Next projects B review : October 15 2020 Proposal must be submitted before September 30 2020.
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 :
2020 |
Paul G Chen; J M Lyu; M Jaeger; M Leonetti Shape transition and hydrodynamics of vesicles in tube flow Journal Article In: Phys. Rev. Fluids, 5 , pp. 043602, 2020. @article{PhysRevFluids.5.043602, title = {Shape transition and hydrodynamics of vesicles in tube flow}, author = {Paul G Chen and J M Lyu and M Jaeger and M Leonetti}, url = {https://link.aps.org/doi/10.1103/PhysRevFluids.5.043602}, doi = {10.1103/PhysRevFluids.5.043602}, year = {2020}, date = {2020-04-01}, journal = {Phys. Rev. Fluids}, volume = {5}, pages = {043602}, publisher = {American Physical Society}, abstract = {The steady motion and deformation of a lipid-bilayer vesicle translating through a circular tube in low Reynolds number pressure-driven flow are investigated numerically using an axisymmetric boundary element method. This fluid-structure interaction problem is determined by three dimensionless parameters: reduced volume (a measure of the vesicle asphericity), geometric confinement (the ratio of the vesicle effective radius to the tube radius), and capillary number (the ratio of viscous to bending forces). The physical constraints of a vesicle—fixed surface area and enclosed volume when it is confined in a tube—determine critical confinement beyond which it cannot pass through without rupturing its membrane. The simulated results are presented in a wide range of reduced volumes [0.6, 0.98] for different degrees of confinement; the reduced volume of 0.6 mimics red blood cells. We draw a phase diagram of vesicle shapes and propose a shape transition line separating the parachutelike shape region from the bulletlike one in the reduced volume versus confinement phase space. We show that the shape transition marks a change in the behavior of vesicle mobility, especially for highly deflated vesicles. Most importantly, high-resolution simulations make it possible for us to examine the hydrodynamic interaction between the wall boundary and the vesicle surface at conditions of very high confinement, thus providing the limiting behavior of several quantities of interest, such as the thickness of lubrication film, vesicle mobility and its length, and the extra pressure drop due to the presence of the vesicle. This extra pressure drop holds implications for the rheology of dilute vesicle suspensions. Furthermore, we present various correlations and discuss a number of practical applications. The results of this work may serve as a benchmark for future studies and help devise tube-flow experiments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The steady motion and deformation of a lipid-bilayer vesicle translating through a circular tube in low Reynolds number pressure-driven flow are investigated numerically using an axisymmetric boundary element method. This fluid-structure interaction problem is determined by three dimensionless parameters: reduced volume (a measure of the vesicle asphericity), geometric confinement (the ratio of the vesicle effective radius to the tube radius), and capillary number (the ratio of viscous to bending forces). The physical constraints of a vesicle—fixed surface area and enclosed volume when it is confined in a tube—determine critical confinement beyond which it cannot pass through without rupturing its membrane. The simulated results are presented in a wide range of reduced volumes [0.6, 0.98] for different degrees of confinement; the reduced volume of 0.6 mimics red blood cells. We draw a phase diagram of vesicle shapes and propose a shape transition line separating the parachutelike shape region from the bulletlike one in the reduced volume versus confinement phase space. We show that the shape transition marks a change in the behavior of vesicle mobility, especially for highly deflated vesicles. Most importantly, high-resolution simulations make it possible for us to examine the hydrodynamic interaction between the wall boundary and the vesicle surface at conditions of very high confinement, thus providing the limiting behavior of several quantities of interest, such as the thickness of lubrication film, vesicle mobility and its length, and the extra pressure drop due to the presence of the vesicle. This extra pressure drop holds implications for the rheology of dilute vesicle suspensions. Furthermore, we present various correlations and discuss a number of practical applications. The results of this work may serve as a benchmark for future studies and help devise tube-flow experiments. |
