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Parallel biological in silico simulation
No full textInternational audienceIt is crucial to understand how biological systems work, in particular the metabolic pathways, if we want to be able to understand diseases. For instance, why and how the apoptosis mechanisms are disturbed in some cancers. One of the author has developed HSIM, a simulator dedicated to the biochemical simulation of the reactions inside the compartments of a virtual cell. Another author is the leader in the development of BOBPP a high level parallelization framework. In this article, we propose an important improvement of BOBPP in order to run HSIM in parallel. This will allow us to simulate more complex models, involving more chemical species and reactions, leading to more realistic results using a smaller amount of computing time
On the (anticipated) diversity of terrestrial planet atmospheres
No full textInternational audienceOn our way toward the characterization of smaller and more temperate planets, missions dedicated to the spectroscopic observation of exoplanets will teach us about the wide diversity of classes of planetary atmospheres, many of them probably having no equivalent in the Solar System. But what kind of atmospheres can we expect? To start answering this question, many theoretical studies have tried to understand and model the various processes controlling the formation and evolution of planetary atmospheres, with some success in the Solar System. Here, we shortly review these processes and we try to give an idea of the various type of atmospheres that these processes can create. As will be made clear, current atmosphere evolution models have many shortcomings yet, and need heavy calibrations. With that in mind, we will thus discuss how observations with a mission similar to EChO would help us unravel the link between a planet's environment and its atmosphere. © 2014 Springer Science+Business Media Dordrecht
Multisymplectic Lie group variational integrator for a geometrically exact beam in R-3
No full textInternational audienceIn this paper we develop, study, and test a Lie group multisymplectic integrator for geometrically exact beams based on the covariant Lagrangian formulation. We exploit the multisymplectic character of the integrator to analyze the energy and momentum map conservations associated to the temporal and spatial discrete evolutions. (C) 2014 Elsevier B.V. All rights reserved
Interactions non-covalentes et propriétés physico-chimiques de petits systèmes biologiques : approches théoriques
No full textThe three-dimensional structure and physico-chemical properties of biomolecules such as peptides are not only governed by their elementary composition but also various non-covalent intra-and inter-molecular interactions. The characterization, measurement and effects of these interactions are currently at the center of many researches at the interface between biology and physical chemistry. In this context, the aim of our thesis is a better understanding of these interactions in biomolecules and aggregates using the tools of quantum chemistry and molecular modeling. In this regard, due to the complexity and size of the real biological systems, chemical models have been developed. These have allowed us to study and understand the nature and effects of these interactions taken "individually" on the geometric and electronic structure of molecular systems such as small peptides and aggregates of glycine betaine. The role of non-covalent interactions on the reactivity of various physico-chemical conditions (electronic reduction, gas phase, microsolvation) is also one of the several approaches of our work. Among the systems examined, many of them included at least one ammonium, guanidinium or imidazolium charged groups, which are founded in the side chains of the amino acids lysine, arginine and histidine. We have shown that the chemical environment of these electronic charges greatly influences the structure and reactivity of the molecules that contain these groups. Eventually, we both performed a calibration of modeling methods for the study of the electronic properties of radical peptides and developed new protocols for the potential energy surface exploration starting from the AMOEBA polarizable force field, in order to optimize the conformational searches exhaustivity for flexible biological systems.La structure tridimensionnelle et les propriétés physico-chimiques des biomolécules telles que les peptides sont gouvernées non seulement par leur composition primaire mais aussi par diverses interactions non-covalentes, inter- et intra-moléculaires. La description, la mesure et les effets de ces interactions sont actuellement au cœur de nombreux travaux de recherches à l’interface entre la biologie et la physico-chimie. Dans ce cadre, nos travaux de thèse visent à une meilleure compréhension de ces interactions au sein de biomolécules et d’agrégats en utilisant les outils de la chimie quantique et de la modélisation moléculaire. Pour cela, du fait de la complexité et de la taille des systèmes biologiques réels, des modèles chimiques simplifiés ont été élaborés. Ceux-ci nous ont permis d’étudier et de comprendre la nature et les effets de ces interactions prises « individuellement » sur la structure géométrique et électronique de systèmes moléculaires tels que de petits peptides et des agrégats de la glycine bétaïne. Le rôle