Next projects B review : February 15 2023 Proposal must be submitted before January 31 2023.

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 :
2022
Huang, Liangzhao; Eymeoud, Paul; Maugis, Philippe
Atomistic investigation on the impact of substitutional Al and Si atoms on the carbon kinetics in ferrite Journal Article
In: 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.
Taileb, Said; Millan-Merino, Alejandro; Zhao, Song; Boivin, Pierre
Lattice-Boltzmann modeling of lifted hydrogen jet flames: A new model for hazardous ignition prediction Journal Article
In: 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.
Kumar, Sanjeev; Medale, Marc; Brutin, David
Numerical model for sessile drop evaporation on heated substrate under microgravity Journal Article
In: 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.
Braun, Gabriel; Jr, Itamar Borges; Aquino, Adelia J. A.; Lischka, Hans; Plasser, Felix; Monte, Silmar A.; Ventura, Elizete; Mukherjee, Saikat; Barbatti, Mario
Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states Journal Article
In: 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).
Restrepo, S. Rendon; Barge, P.
Morphology and dynamical stability of self-gravitating vortices Numerical simulations Journal Article
In: 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.
Abiola, Temitope T.; Toldo, Josene M.; Casal, Mariana T.; Flourat, Amandine L.; Rioux, Benjamin; Woolley, Jack M.; Murdock, Daniel; Allais, Florent; Barbatti, Mario; Stavros, Vasilios G.
Direct structural observation of ultrafast photoisomerization dynamics in sinapate esters Journal Article
In: 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.
Kadoch, Benjamin; del-Castillo-Negrete, Diego; Bos, Wouter J. T.; Schneider, Kai
Lagrangian conditional statistics and flow topology in edge plasma turbulence Journal Article
In: 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.
Casal, Mariana T.; Toldo, Josene M.; Plasser, Felix; Barbatti, Mario
Using diketopyrrolopyrroles to stabilize double excitation and control internal conversion Journal Article
In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 38, pp. 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.
Combrisson, Etienne; Allegra, Michele; Basanisi, Ruggero; Ince, Robin A. A.; Giordano, Bruno L.; Bastin, Julien; Brovelli, Andrea
Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data Journal Article
In: 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.
Chaussy, Leo; Hagebaum-Reignier, Denis; Humbel, Stephane; Nava, Paola
Accurate computed singlet-triplet energy differences for cobalt systems: implication for two-state reactivity Journal Article
In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 36, pp. 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
Cai, Shang-Gui; Mozaffari, Sajad; Jacob, Jerome; Sagaut, Pierre
Application of immersed boundary based turbulence wall modeling to the Ahmed body aerodynamics Journal Article
In: 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.
Couston, Louis-Alexandre; Nandaha, Joseph; Favier, Benjamin
Competition between Rayleigh-Benard and horizontal convection Journal Article
In: 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.
Polak, Daniel W.; Casal, Mariana T.; Toldo, Josene M.; Hu, Xiantao; Amoruso, Giordano; Pomeranc, Olivia; Heeney, Martin; Barbatti, Mario; Ashfold, Michael N. R.; Oliver, Thomas A. A.
Probing the electronic structure and photophysics of thiophene-diketopyrrolopyrrole derivatives in solution Journal Article
In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 34, pp. 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.
Polak, Daniel W.; Casal, Mariana T.; Toldo, Josene M.; Hu, Xiantao; Amoruso, Giordano; Pomeranc, Olivia; Heeney, Martin; Barbatti, Mario; Ashfold, Michael N. R.; Oliver, Thomas A. A.
Probing the electronic structure and photophysics of thiophene-diketopyrrolopyrrole derivatives in solution Journal Article
In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 34, pp. 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.
Mukherjee, Saikat; Barbatti, Mario
A Hessian-Free Method to Prevent Zero-Point Energy Leakage in Classical Trajectories Journal Article
In: 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.
