The knowledge of solid-state second phase heterogeneous nucleation process is limited due to the experimental difficulty, such as tiny length scale, short time period, and high temperature condition. In recent years, some significant breakthroughs in nucleation studies have been achieved by aid of computational techniques. In this study, we apply molecular dynamics (MD) simulations to perform with heterogeneous nucleation occurring at grain boundaries (GB) during the austenite (FCC) phase to ferrite (BCC) phase transformation in a pure Fe polycrystalline system. A neighbor vector analysis (NVA) method has been introduced and it is shown how the NVA can be used to determine the misorientation of grain or interphase boundaries, which allow a further investigation of the boundary structure correlated to interfacial energy and mobility during the nucleation and early grain growth stage. Meanwhile, benefited from the MD technique, the bulk energy, grain boundary energy, and interfacial energy can be individually captured during the simulations, which allow a detail analyze of the shape, critical size and nucleation energy of specific nuclei, through the classical nucleation theory (CNT) and according to a faceted-spherical cap geometric model (FSC). In addition, we also compared the results from the classical approach with a new algorithm that combination of the multi-phase field model (MPFM) and the nudged elastic band (NEB) method to demonstrate the CNT in the solid-state conduction. Finally, we extend our simulation method to a more complex triple GB junction nucleation event, and investigate the non-classical barrier-free nucleation behaviors. The results support the critical informations to clarify the initial state of austenite to ferrite transition, and improve our knowledge of the heterogeneous nucleation process, which help to bridge the gap between the experimental measurements and the theoretical calculations. The simulation method also provided a new approach for studying the complicate heterogeneous nucleation phenomenon in solid-state for a wide variety of polycrystalline material systems. / Thesis / Doctor of Philosophy (PhD)

Molekulardynamik (MD) Simulationen wurden an zwei verschiedenen Systemen durchgeführt: 1. Grenzfläche zwischen Polyethylen und isotaktischem Polypropylen (PE-iPP) und 2. Zylindrische Mizellen, bestehend aus Tetradecyltrimethylammoniumbromid (C14TAB), in wässriger Lösung und an Fest-Flüssig-Grenzflächen. Die allgemeinen Schwierigkeiten bei der Simulation von Grenzflächen kristalliner Polymere wurden diskutiert und eine Methode für solche Simulationen vorgeschlagen. Diese Methode wurde zur epitaxialen Kristallisation von PE auf iPP benutzt. Experimentelle Ergebnisse der epitaxialen Kristallisation konnten durch die Simulation bestätigt werden. Ferner konnte vorhergesagt werden, dass PE bevorzugt auf einer iPP-Oberfläche mit hoher Methylgruppenkonzentration kristallisiert. Ebenso wurde durch die MD Simulation vorhergesagt, dass PE in der Grenzflächenregion von einer orthorhombischen zur monoklinischen Kristallstruktur wechselt. Die Simulationsdauer für die Mizellen betrug einige Nanosekunden. Die Ergebnisse für die Mizellen in wässriger Lösung stehen hierbei in guter Übereinstimmung mit experimentellen Werten. Im Widerspruch zur allgemein üblichen Vorstellung führte die Simulation der Mizellen zur Ausbildung eines Hohlraums in ihrer Mitte sowie zu einer inhomogenen Dichte des hydrophoben Mizellkerns. Dies wurde zum Teil der inhomogenen Verteilung der terminalen Methylgruppen im Mizellkern zugeschrieben. Zylindrische und halbzylindrische Mizellen wurden an den Paraffin/Wasser- und Gold/Wasser-Grenzflächen simuliert. / Molecular Dynamic (MD) simulation of two different systems was performed: 1) Polyethylene- isotactic Polypropylene (PE-iPP) interfaces and 2) cylindrical micelles formed by tetradecyl trimethylammonium bromide (C14TAB) molecules in aqueous solution and at solid liquid interfaces. The general difficulties of simulation of polymer crystalline interfaces were discussed and one method was proposed for such simulations. Thise method was used to simulate epitaxial crystallisation of PE on iPP. The experimental results on epitaxial crystallisation were confirmed by MD simulation and in addition epitaxial crystallisation of PE on iPP surface with high dencity of methyl groups was predicted. MD simulation also predicted that PE should change at the interfacial region from the orthorhombic to monoclinic crystalline structure. Several nanoseconds of life of cylindrical micelles were simulated. The simulation results for the micelle in aqueous solution were favourably compared with experimental results. In contradiction to the standard picture of an ionic micelle the simulated micelle formed hole in its centre and the density of the hydrophobic micelle core was inhomogeneous. This effect partially was explained by the inhomogeneous distribution of the terminal methyl groups in the micelle core. Cylindrical and half cylindrical micelles of C14TAB molecules were simulated at the paraffin- and gold-aqueous interfaces.

