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.

<div>Organic mixed ion-electron conducting (OMIEC) polymers are capable of transporting both electrons and ions. This unique functionality underpins many emerging applications, including biosensors, electrochemical transistors, and batteries. The fundamental operating principles and structure-function relationships of OMIECs are still being investigated. Computational tools such as coarse-grained molecular dynamics (CGMD), which use simpler representations than in atomistic modeling, are ideal to study OMIECs, as they can explore the slow dynamics and large length scale features of polymers. Nevertheless, methods development is still required for CGMD simulations to accurately describe OMIECs.</div><div><br></div><div>In this thesis, two CGMD simulation approaches have been adopted. One is a so-called "top-down" approach to develop a generic model of OMIECs. Top-down models are phenomenological but capable of exploring a broad space of materials variables, including backbone anisotropy, persistence length, side-chain density, and hydrophilicity. This newly developed model was used to interrogate the effect of side-chain polarity and patterning on OMIEC physics. These studies reproduce experimentally observed polymer swelling while for the first time clarifying several molecular factors affecting charge transport, including the role of trap sites, polaron delocalization, electrolyte percolation, and suggesting side-chain patterning as a potential tool to improve OMIEC performance.</div><div><br></div><div>The second strategy pursued in this thesis is bottom-up CGMD modeling of specific atomistic systems. The bottom-up approach enables CGMD simulations to be quantitatively related to specific materials; yet, the sources of error and methods for addressing them have yet to be systematically established. To address this gap, we have studied the effect of the CG mapping operator, an important CG variable, on the fidelity of atomistic and CGMD simulations. A major observation from this study is that prevailing CGMD methods are underdetermined with respect to atomistic training data. In a separate study, we have proposed a hybrid machine-learning and physics-based CGMD framework that utilizes information from multiple sources and improves on the accuracy of ML-only bottom-up CGMD approaches. </div>

Membranes made of composite polymer material are widely employed to separate gas mixtures in industrial processes. These membranes have better performance than membranes consisting of polymer alone. To understand the mechanism and therefore aid membrane design it is essential to explore the penetrant transport in the complex composites from the molecular level, but few researchers have done such research to our knowledge. Herein the penetrant transport in the composite Poly (4-methyl-2-pentyne) (PMP) and silica nanoparticle is being explored with molecular dynamics (MD) simulations. The structure of the PMP and amorphous silica nanoparticle composite was modeled and with the structure the variation of the cavity size distribution was established due to the existence of nanoparticles. The diffusivity of different penetrants, including H2, O2, Ar, CH4 and n-C4H10 was determined through least square fit of the data of mean square displacement at different times in the Fickian diffusive regime. The solubility coefficients and the permeability of different penetrants in PMP and the composite were calculated and the distribution of potential difference due to the penetrant insertion was analyzed in detail to find the reason of higher solubility in composite than pure PMP. Silica has different crystalline form. In faujasite silica, there are pores that are large enough to allow penetrants to pass through, while in cristobalite silica, the Si and O atoms are densely packed and there are no pores that penetrants can pass through. The transport properties of penetrants in the composite of PMP and nanoparticles of these two types of silica are therefore different. The molecular dynamics method was employed in the research to explore the transport of different penetrants in the composites of PMP and nanoparticles of two forms of silica, namely the cristobalite form and the faujasite form. The structures of the PMP and nanoparticle of cristobalite silica composite (PMPC) and the PMP and nanoparticle of faujasite silica composite (PMPF) were established and relaxed. With the relaxed structure, the cavity size change due to the insertion of both types of nanoparticle was analyzed. The diffusivity of different penetrants was determined through least square fit of the data of mean square displacement at different time in Fickian diffusive regime. The solubility coefficients and the permeability of different penetrants in PMPC and PMPF were calculated and compared. The parameters of "Ti" in the Lennard-Jones potential equation were estimated; MD simulation of penetrants transport in composite poly (4-methyl-2-pentyne) and TiO2 nanoparticles were done; the simulation results were compared with composite poly (4-methyl-2-pentyne) and silica nanoparticles. / Ph. D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1982. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Includes bibliographical references. / by Francisco Javier Carrion. / M.S.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1982. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Includes bibliographical references. / by Khaled Awni Touqan. / Ph.D.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18117号 / 理博第3995号 / 新制||理||1576(附属図書館) / 30975 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 高田 彰二, 教授 大野 睦人, 准教授 土井 知子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18816号 / 理博第4074号 / 新制||理||1586(附属図書館) / 31767 / 京都大学大学院理学研究科化学専攻 / (主査)教授 長谷川 健, 准教授 安藤 耕司, 教授 林 重彦 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19521号 / 理博第4181号 / 新制||理||1600(附属図書館) / 32557 / 京都大学大学院理学研究科化学専攻 / (主査)教授 林 重彦, 教授 谷村 吉隆, 教授 松本 吉泰 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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