Gregoire, Claude; Spinelli, Lionel; Villazala-Merino, Sergio; Gil, Laurine; Holgado, Maria Pia; Moussa, Myriam; Dong, Chuang; Zarubica, Ana; Fallet, Mathieu; Navarro, Jean-Marc; Malissen, Bernard; Milpied, Pierre; Gaya, Mauro
Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism Journal Article
In: IMMUNITY, vol. 55, no. 7, pp. 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.
Kandaskalov, Dmytro; Huang, Liangzhao; Emo, Johnathan; Maugis, Philippe
Carbon diffusion in bcc- and bct-Fe: Influence of short-range C-C pair interactions studied from first-principles calculations Journal Article
In: 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.%).
Bhairapurada, Karthik; Denet, Bruno; Boivin, Pierre
A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities Journal Article
In: 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.
Taha, M.; Zhao, S.; Lamorlette, A.; Consalvi, J. L.; Boivin, P.
Lattice-Boltzmann modeling of buoyancy-driven turbulent flows Journal Article
In: 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.
Fan, Jianhua; Luu, Li-Hua; Philippe, Pierre; Noury, Gildas
Discharge rate characterization for submerged grains flowing through a hopper using DEM-LBM simulations Journal Article
In: 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.
Bonnet, G.; Nezri, E.; Kraljic, K.; Schimd, C.
Morphology of dark matter haloes beyond triaxiality Journal Article
In: MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, vol. 513, no. 4, pp. 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.
Mansour, Ritam; Mukherjee, Saikat; Pinheiro, Max Jr.; Noble, Jennifer A.; Jouvet, Christophe; Barbatti, Mario
Pre-Dewar structure modulates protonated azaindole photodynamics Journal Article
In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 24, no. 20, pp. 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.
Galko, Antoine; Gsell, Simon; D'Ortona, Umberto; Morin, Laurent; Favier, Julien
Pulsated Herschel-Bulkley flows in two-dimensional channels: A model for mucus clearance devices Journal Article
In: 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.
Wissocq, G.; Coratger, T.; Farag, G.; Zhao, S.; Boivin, P.; Sagaut, P.
Restoring the conservativity of characteristic-based segregated models: Application to the hybrid lattice Boltzmann method Journal Article
In: 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.
Truong, Hung; Engels, Thomas; Wehmann, Henja; Kolomenskiy, Dmitry; Lehmann, Fritz-Olaf; Schneider, Kai
An experimental data-driven mass-spring model of flexible Calliphora wings Journal Article
In: 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.
Bufferand, H; Balbin, J; Baschetti, S; Bucalossi, J; Ciraolo, G; Ghendrih, Ph; Mao, R; Rivals, N; Tamain, P; Yang, H; Giorgiani, G; Schwander, F; d'Abusco, M Scotto; Serre, E; Denis, J; Marandet, Y; Raghunathan, M; Innocente, P; Galassi, D
Implementation of multi-component Zhdanov closure in SOLEDGE3X Journal Article
In: Plasma Physics and Controlled Fusion, vol. 64, no. 5, pp. 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}
}
Scaramuzzino, Sara; Potier, Delphine; Ordioni, Robin; Grenot, Pierre; Payet-Bornet, Dominique; Luche, Herve; Malissen, Bernard
Single-cell transcriptomics uncovers an instructive T-cell receptor role in adult gamma delta T-cell lineage commitment Journal Article
In: 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.
D'Ortona, Umberto; Thomas, Nathalie; Lueptow, Richard M.
Mechanisms for recirculation cells in granular flows in rotating cylindrical rough tumblers Journal Article
In: 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}
}
Alekseenko, Elena; Roux, Bernard; Kuznetsov, Konstantin
Wind-Induced Resuspension and Transport of Contaminated Sediment from the Rove Canal into the Etang De Berre, France Journal Article
In: 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}
}
Bouffard, M.; Favier, B.; Lecoanet, D.; Bars, M. Le
Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell Journal Article
In: GEOPHYSICAL JOURNAL INTERNATIONAL, vol. 228, no. 1, pp. 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.
Bhairapurada, Karthik; Denet, Bruno; Boivin, Pierre
A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities Journal Article
In: Combustion and Flame, vol. 240, pp. 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}
}