropy production for conservation laws. Article de journal
Dans: Central European Journal of Mathematics, vol. 11, p. 1392-1415, 2013.
@article{ersoy:hal-00980132,
title = {Adaptive multi scale scheme based on numerical density of entropy production for conservation laws.},
author = {Ersoy, Mehmet and Golay, Frederic and Yushchenko, Lyudmyla},
url = {https://hal-univ-tln.archives-ouvertes.fr/hal-00980132},
doi = {10.2478/s11533-013-0252-6},
year = {2013},
date = {2013-01-01},
journal = {Central European Journal of Mathematics},
volume = {11},
pages = {1392-1415},
publisher = {Springer Verlag},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maget, Patrick; Mellet, Nicolas; Lütjens, Hinrich; Meshcheriakov, Dmytro; Garbet, Xavier
Curvature effect on tearing modes in presence of neoclassical friction Article de journal
Dans: Physics of Plasmas, vol. 20, no. 11, 2013.
@article{:/content/aip/journal/pop/20/11/10.1063/1.4829038,
title = {Curvature effect on tearing modes in presence of neoclassical friction},
author = {Maget, Patrick and Mellet, Nicolas and Lütjens, Hinrich and Meshcheriakov, Dmytro and Garbet, Xavier},
url = {http://scitation.aip.org/content/aip/journal/pop/20/11/10.1063/1.4829038},
doi = {http://dx.doi.org/10.1063/1.4829038},
year = {2013},
date = {2013-01-01},
journal = {Physics of Plasmas},
volume = {20},
number = {11},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Boris Le Guennic, Nicolas Ferré
Analysis of the Magnetic Exchange Interaction in Halide-Bridged Cu(II) Binuclear Complexes: Deciphering the Paths Article de journal
Dans: Current Inorganic Chemistry 3(3), 2013.
@article{Guennic2013,
title = {Analysis of the Magnetic Exchange Interaction in Halide-Bridged Cu(II) Binuclear Complexes: Deciphering the Paths},
author = {Boris Le Guennic, Nicolas Ferré},
url = {https://www.researchgate.net/publication/263338004_Analysis_of_the_Magnetic_Exchange_Interaction_in_Halide-Bridged_CuII_Binuclear_Complexes_Deciphering_the_Paths},
doi = {10.2174/1877944103666140110225547},
year = {2013},
date = {2013-01-01},
journal = {Current Inorganic Chemistry 3(3)},
abstract = {Following a recently reported synthesis of linearly halide-bridged Cu(II) complexes [Inorg. Chem. 2012, 51, 7966-7968] characterized by strong antiferromagnetic exchange couplings (J), we applied Difference Dedicated Configuration Interaction (DDCI) and Broken-Symmetry Density Functional Theory (BS-DFT) approaches in order to analyze theoretically the trend observed, in which the decreasing electronegativity of the central halide induces an exacerbed magnetic coupling. The importance of the magnetic orbitals in DDCI calculations is acknowledged. The use of reduced molecular models is shown to lead to significant differences in J, in the case of chloride and bromide bridges. Finally, the BS-DFT decomposition of J in its main physical contributions confirms the importance of the kinetic exchange mediated by the halide bridge, but also points towards an increasing core polarization contribution when going from fluoride to bromide.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
K. Gavrilov; D. Morvan; G. Accary; D. Lyubimov; S. Meradji
Numerical simulation of coherent turbulent structures and of passive scalar dispersion in a canopy sub-layer Article de journal
Dans: Computers & Fluids, vol. 78, p. 54 - 62, 2013, ISSN: 0045-7930, (LES of turbulence aeroacoustics and combustion).
