Le développement de nouveaux ligands capables d’orienter sélectivement la réponse des cellules Natural Killer T invariantes (iNKT) vers un profil immunostimulant (Th1) ou immunorégulateur (Th2) est un challenge important qui peut mener à de nouvelles opportunités thérapeutiques dans le traitement de nombreuses maladies auto-Immunes et de cancers. Dans ce contexte, il est indispensable de comprendre le mécanisme de polarisation des iNKT. L’hypothèse principale est que l’intensité et la nature de la réponse biologique dépendent de la stabilité de l’interaction CD1d/TCR (Récepteur des Cellules T) qui serait elle-Même influencée par la forme du CD1d et donc par l’antigène qui y est chargé. C’est pourquoi nous avons étudié l’impact des activateurs des iNKT sur la structure du CD1d dans le but de faciliter la conception de molécules induisant sélectivement un profil de réponse Th1 ou Th2.En s’aidant des relations structure-Activité, du « docking-Scoring » et de dynamiques moléculaires de complexes CD1d/ligand analysées par différents outils, nous avons comparé la structure des CD1d humain et murins en fonction des profils de réponse.A partir de l’analyse des trajectoires de dynamique moléculaire, nous avons identifié des différences notables dans le comportement des CD1d humains et murins, les plus remarquables étant des changements dans les distances inter-Hélice et une mobilité du ligand accrue dans les systèmes humains. Un autre résultat majeur est l’identification d’une conformation spécifique de la tête polaire du ligand qui pourrait être corrélée à une réponse préférentiellement Th2.Ces différentes méthodes et la combinaison des descripteurs protéiques et moléculaires utilisés pour analyser la dynamique des complexes binaires nous donne suffisamment d’indices structuraux pour tenter de prédire le comportement de ligands dans le CD1d et aider à la conception de nouveaux modulateurs des cellules iNKT. / Development of new ligands able to switch invariant Natural Killer T (iNKT) cells toward an immunostimulant Th1 or an immunoregulative Th2 profile is a great challenge that can lead to new therapeutic opportunities in the treatment of various auto-Immune diseases or cancers. In this context, understanding the polarizing effect of iNKT ligands is of a major interest. We hypothesized that the intensity and nature of the biological response could depend on the stability of the CD1d-T Cell Receptor (TCR) interactions under the influence of the antigen which could modulate the shape of CD1d. Thus, our goal was to study the impact of iNKT ligands on the structure of the CD1d molecule and find clues to help design Th1/Th2 selective ligands.Using structure-Activity relationships, docking and molecular dynamic analyzed by a mix of classical and in house tools, we compared the structural behavior of the human and mouse CD1d molecule loaded with different ligands inducing Th1 or Th2 immune response profile. From the analysis of our molecular dynamics trajectories, it appears that there are noticeable differences in the behaviour of human and mouse CD1d molecules, mainly caracterized by changes at the inter-Helix distance and an increase ligand mobility for human systems.One major result is the identification of a specific conformational state of the ligand sugar group which could be correlated, in the present study, to the biological Th2 biased response. The different methods and combinations of ligand and protein descriptors used to analyze the dynamics of the binary complexes provide a structural basis for predicting the very different dynamical behaviors of ligands in CD1d and might aid in the future design of new iNKT modulators.

<p>Granular systems are ensembles of inelastic particles which dissipate energy during collisions. Granular systems serve as excellent models for a wide variety of materials such as sand, soils, corn, and powder. A rather remarkable property of granular systems is when excited, whether due to an interstitial fluid or via the boundaries, the granular particlesdisplay fluid-like behavior. As a result, there has been decades of granular research with the overarching goal of formulating a general granular hydrodynamic theory.</p> <p>However, the granular hydrodynamic theory is limited, and the underlying transport coefficients often require modifications which are based on empirical observations, and assuch, are system-specific. It is ideally better to devise a general theory which minimizes the information needed about the systema priori. The main thrust of the work undertaken shown here strives to develop such a model by using kinetic theory as the basis. More specifically, I investigate granular gases via the direct simulation Monte Carlo (DSMC) methodand modify the governing equations. In this thesis, two idealized cases of granular gases areconsidered: the homogeneous cooling state and a boundary-heated gas (or the pure conduc-tion case). In the former, the effects of polydispersity are probed. In the latter, the evolutionof the local hydrodynamics due to strong rarefaction effects are divulged. Additionally, amodified, more generalized constitutive relation for the heat flux is proposed and comparedwith DSMC results. Extensions of the DSMC method for dense granular gases and granulargases composed of non-spherical particles are also discussed.</p>