des interactions non-covalentes sur la réactivité dans des conditions physico-chimiques variées (réduction électronique, phase gazeuse, microsolvatation) constitue également une des approches de notre travail. Parmi les systèmes étudiés, nombres d’entre eux comportent un ou plusieurs groupes chargés ammonium, guanidinium ou imidazolium, présents dans les chaines latérales des acides aminés lysine, arginine et histidine. Nous avons montré que l’environnement chimique et électronique de ces groupes chargés influence largement la structure et la réactivité des molécules qui les contiennent. Enfin, au cours de nos travaux, nous avons réalisé une calibration des méthodes de modélisation pour l’étude des propriétés électroniques de peptides radicalaires et mis au point des protocoles d’exploration de surface d’énergie potentielle à partir du champ de force polarisable AMOEBA, ceci afin d’optimiser l’exhaustivité des recherches conformationnelles pour des systèmes biologiques flexibles
Volume Viscosity and Internal Energy Relaxation : Error Estimates
No full textWe investigate the fast relaxation of internal energy in nonequilibrium gas models derived from the kinetic theory of gases. We establish a priori estimates and existence theorems for symmetric hyperbolic-parabolic systems of partial differential equations with small second order terms and stiff sources. We also establish the stability of the corresponding equilibrium systems. We then prove local in time error estimates between the out of equilibrium solution and the one-temperature equilibrium fluid solution for well prepared data and justify the apparition of volume viscosity terms. The situation of ill prepared data with initial layers is also addressed
CORECLUSTER: A Degeneracy Based Graph Clustering Framework
No full textInternational audienceGraph clustering or community detection constitutes an important task forinvestigating the internal structure of graphs, with a plethora of applications in several domains. Traditional tools for graph clustering, such asspectral methods, typically suffer from high time and space complexity. In thisarticle, we present \textsc{CoreCluster}, an efficient graph clusteringframework based on the concept of graph degeneracy, that can be used along withany known graph clustering algorithm. Our approach capitalizes on processing thegraph in a hierarchical manner provided by its core expansion sequence, anordered partition of the graph into different levels according to the -coredecomposition. Such a partition provides a way to process the graph inan incremental manner that preserves its clustering structure, whilemaking the execution of the chosen clustering algorithm much faster due to thesmaller size of the graph's partitions onto which the algorithm operates
Comprehensive analysis of glaciated martian crater Greg
No full textInternational audienceDespite a substantial hemispheric asymmetry in clear-sky albedo, observations of Earth’s radiation budget reveal that the two hemispheres have the same all-sky albedo. Here, aquaplanet simulations with the atmosphere general circulation model ECHAM6 coupled to a slab ocean are performed to study to what extent and by which mechanisms clouds compensate hemispheric asymmetries in clear-sky albedo. Clouds adapt to compensate the imposed asymmetries because the intertropical convergence zone (ITCZ) shifts into the dark surface hemisphere. The strength of this tropical compensation mechanism is linked to the magnitude of the ITCZ shift. In some cases the ITCZ shift is so strong as to overcompensate the hemispheric asymmetry in clear-sky albedo, yielding a range of climates for which the hemisphere with lower clear-sky albedo has a higher all-sky albedo. The ITCZ shift is sensitive to the convection scheme and the depth of the slab ocean. Cloud–radiative feedbacks explain part of the sensitivity to the convection scheme as they amplify the ITCZ shift in the Tiedtke (TTT) scheme but have a neutral effect in the Nordeng (TNT) scheme. A shallower slab ocean depth, and thereby reduced thermal inertia of the underlying surface and increased seasonal cycle, stabilizes the ITCZ against annual-mean shifts. The results lend support to the idea that the climate system adjusts so as to minimize hemispheric albedo asymmetries, although there is no indication that the hemispheres must have exactly the same albedo
Thin films characterizations to design high-reflective coatings for ultrafast high power laser systems
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Simultaneous satellite measurements of NH<sub>3</sub> and NO<sub>2</sub> emitted by fires
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Large scale Tesla coil guided discharges initiated by femtosecond laser filamentation in air
No full textInternational audienceThe guiding of meter scale electric discharges produced in air by a Tesla coil is realized in laboratory using a focused terawatt laser pulse undergoing filamentation. The influence of the focus position, the laser arrival time or the gap length is studied to determine the best conditions for efficient laser guiding. Discharge parameters such as delay, jitter and resistance are characterized. An increase of the discharge length by a factor 5 has been achieved with the laser filaments, corresponding to a mean breakdown field of 2 kV/cm for a 1.8 m gap length. Consecutive guided discharges at a repetition rate of 10 Hz are also reported