No description available.

A multiscale model is proposed to study the influence of interfacial interactions at the nanoscale in carbon nanotube(CNT)-polymer nanocomposites on the macroscale bulk elastic material properties. The efficiency of CNT reinforcement in terms of interfacial load transferring is assessed for the non-functionalized and functionalized interfaces between the CNTs and polymer matrix using force field based molecular dynamic simulations at the nanoscale. Polyethylene (PE) as a thermoplastic material is adopted and studied first because of its simplicity. Characterization of the nanoscale load transfer has been done through the identification of representative nanoscale interface elements for unfunctionalized CNT-PE interface models which are studied parametrically in terms of the length of the PE chains, the number of the PE chains and the "grip" position. Referring to the non-functionalized interface, CNTs interact with surrounding polymer only through weakly nonbonded van der Waals (vdW) forces in our study. Once appropriate values of these parameters are deemed to yield sufficiently converged results, the representative interface elements are subjected to normal and sliding mode simulations in order to obtain the force-separation responses at 100K and 300K for unfunctionalized CNT-PE interfaces. To study the functionalization effects, atomistic interface representative elements for functionalized CNT-PE interface are built based on non-functionalized interface models by grafting functional groups between the PE matrix and the graphene sheet. This introduces covalent bonding forces in addition to the non-bonded vdW forces. A modified consistent covalent force field (CVFF) and adaptive intermolecular reactive empirical bond order (AIREBO) potentials, both of which account for bond breaking, are applied to investigate the interfacial characteristic of functionalized CNT-PE interface in terms of the force-separation responses at 100K in both normal opening and sliding mode separations. In these studies, the focus has been on the influence of the functionalization density on the load transfer at the nanoscale interface. As an important engineering material, Epon 862/DETDA epoxy polymer,a thermoset plastic, has also been used as the polymer matrix material in order to see the difference in interfacial load transfer between a network structured polymer and the amorphous entangled structure of the PE matrix. As for thermoset epoxy polymer, emphasis has been put on investigating the effects of the crosslink density of the epoxy network on the interfacial load transfer ability for both non-functionalized and functionalized CNT-Epoxy interface at different temperatures(100K and 300K) and on the functionalization effect influenceing the interfacial interactions at the functionalized CNT-Epoxy interface. Cohesive zone traction-displacement laws are developed based on the force-separation responses obtained from the MD simulations for both non-functionalied and functionalized CNT-PE/epoxy interfaces. Using the cohesive zone laws, the influence of the interface on the effective elastic material properties of the nanocomposites are observed and determined in continuum level models using analytic and computational micromechanics approaches, allowing for the assessment of the improvement in reinforcement efficiency of CNTs due to the functionalization. It is found that the inclusion of the nanoscale interface in place of the perfectly bonded interface results in effective elastic properties which are dependent on the applied strain and temperature in accordance with the interface sensitivity to those effects, and which are significantly diminished from those obtained under the perfect interface assumption for non-functionalized nanocomposites. Better reinforcement efficiency of CNTs are also observed for the nanocomposites with the functionalized interface between CNTs and polymer matrix, which results in large increasing for the effective elastic material properties relative to the non-functionalized nanocomposites with pristine CNTs. Such observations indicates that trough controlling the degree of functionalization, i.e. the number and distribution of covalent bonds between the embedded CNTs and the enveloping polymer, one can tailor to some degree the interfacial load transfer and hence, the effective mechanical properties. The multiscale model developed in this study bridges the atomistic modeling and micromechanics approaches with cohesive zone models, which demonstrates to deepen the understanding of the nanoscale load transfer mechanism at the interface and its effects on the effective mechanical properties of the nanocomposites. It is anticipated that the results can offer insights about how to engineer the interface and improve the design of nanocomposites. / Ph. D.