@article{Gavrilov201354,
title = {Numerical simulation of coherent turbulent structures and of passive scalar dispersion in a canopy sub-layer},
author = {K. Gavrilov and D. Morvan and G. Accary and D. Lyubimov and S. Meradji},
url = {http://www.sciencedirect.com/science/article/pii/S0045793012003374},
doi = {http://dx.doi.org/10.1016/j.compfluid.2012.08.021},
issn = {0045-7930},
year = {2013},
date = {2013-01-01},
journal = {Computers & Fluids},
volume = {78},
pages = {54 - 62},
abstract = {This study deals with the problem of turbulent atmospheric boundary-layer flow over a forest canopy. Numerous previous works showed that this flow presents more similarities with a mixing-layer flow than with the standard boundary-layer flow. In this paper, this problem was studied for homogeneous canopies, using large eddy simulation (LES). The numerical results reproduced correctly the various steps of development of this flow: the appearance of a first generation of coherent structures resulting from the development of a primary Kelvin–Helmholtz instability, the reorganization of these structures, by vortex pairing and kinking, the development of a secondary instability and the formation of horseshoe vortices. Then, the process of transport of a passive scalar from a forest canopy into a clear atmosphere was studied in two cases, i.e., when the passive scalar concentration at the surface foliage is either constant or time-varying. Even though this small difference has little influence on the concentration patterns, the results showed that it can significantly affect the concentration magnitude as well as the dynamics of the total concentration in the atmosphere.},
note = {LES of turbulence aeroacoustics and combustion},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dominique Morvan; Sofiane Meradji; William Mell
Interaction between head fire and backfire in grasslands Article de journal
Dans: Fire Safety Journal, vol. 58, p. 195 - 203, 2013, ISSN: 0379-7112.
@article{Morvan2013195,
title = {Interaction between head fire and backfire in grasslands},
author = {Dominique Morvan and Sofiane Meradji and William Mell},
url = {http://www.sciencedirect.com/science/article/pii/S0379711213000295},
doi = {http://dx.doi.org/10.1016/j.firesaf.2013.01.027},
issn = {0379-7112},
year = {2013},
date = {2013-01-01},
journal = {Fire Safety Journal},
volume = {58},
pages = {195 - 203},
abstract = {This paper deals with 3D numerical simulations of two fires fronts (head and backfire) propagating simultaneously through a grassland fuel. The simulations were carried out using a “fully” physical and three-dimensional fire model (namely WFDS). One of the objectives of this work, was to evaluate the potential for fully physical fire model to simulate the interactions between two fire fronts (a head fire and a backfire), in conditions similar to those encountered during suppression fire operations. A set of numerical simulations was first carried out for standalone head fires propagating through grasslands on a flat terrain and for various wind conditions ranging between 1 and 10 m/s. These results were compared with experimental data and numerical results from the literature. The same calculations were then repeated, with a backfire ignited at the downwind side of the plot. The numerical results highlighted that, for these particular conditions, head fire and backfire can interact, mainly, via two mechanisms:• at relatively large distances (greater than 10 m) the head fire acts on backfire as a screen and reduces the direct action of the wind flow on the backfire, • at relative small distances (nearly equal to 10 m) the gas flow (entrainment) generated in the vicinity of the head fire promotes the aspiration of the backfire towards the main fire front.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dominique Morvan
Numerical study of the effect of fuel moisture content (FMC) upon the propagation of a surface fire on a flat terrain Article de journal
Dans: Fire Safety Journal, vol. 58, p. 121 - 131, 2013, ISSN: 0379-7112.
@article{Morvan2013121,
title = {Numerical study of the effect of fuel moisture content (FMC) upon the propagation of a surface fire on a flat terrain},
author = {Dominique Morvan},
url = {http://www.sciencedirect.com/science/article/pii/S037971121300012X},
doi = {http://dx.doi.org/10.1016/j.firesaf.2013.01.010},
issn = {0379-7112},
year = {2013},
date = {2013-01-01},
journal = {Fire Safety Journal},
volume = {58},
pages = {121 - 131},
abstract = {This paper was devoted to clarify and evaluate how fuel moisture content (FMC) characterising a homogeneous vegetation layer (grass or shrubs), can affect the behaviour of surface fire. The approach used in this study was based on numerical simulations performed using a detailed fire physical model. The numerical results were analysed in terms of fire residence time, fire front depth, mass loss rate and rate of spread (ROS). Two windy conditions (calm and weak) were studied to evaluate the decay of the rate of spread (ROS) resulting from an increase of the fuel moisture content. The effect of wind velocity upon marginal burning conditions was also analysed. The numerical results were compared with empirical data of the literature.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}