Next projects B review : October 15 2023 Proposal must be submitted before September 30 2023.
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Publications and communications which have benefited of mésocentre resources should contain : « Centre de Calcul Intensif d’Aix-Marseille is acknowledged for granting access to its high performance computing resources. »
Recent publications :
2023
Bourne, Emily; Leleux, Philippe; Kormann, Katharina; Kruse, Carola; Grandgirard, Virginie; Guclu, Yaman; Kuhn, Martin J.; Rude, Ulrich; Sonnendrucker, Eric; Zoni, Edoardo
Solver comparison for Poisson-like equations on tokamak geometries Journal Article
In: 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.
Bourne, Emily; Munschy, Yann; Grandgirard, Virginie; Mehrenberger, Michel; Ghendrih, Philippe
Non-uniform splines for semi-Lagrangian kinetic simulations of the plasma sheath Journal Article
In: 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.
Zhao, Song; Bhairapurada, Karthik; Tayyab, Muhammad; Mercier, Renaud; Boivin, Pierre
Lattice-Boltzmann modeling of the quiet and unstable PRECCINSTA burner modes Journal Article
In: 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.
Cai, Shang-Gui; Jacob, Jerome; Sagaut, Pierre
Immersed boundary based near-wall modeling for large eddy simulation of turbulent wall-bounded flow Journal Article
In: 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.
Dufaure, A.; Eyraud, C.; Sorsa, L. - I; Yusuf, Y. O.; Pursiainen, S.; Geffrin, J. -M
Imaging of the internal structure of an asteroid analogue from quasi-monostatic microwave measurement data I. The frequency domain approach Journal Article
In: 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.
Sorsa, Liisa-Ida; Yusuf, Yusuf Oluwatoki; Dufaure, Astrid; Geffrin, Jean-Michel; Eyraud, Christelle; Pursiainen, Sampsa
Imaging of the internal structure of an asteroid analogue from quasi-monostatic microwave measurement data II. The time domain approach Journal Article
In: 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.
Jonckheere, T.; Rech, J.; Gremaud, B.; Martin, T.
Anyonic Statistics Revealed by the Hong-Ou-Mandel Dip for Fractional Excitations Journal Article
In: 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.
Li, Qing; Chen, Jieyi; Faux, Pierre; Delgado, Miguel Eduardo; Bonfante, Betty; Fuentes-Guajardo, Macarena; Mendoza-Revilla, Javier; Chacon-Duque, J. Camilo; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Jaramillo, Claudia; Arias, William; Barquera, Rodrigo; Everardo-Martinez, Paola; Sanchez-Quinto, Mirsha; Gomez-Valdes, Jorge; Villamil-Ramirez, Hugo; de Cerqueira, Caio C. Silva; Huenemeier, Tabita; Ramallo, Virginia; Wu, Sijie; Du, Siyuan; Giardina, Andrea; Paria, Soumya Subhra; Khokan, Mahfuzur Rahman; Gonzalez-Jose, Rolando; Schueler-Faccini, Lavinia; Bortolini, Maria-Catira; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Gallo, Carla; Poletti, Giovanni; Rojas, Winston; Rothhammer, Francisco; Navarro, Nicolas; Wang, Sijia; Adhikari, Kaustubh; Ruiz-Linares, Andres
Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape Journal Article
In: 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.
Terrien, Louise; Favier, Benjamin; Knobloch, Edgar
Suppression of Wall Modes in Rapidly Rotating Rayleigh-Be ` nard Convection by Narrow Horizontal Fins Journal Article
In: 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.
Valente, Michael; Collinet, Nils; Manh, Thien-Phong Vu; Popoff, Dimitri; Rahmani, Khalissa; Naciri, Karima; Bessou, Gilles; Rua, Rejane; Gil, Laurine; Mionnet, Cyrille; Milpied, Pierre; Tomasello, Elena; Dalod, Marc
Novel mouse models based on intersectional genetics to identify and characterize plasmacytoid dendritic cells Journal Article
In: NATURE IMMUNOLOGY, vol. 24, no. 4, pp. 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.
Casal, Mariana T. T.; Toldo, Josene M. M.; Barbatti, Mario; Plasser, Felix
Classification of doubly excited molecular electronic states Journal Article
In: CHEMICAL SCIENCE, vol. 14, no. 15, pp. 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.
Loisy, Aurore; Heinonen, Robin A. A.
Deep reinforcement learning for the olfactory search POMDP: a quantitative benchmark Journal Article
In: 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.
Benseghier, Zeyd; Luu, Li-Hua; Cuellar, Pablo; Bonelli, Stephane; Philippe, Pierre
On the erosion of cohesive granular soils by a submerged jet: a numerical approach Journal Article
In: 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.
Jr, Max Pinheiro; Zhang, Shuang; Dral, Pavlo O. O.; Barbatti, Mario
WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets Journal Article
In: 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.
Lyu, Jinming; Chen, Paul G.; Farutin, Alexander; Jaeger, Marc; Misbah, Chaouqi; Leonetti, Marc
Swirling of vesicles: Shapes and dynamics in Poiseuille flow as a model of RBC microcirculation Journal Article
In: 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
Lemasquerier, D.; Favier, B.; Bars, M. Le
Zonal jets experiments in the gas giants' zonostrophic regime Journal Article
In: Icarus, vol. 390, pp. 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}
}
Chachanidze, Revaz; Xie, Kaili; Lyu, Jinming; Jaeger, Marc; Leonetti, Marc
Breakups of Chitosan microcapsules in extensional flow Journal Article
In: JOURNAL OF COLLOID AND INTERFACE SCIENCE, vol. 629, no. A, pp. 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.
Xia, Ming; Record, Marie-Christine; Boulet, Pascal
Investigation of PbSnTeSe High-Entropy Thermoelectric Alloy: A DFT Approach Journal Article
In: 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.
Bonfrate, Simone; Ferre, Nicolas; Huix-Rotllant, Miquel
In: 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.