Daphné Lemasquerier; Giulio Facchini; Benjamin Favier ; Michael Le Bars Remote determination of the shape of Jupiter’s vortices from laboratory experiments Journal Article In: Nature Physics, 2020. @article{Lemasquerier2020, title = {Remote determination of the shape of Jupiter’s vortices from laboratory experiments}, author = {Daphné Lemasquerier; Giulio Facchini; Benjamin Favier ; Michael Le Bars}, url = {https://doi.org/10.1038/s41567-020-0833-9}, doi = {10.1038/s41567-020-0833-9}, year = {2020}, date = {2020-03-16}, journal = {Nature Physics}, abstract = {Jupiter’s dynamics shapes its cloud patterns but remains largely unknown below this natural observational barrier. Unravelling the underlying three-dimensional flows is thus a primary goal for NASA’s ongoing Juno mission, which was launched in 2011. Here, we address the dynamics of large Jovian vortices using laboratory experiments complemented by theoretical and numerical analyses. We determine the generic force balance responsible for their three-dimensional pancake-like shape. From this, we define scaling laws for their horizontal and vertical aspect ratios as a function of the ambient rotation, stratification and zonal wind velocity. For the Great Red Spot in particular, our predicted horizontal dimensions agree well with measurements at the cloud level since the Voyager mission in 1979. We also predict the Great Red Spot’s thickness, which is inaccessible to direct observation. It has remained surprisingly constant despite the observed horizontal shrinking. Our results now await comparison with upcoming Juno observations. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Jupiter’s dynamics shapes its cloud patterns but remains largely unknown below this natural observational barrier. Unravelling the underlying three-dimensional flows is thus a primary goal for NASA’s ongoing Juno mission, which was launched in 2011. Here, we address the dynamics of large Jovian vortices using laboratory experiments complemented by theoretical and numerical analyses. We determine the generic force balance responsible for their three-dimensional pancake-like shape. From this, we define scaling laws for their horizontal and vertical aspect ratios as a function of the ambient rotation, stratification and zonal wind velocity. For the Great Red Spot in particular, our predicted horizontal dimensions agree well with measurements at the cloud level since the Voyager mission in 1979. We also predict the Great Red Spot’s thickness, which is inaccessible to direct observation. It has remained surprisingly constant despite the observed horizontal shrinking. Our results now await comparison with upcoming Juno observations. |
Joackim Bernier; Michel Mehrenberger LONG-TIME BEHAVIOR OF SECOND ORDER LINEARIZED VLASOV-POISSON EQUATIONS NEAR A HOMOGENEOUS EQUILIBRIUM Journal Article In: KINETIC AND RELATED MODELS, 13 (1), pp. 129-168, 2020, ISSN: 1937-5093. @article{ISI:000500816900007, title = {LONG-TIME BEHAVIOR OF SECOND ORDER LINEARIZED VLASOV-POISSON EQUATIONS NEAR A HOMOGENEOUS EQUILIBRIUM}, author = {Joackim Bernier and Michel Mehrenberger}, doi = {10.3934/krm.2020005}, issn = {1937-5093}, year = {2020}, date = {2020-02-01}, journal = {KINETIC AND RELATED MODELS}, volume = {13}, number = {1}, pages = {129-168}, publisher = {AMER INST MATHEMATICAL SCIENCES-AIMS}, address = {PO BOX 2604, SPRINGFIELD, MO 65801-2604 USA}, abstract = {The asymptotic behavior of the solutions of the second order linearized Vlasov-Poisson system around homogeneous equilibria is derived. It provides a fine description of some nonlinear and multidimensional phenomena such as the existence of Best frequencies. Numerical results for the 1D x 1D and 2D x 2D Vlasov-Poisson system illustrate the effectiveness of this approach.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The asymptotic behavior of the solutions of the second order linearized Vlasov-Poisson system around homogeneous equilibria is derived. It provides a fine description of some nonlinear and multidimensional phenomena such as the existence of Best frequencies. Numerical results for the 1D x 1D and 2D x 2D Vlasov-Poisson system illustrate the effectiveness of this approach. |