Les protéines amyloïdes sont retrouvées sous forme de fibres dans de nombreuses maladies neurodégénératives. En tentant d’élucider le mécanisme de fibrillation, les chercheurs ont découvert que cette réaction se fait par un phénomène de nucléation passant par des oligomères. Il semblerait que ces espèces soient la principale cause de la toxicité observée dans les cellules des patients atteints d’amyloïdose. C’est pourquoi un intérêt particulier est donc porté aux premières étapes d’oligomérisation. Dans ce mémoire, nous nous intéressons à une séquence d’acide aminé fortement hydrophobe de l’α-synucléine appelée composante non β -amyloïde (Non-Amyloid β Component ou NAC). Cette dernière est retrouvée sous forme de fibres dans les corps et les neurites de Lewy des patients atteints de la maladie de Parkinson. De plus, elle constitue une composante minoritaire des fibres impliquées dans la maladie d’Alzheimer. Nous avons observé les changements structuraux qui ont lieu pour le monomère, le dimère et le trimère de la séquence NAC de l’α-synucléine. Nous nous sommes aussi intéressés aux conséquences structurelles observées dans des oligomères hétérogènes qui impliqueraient, Aβ1−40. Pour cela nous utilisons des dynamiques moléculaires, d’échange de répliques couplées au potentiel gros-grain, OPEP. Nous constatons une disparition des hélices α au profit des feuillets β , ainsi que le polymorphisme caractéristique des fibres amyloïdes. Certaines régions se sont démarquées par leurs capacités à former des feuillets β . La disparition de ces régions lorsque NAC est combinée à Aβ laisse entrevoir l’importance de l’emplacement des résidus hydrophobes dans des structures susceptibles de former des fibres amyloïdes. / Amyloid proteins are found in fiber form in many neurodegenerative diseases. In attempting to elucidate the mechanism of fibrillation, researchers have found that fibril formation occurs by a nucleation mechanisms involving oligomers. It seems, in particular, that the latter species are responsible for the toxicity observed in the cells of patients suffering from amyloidosis. That is why special interest is focused in the early stages of oligomerization. In this this work, we focus on a highly hydrophobic amino acid sequence of the α-synuclein called Non-Amyloid β Component (NAC). The NAC is recovered in the form of fibers in the body and Lewy neurites in patients with Parkin- son’s disease. Moreover, it is a minority component of the fibers involved in Alzheimer’s disease. In particular, we observe the structural changes taking place for the monomer, dimer and trimer of the NAC region of α-synuclein. We are also interested in the structural consequences observed in heterogeneous oligomers which involve Aβ1−40. We use Hamiltonian and temperature replica exchange molecular dynamics (HT-REMD) simulations combined with the coarse-grained OPEP potential. We observe a loss of α-helices in favor of β -strands and the characteristic polymorphism of amyloid fibers. We also find that some regions are distinguished by their ability to form β -strands. The disappearance of these regions when combined Aβ with NAC suggests the importance of the location of hydrophobic residues in amyloid fibers structures.

