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}
}
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.
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.
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}
}
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.
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.
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}
}
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.
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.
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}
}
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.
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}
}
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.
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}
}
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.%).
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.%).
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.
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.
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.
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}
}
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.