Patrick Maget; Judith Frank; Timothee Nicolas; Olivier Agullo; Xavier Garbet; Hinrich Lutjens Natural poloidal asymmetry and neoclassical transport of impurities in tokamak plasmas Journal Article In: PLASMA PHYSICS AND CONTROLLED FUSION, 62 (2), 2020, ISSN: 0741-3335. @article{ISI:000500812100001, title = {Natural poloidal asymmetry and neoclassical transport of impurities in tokamak plasmas}, author = {Patrick Maget and Judith Frank and Timothee Nicolas and Olivier Agullo and Xavier Garbet and Hinrich Lutjens}, doi = {10.1088/1361-6587/ab53ab}, issn = {0741-3335}, year = {2020}, date = {2020-02-01}, journal = {PLASMA PHYSICS AND CONTROLLED FUSION}, volume = {62}, number = {2}, publisher = {IOP PUBLISHING LTD}, address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND}, abstract = {The neoclassical transport of impurities is investigated for a plasma without toroidal rotation nor anisotropic ion temperature. It is shown that a natural poloidal asymmetry of the impurity density exists in this case, and that it can be described with a simple analytical model. The poloidal asymmetry tends naturally to cancel as the impurity profile evolves towards its steady state, so that the main effect of the poloidal asymmetry is to slow down the impurity flux compared to its predicted value without poloidal asymmetry. The contribution of the asymmetries of the electrostatic potential and of the main ion density can be included in the analytical derivation, thus forming a self-consistent description of the neoclassical impurity flux together with its poloidal distribution. Numerical simulations with a non linear fluid code confirm the analytical findings, showing that the neoclassical transport of impurities is strongly modified by its natural poloidal distribution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The neoclassical transport of impurities is investigated for a plasma without toroidal rotation nor anisotropic ion temperature. It is shown that a natural poloidal asymmetry of the impurity density exists in this case, and that it can be described with a simple analytical model. The poloidal asymmetry tends naturally to cancel as the impurity profile evolves towards its steady state, so that the main effect of the poloidal asymmetry is to slow down the impurity flux compared to its predicted value without poloidal asymmetry. The contribution of the asymmetries of the electrostatic potential and of the main ion density can be included in the analytical derivation, thus forming a self-consistent description of the neoclassical impurity flux together with its poloidal distribution. Numerical simulations with a non linear fluid code confirm the analytical findings, showing that the neoclassical transport of impurities is strongly modified by its natural poloidal distribution. |
Benjamin Kadoch; Wouter Bos; Kai Schneider Efficiency of laminar and turbulent mixing in wall-bounded flows Journal Article In: Physical Review E, 101 , 2020. @article{articlec, title = {Efficiency of laminar and turbulent mixing in wall-bounded flows}, author = {Benjamin Kadoch and Wouter Bos and Kai Schneider}, doi = {10.1103/PhysRevE.101.043104}, year = {2020}, date = {2020-01-01}, journal = {Physical Review E}, volume = {101}, abstract = {A turbulent flow mixes in general more rapidly a passive scalar than a laminar flow does. From an energetic point of view, for statistically homogeneous or periodic flows, the laminar regime is more efficient. However, the presence of walls may change this picture. We consider in this investigation mixing in two-dimensional laminar and turbulent wall-bounded flows using direct numerical simulation. We show that for sufficiently large Schmidt number, turbulent flows more efficiently mix a wall-bounded scalar field than a chaotic or laminar flow does. The mixing efficiency is shown to be a function of the Péclet number, and a phenomenological explanation yields a scaling law, consistent with the observations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A turbulent flow mixes in general more rapidly a passive scalar than a laminar flow does. From an energetic point of view, for statistically homogeneous or periodic flows, the laminar regime is more efficient. However, the presence of walls may change this picture. We consider in this investigation mixing in two-dimensional laminar and turbulent wall-bounded flows using direct numerical simulation. We show that for sufficiently large Schmidt number, turbulent flows more efficiently mix a wall-bounded scalar field than a chaotic or laminar flow does. The mixing efficiency is shown to be a function of the Péclet number, and a phenomenological explanation yields a scaling law, consistent with the observations. |