La compréhension de la relation structure-propriétés des parois des cellules végétales s'appuie de plus en plus sur l'utilisation d'approches de modélisation moléculaire en général et de dynamique moléculaire en particulier. A ce jour, le poids numérique que représente une telle démarche à l'échelle de l'atome est la plupart du temps incompatible avec les puissances de calcul disponibles. C'est pourquoi des méthodes d'approximation sont indispensables pour pouvoir mettre en œuvre des simulations numériques à l'échelle de systèmes supramoléculaires réalistes. Dans le cadre de cette thèse, un modèle de dynamique moléculaire, dit « gros grain » a été mis au point à l'échelle du monomère de macromolécules pariétales. Les paramètres de ce modèle ont été calibrés à l'aide de simulations de dynamique moléculaire à l'échelle de l'atome. Ce modèle a fait l'objet de quatre applications : adsorption d'une chaine de xylane sur une surface de cellulose cristalline, arrachement d'une chaine de xylane adsorbée sur une surface de cellulose cristalline par une pointe AFM, adsorption d'une phase amorphe de xylane sur une surface de cellulose cristalline et adsorption d'une phase amorphe de xylane sur un monocristal de cellulose exposant trois surfaces différentes. Des effets de structuration au voisinage de la cellulose sont observés. / Nowadays, the understanding of plant cell walls' structure-properties relationship leans more and more on the use of molecular modeling approaches and of molecular dynamics in particular. To date, numerical weight of such an approach is usually out of the reach of available computing power if the atomic scale is used. As a consequence, building approximate methods is of crucial importance to perform numerical simulation of realistic supramolecular systems. Within the framework of this PhD, a “coarse grain” molecular dynamics model was built at plant cell wall macromolecule monomer's scale, it's parameters being fixed with the help of atom-scale molecular dynamics simulations. Then, several numerical studies were carried out: a single xylan chain was adsorbed on a crystalline cellulose surface, a single xylan chain was pulled from a crystalline cellulose surface with the help of the tip of an AFM cantilever, an amorphous xylan phase was adsorbed on a cellulose surface and an amorphous xylan phase was adsorbed on a cellulose crystal, which three surfaces were exposed. Local structuring effects were observed.

Le but de cette thèse est de mettre en relation les propriétés structurale, dynamique et fonctionnelle de la forme humaine d’une nouvelle protéine découverte dans le cerveau des vertébrés en 2000 : la Neuroglobine. Dans un premier temps, j’ai réalisé une étude théorique dans laquelle un mécanisme à deux voies menant à la forme pentacoordinée avec cystéines oxydées a été mis en avant. A travers ce mécanisme, un conformère de la Neuroglobine au sein duquel le groupe prosthétique hème a basculé au cœur de la structure protéique a été déterminé. A partir des structures de ce mécanisme, une étude sur la diffusion de petits ligands au sein des cavités internes de la protéine à l’aide de la méthode de métadynamique a mis en évidence que la formation du pont disufure intramoléculaire favorisait la poche de ligation. De plus un certain nombre de voies de sortie pour les ligands a pu être obtenu. Pour compléter ce premier aspect de la thèse, une étude des propriétés mécaniques, communes avec les autres globines, a montré l’importance de quatre résidus centraux, dit mécaniquement sensibles, qui régulent les canaux d’accès aux différentes poches internes de la protéine, appelé phénomène de respiration. Dans un second temps, je me suis intéressé à l’interaction de la Neuroglobine avec un petit ligand via une étude expérimentale par ITC. La première conclusion importante est que la cinétique de ligation est plus importante lorsque le pont disulfure est formé. De plus j’ai observé une diminution de la cinétique lors du passage Wild Type vers C120S puis réaugmentation de la cinétique lors du passage C120S vers C46G/C55S/C120. Afin de comprendre ce phénomène, une simulation de la Neuroglobine triplement mutée a été réalisée au cours de laquelle un réseau de deux liaisons hydrogènes a été mis en avant. Ce réseau change considérablement les voies d’entrée/sortie pour les ligands. Ainsi la mutation 120 ferme une/ou plusieurs voies de sortie alors que la mutation 46 ouvre la voie naturelle des globines. Le changement observé étant important, une étude par RMN de Ngb TM et WT cystéines réduites a montré qu’il y avait une différence de structure entre ces formes pas seulement au niveau des points de mutation mais sur l’ensemble de la structure. Ces nouveaux résultats mettent ainsi en évidence le rôle important des trois cystéines chez la Neuroglobine humaine. / In this PhD work, I tried to link together the different structural, dynamic and fonctional properties of a new human protein discovered in the mamals brain in 2000: the Neuroglobin. First of all, I established a new two ways mecanism in order to get the pentacoodinated oxydized cysteins state using theoritical method. One of this mecanism’s conformer shows an important heme sliding inside of the proteic structure. Furthermore with help of metadynamic method, I studied the small ligand diffusion and migration in the internal cavity network. I showed the higher ligand affinity when the disulfide bridge is bond and we proposed an important number of exit pathways. Then we developed a method to understand the mechanical properties of the globins and we found four residues mechanically sensitive which form together a control access pathway between internal cavities, called breath phenomenon. Secondly I used ITC method in order to characterize the interaction between the Neuroglobin and a small ligand. From this experiment we highlighted that the kinetic ligation is faster when the disulfide bridge is formed. Then I noticed a relative decrease of the velocity when the mutation C120S is operated followed by a relative increase of the velocity for the triple mutation C46G/C55S/C120 compared to the Wild Type data. To understand these results, I performed a molecular simulation of the triple mutation Neuroglobin form. During this trajectory, I discovered a structure with a two hydrogen bonds network, which significantly changes the ligand entry/exit pathways. The 120 mutation closes one/several exit pathways while the 46 mutation opens the natural globin exit pathway. Because of the considerable structural change observed in the triple mutation Neuroglobin form, I decided to produce NMR results. These last points reveal a relative structure difference between the Wild Type oxidized cysteins form and the triple mutation form not only on the mutation points but also on the global structure. All these new results highlight the essential role of the three cysteins in the human Neuroglobin.

Dans cette thèse nous avons réalisé une étude théorique concernant les mécanismes de formation et les propriétés de transport électronique de fils de section atomique d’Au et de Pt.Pour cela, nous avons utilisé un Hamiltonien de Liaisons Fortes donnant accès aux propriétés électroniques et à l’énergie totale. Lors de nos simulations de traction de nanofils cristallins en Dynamique Moléculaire nous avons observé la formation de structures assimilables `a des nanotubes dont la chiralité évolue au cours de la déformation. En poursuivant la traction, nous avons observé la formation de structures planes (ou rubans) dans le cas de l’Au et du Pt. Ces rubans permettent de former des fils de section atomique pour l’Au mais pas pour le Pt, la différence étant liée aux propriétés mécaniques des éléments. Les calculs réalisés sur les propriétés de transport ont mis en évidence des effets d’interférence destructive induits par la géométrie du système. / In this thesis we study the formation mechanisms and the electronic transport propertiesof Au and Pt atomic wires. We have used a Tight Binding Hamiltonian giving access to theelectronic structure and to the total energy. By performing traction simulations of cristallinenanowires by Molecular Dynamics we observe the formation of structures similar to nanotubeswhose chirality evolve during the deformation. Following the traction process we observe theformation of planar structures (or ribbons) for both Au and Pt. These ribbons give rise to theformation of wires of atomic section for Au but not for Pt, the different behavior is related withthe different elastic properties of the two elements. Our preliminary results on the electronictransport properties show interference effects induced by the geometry which can cancel out theconductance.

This thesis presents the first-principles studies of materials properties within the framework of the density functional theory (DFT). The thesis constitutes three main parts, i. e., pressure-induced phase transitions in solids, data-storage and clean-energy materials. The first part focuses on the predictions of crystal structures and the determinations of electronic properties of Xe-H2, FeB4 and Co3O4. Pressurizing Xe-H2 compound yields the formation of H-rich Xe(H2)8, which can exhibit a metallic feature at comparatively lower pressure than pure hydrogen. Hard superconducting FeB4 gets transformed into a novel transparent phase under pressure owing to the enhanced overlap of atomic cores. Spinel Co3O4 undergoes the phase transition from a cubic to a monoclinic because of the charge transfer between cations via the increased 3d-3d interactions. The second part involves the study of structural and electronic properties of phase-change memory materials (PCMs), i. e., Ge2Sb2Te5 (GST) and Ga-doped In2O3. Van der Waals (vdW) interaction must be considered to obtain accurate crystal structure of layered GST. For Ga-doped In2O3 (GIO), the local structure of amorphous GIO is found to resemble that of amorphous In2O3, except the vicinity of doping atoms. The electronic property of a-GIO is metallic, which considerably differs from the semiconducting feature of the crystalline GIO. This emphasizes the contrast in the conductivity of the crystalline and amorphous upon phase switching of GIO. The third part associates with the search for clean-energy materials, viz., hydrogen production, hydrogen storage and green Mg-ion batteries. For hydrogen production, the role of intrinsic point defects to water adsorption on ZnO(10-10) surface is investigated. The findings show that the Zn and O defect-sites are energetically not favorable for the water adsorption and dissociation. For the purpose of storing hydrogen in a solid phase, silicene, doped by alkaline and alkaline earth metals, is investigated. We find that Li-doped and Na-doped silicene can attain the superior storage capacity. For cathode material of Mg-ion batteries, Mg2Mo6S8, the diffusivity of Mg ions occurs through an available channel in the bulk with the onset temperature of 200 K.