Benjamin Favier; Edgar Knobloch Robust wall states in rapidly rotating Rayleigh–Bénard convection Journal Article In: Journal of Fluid Mechanics, 895 , pp. R1, 2020. @article{favier_knobloch_2020, title = {Robust wall states in rapidly rotating Rayleigh–Bénard convection}, author = {Benjamin Favier and Edgar Knobloch}, doi = {10.1017/jfm.2020.310}, year = {2020}, date = {2020-01-01}, journal = {Journal of Fluid Mechanics}, volume = {895}, pages = {R1}, publisher = {Cambridge University Press}, abstract = {We show, using direct numerical simulations with experimentally realizable boundary conditions, that wall modes in Rayleigh–Bénard convection in a rapidly rotating cylinder persist even very far from their linear onset. These nonlinear wall states survive in the presence of turbulence in the bulk and are robust with respect to changes in the shape of the boundary of the container. In this sense, these states behave much like the topologically protected states present in two-dimensional chiral systems even though rotating convection is a three-dimensional nonlinear driven dissipative system. We suggest that the robustness of this nonlinear state may provide an explanation for the strong zonal flows observed recently in experiments and simulations of rapidly rotating convection at high Rayleigh number.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show, using direct numerical simulations with experimentally realizable boundary conditions, that wall modes in Rayleigh–Bénard convection in a rapidly rotating cylinder persist even very far from their linear onset. These nonlinear wall states survive in the presence of turbulence in the bulk and are robust with respect to changes in the shape of the boundary of the container. In this sense, these states behave much like the topologically protected states present in two-dimensional chiral systems even though rotating convection is a three-dimensional nonlinear driven dissipative system. We suggest that the robustness of this nonlinear state may provide an explanation for the strong zonal flows observed recently in experiments and simulations of rapidly rotating convection at high Rayleigh number. |
Karno Schwinn; Nicolas Ferré; Miquel Huix-Rotllant UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein Journal Article In: Phys. Chem. Chem. Phys., 22 , pp. 12447-12455, 2020. @article{D0CP01714K, title = {UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein}, author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant}, url = {http://dx.doi.org/10.1039/D0CP01714K}, doi = {10.1039/D0CP01714K}, year = {2020}, date = {2020-01-01}, journal = {Phys. Chem. Chem. Phys.}, volume = {22}, pages = {12447-12455}, publisher = {The Royal Society of Chemistry}, abstract = {Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered. |
Karno Schwinn; Nicolas Ferré; Miquel Huix-Rotllant Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome Journal Article In: Journal of Chemical Theory and Computation, 16 (6), pp. 3816-3824, 2020. @article{doi:10.1021/acs.jctc.9b01145, title = {Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome}, author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant}, url = {https://doi.org/10.1021/acs.jctc.9b01145}, doi = {10.1021/acs.jctc.9b01145}, year = {2020}, date = {2020-01-01}, journal = {Journal of Chemical Theory and Computation}, volume = {16}, number = {6}, pages = {3816-3824}, abstract = {Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an environment represented as a classical electrostatic potential. The main bottleneck of EE-QM/MM second derivatives is the solution of coupled perturbed equations for each MM atom perturbation. Here, we exploit the Q-vector method [J. Chem. Phys., 2019, 151, 041102] to workaround this bottleneck. We derive the full analytic second derivative of the EE-QM/MM energy, which allows us to compute QM, MM, and QM-MM Hessian blocks in an efficient and easy to implement manner. To show the capabilities of our method, we compute the normal modes for the full Arabidopsis thaliana plant cryptochrome. We show that the flavin adenine dinucleotide vibrations (QM subsystem) strongly mix with protein modes. We compute approximate vibronic couplings for the lowest bright transition, from which we extract spectral densities and the homogeneous broadening of FAD absorption spectrum in protein using vibrationally resolved electronic spectrum simulations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an environment represented as a classical electrostatic potential. The main bottleneck of EE-QM/MM second derivatives is the solution of coupled perturbed equations for each MM atom perturbation. Here, we exploit the Q-vector method [J. Chem. Phys., 2019, 151, 041102] to workaround this bottleneck. We derive the full analytic second derivative of the EE-QM/MM energy, which allows us to compute QM, MM, and QM-MM Hessian blocks in an efficient and easy to implement manner. To show the capabilities of our method, we compute the normal modes for the full Arabidopsis thaliana plant cryptochrome. We show that the flavin adenine dinucleotide vibrations (QM subsystem) strongly mix with protein modes. We compute approximate vibronic couplings for the lowest bright transition, from which we extract spectral densities and the homogeneous broadening of FAD absorption spectrum in protein using vibrationally resolved electronic spectrum simulations. |