L’ADN, support de l’information génétique, est constamment altéré par des agents physiques ou chimiques d’origines endogènes (métabolisme) et exogènes (UV, radiations ionisantes, produits chimiques) dont les effets sont génotoxiques. Ces modifications structurales délétères de l’ADN sont éliminées par de nombreux mécanismes de réparation. Parmi eux, le système de réparation par excision de bases (BER) est initié par les ADN glycosylases qui reconnaissent et éliminent les bases endommagées. Dans certaines stratégies anti-cancéreuses, l’utilisation de la chimiothérapie et la radiothérapie ont pour but la destruction des cellules cancéreuses en altérant leur ADN. Dans ce contexte, les ADN glycosylases réparent l’ADN des cellules traitées et induisent une résistance non désirée au traitement, faisant de ces enzymes des cibles thérapeutiques intéressantes. Le but de ces travaux est d’approfondir la compréhension des mécanismes de réparation des ADN glycosylases de la superfamille structurale Fpg/Nei grâce à la modélisation moléculaire et de pouvoir identifier et concevoir des inhibiteurs de ces enzymes. Les simulations de dynamique moléculaire (DM) nous ont permis d’étudier la « Lesion Capping Loop » (LCL) et de l’associer à la stabilisation de la base endommagée positionnée dans le site actif. Nous avons également étudié les chemins de sortie possibles de la base après coupure par l’enzyme et l’implication de la boucle LCL dans ce phénomène grâce à des simulations de DM ciblée (TMD-1). De plus, les simulations de DM couplées à un protocole d’amarrage moléculaire « aveugle » nous ont permis d’identifier 2 sites de fixations possibles majoritaires pour des petites molécules potentiellement inhibitrices. Un de ces sites correspondant au site actif de hNEIL1 a fait l’objet d’un criblage virtuel d’une partie de la base de molécules Ambinter. Ceci nous a permis d’identifier des molécules potentiellement inhibitrices dont les effets seront prochainement testés in vitro dans l’équipe sur la protéine humaine hNeil1. / The DNA, genetic information support, is frequently damaged by physical or chemical agents from endogenous (cell metabolism) and exogenous (UV, ionizing radiations, chemicals) factors whose effects are genotoxic. These deleterious DNA structural alterations are removed by many DNA repair mechanisms. Among them, the base excision repair (BER) is initiated by DNA glycosylases which recognize and remove damaged bases. In some anti-cancer strategies, the use of chemo- and radiotherapy is aimed to cancerous cells destruction by altering their DNA. In that specific context, DNA glycosylases repair the DNA of treated cells and induce unwanted resistance to treatments, making these enzymes interesting therapeutic targets. The purpose of this work is to deepen the repair mechanism knowledge of Fpg/Nei structural superfamily of DNA glycosylases using molecular modeling and designing inhibitors of these enzymes. Molecular dynamic simulations allowed us to study the « Lesion Capping Loop » (LCL) and to associate its role to substrate stabilization in the enzyme active site. We also studied some possible excision’s product release pathways and LCL implication in this phenomena by targeted molecular dynamic simulations (TMD-1). Furthermore, molecular dynamic simulations coupled to a blind molecular docking protocol allowed us to identify 2 possible main binding sites of potential inhibitiors. One of these binding sites corresponding to the hNEIL1 active site has been the object of a virtual screening of the Greenpharma database. This allowed us to identify potential inhibitors whom effects will be soon tested in vitro on the humain protein hNEIL1.