The interaction between two proteins into salt aqueous solutions is investigated throughout this thesis. Experiments, modeling and molecular simulations were carried out to get a better understanding of the phenomenon. Bovine serum albumin was used as a model protein. An analytical expression for the structure factor for globular proteins in aqueous solution is presented in this work. This expression was obtained considering an intermolecular potential given by the sum of a hard core, a van der Waals attractive and a screened Coulomb contribution. Experimental data of Small Angle X-Ray Scattering for bovine serum albumin in aqueous solutions containing sodium salts at different protein concentrations and pH values are also presented. The expression developed for the structure factor describes accurately these experimental data provided a dependence of the attractive parameter on protein concentration is established. An expression for the osmotic pressure was derived from the structure factor. With attractive parameters adjusted from X-ray scattering data, the osmotic pressure of bovine serum albumin aqueous solutions could be predicted with very good agreement with experimental data. A derivation of the thermodynamic potentials, such as the chemical potential, using the new osmotic equation of state is presented. Applying the phase equilibrium criterion, the fluid-fluid phase equilibrium for bovine serum albumin in salt aqueous solution was calculated. Although such separation was not experimentally observed at the isoelectric point, it was indeed experimentally observed for a pH value below the isoelectric point. The predictions seem to be valuable to discuss how ion specificity affects the phase diagram of proteins. To apply molecular dynamic techniques to simulate how proteins interact to each other in salt aqueous solutions, two new coarse-grained force fields are proposed. The first one, meant for sodium sulfate aqueous solution, avoids the unphysical association observed for non-polarizable atomistic force fields; and allows the prediction of thermodynamic and dynamic properties. The second one, meant for bovine serum albumin in aqueous solution, is used as a new strategy to evaluate the scattering form factor of proteins as a low resolution technique for protein structure prediction. / Nesta tese apresenta-se uma investigação sobre a interação entre duas proteínas em soluções aquosas salinas. Experimentos, modelagem e simulações moleculares foram realizadas para conseguir um melhor entendimento do fenômeno. Albumina de soro bovina foi usada como proteína modelo. Uma expressão para o fator de estrutura de proteínas globulares em solução aquosa é apresentada neste trabalho. Esta expressão foi obtida considerando-se um potencial intermolecular dado pela soma de um núcleo duro, uma contribuição atrativa tipo vander Waals e uma contribuição de potencial coulômbico blindado. Dados experimentais de espalhamento de raios-X a baixos ângulos para a albumina de soro bovino em soluções aquosas contendo sais de sódio com diferentes concentrações de proteína e valores de pH também são apresentados. A expressão desenvolvida para o fator de estrutura descreve com precisão estes dados experimentais, desde que uma dependência entre o parâmetro atrativo com a concentração de proteína seja estabelecida. Uma expressão para a pressão osmótica foi derivada do fator de estrutura. Com parâmetros atrativos ajustados aos dados de espalhamento de raios-X, a pressão osmótica da albumina de soro bovino em solução aquosa pôde ser predita com grande correlação com os dados experimentais. Uma derivação dos potenciais termodinâmicos usando a nova equação osmótica de estado é apresentada. Aplicando o critério de equilíbrio de fases, foi possível calcular o equilíbrio fluido-fluido para a albumina de soro bovino em solução aquosa. Embora tal separação não tenha sido observada experimentalmente em um pH igual ao ponto isoelétrico, ela foi de fato observada experimentalmente para um valor de pH menor do que o ponto isoelétrico. As predições parecem ser valiosas para discutir como a especificidade iônica afeta o diagrama de fases de proteínas. De modo a avaliar como proteínas interagem umas com as outras usando técnicas de dinâmica molecular, dois novos campos de força coarse-grained são propostos. O primeiro, para o sulfato de sódio em solução aquosa, evita a associação não-física que é observada para campos de força atomísticos não-polarizáveis. Este modelo é capaz de prever propriedades dinâmicas e termodinâmicas. O segundo, para a albumina de soro bovino em solução aquosa, é usado como uma nova estratégia para avaliar o fator de forma de espalhamento de proteínas como uma ferramenta de baixa resolução na predição de estruturas proteicas.

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京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20413号 / 工博第4350号 / 新制||工||1674(附属図書館) / 京都大学大学院工学研究科化学工学専攻 / (主査)教授 宮原 稔, 教授 田門 肇, 教授 山本 量一 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Water molecules play a significant role in biological process and are directly involved with bio-molecules and organic compounds and ions. Recent research has focused on the thermal dynamics and kinetics of water molecules in solution, including experimental (infrared spectroscopy and Raman spectroscopy) and computational (Quantum Mechanics and Molecular Dynamics) approaches. The reason that water molecules are so unique, why they have such a profound influence on bio-activity, why water molecules show some anomalies compared to other small molecules, and where and how water molecules exert their influence on solutes are some of the areas under study. We studied some properties of hydrogen bond networks, and the relationship of these properties with solutes in water. Molecular dynamics simulation, followed by an analysis of “water bridges”, which represent protein-water interaction have been carried out on folded and unfolded proteins. Results suggest that the formation of transient water bridges within a certain distance helps to consolidate the protein, possibly in transition states, and may help further guide the correct folding of proteins from these transition states. This is supporting evidence that a hydrophilic interaction is the driving force of protein folding. Biological membranes are complex structures formed mostly by lipids and proteins. For this reason the lipid bilayer has received much attention, through computation and experimental studies in recent years. In this dissertation, we report results of a newly designed pH sensitive lipid MORC16, through all-atom and coarse-grained models. The results did not yield a MORC16 amphiphile which flips its conformation in response to protonation. This may be due to imperfect force field parameters for this lipid, an imperfect protonation definition, or formation of hydrogen bond does not responsible for conformation flip in our models. Despite this, some insights for future work were obtained.

NASCION-type lithium-aluminum-germanium-phosphate (LAGP) glass-ceramic is one of the most promising solid electrolyte (SEs) material for the next generation Li-ion battery. Based on the crystallization of glass-ceramic material, the two-step heat treatment was designed to control the crystallization of Li-ion conducting crystal in the glass matrix. The results show that the LAGP crystal is preferred to internally crystalize, Tg + 60%∆T is the nucleation temperature that provides the highest ion conductivity. The compositional investigation also found that, pure LAGP crystal phase can be synthesized by lowering the amount of GeO2. To fill gap of atomic structure in LAGP glass-ceramic, molecular dynamic (MD) simulation was used to build the crystal, glass, and interfacial structure LAGP. The aliovalent ion substitution induced an simultaneously redistribution of Li to the 36f interstitial site, and the rapid cooperative motion between the Li-ions at 36f can drop the activation energy of LAGP crystal by decreasing the relaxation energy; furthermore, an energy model was built based on the time-based analysis of Li-ion diffusion to articulate the behavior. The glass and interfacial structure show and accumulation of AlO4, GeO4 and Li at the interface, which explains the Li-trapping on the intergranular glass phase. An in-situ synchrotron X-ray study found that, by using two-step heat treatment, the nucleation of Li-ion conducting crystal in the glass-matrix induced large strain from interfacial tension, which can also promote the incorporation of aliovalent ion substitution in the NASICON crystal and enhances the ion conductivity.

The biological membrane, which is composed of a lipid bilayer embedded with numerous proteins, defines the cell boundary, separating the cell interior from the external environment. It serves as a gatekeeper and entry point for various molecular and ionic species. This thesis describes experimental and simulation studies of the interactions of carbon nanotubes (CNTs) with model membranes (lipid bilayers). The unique properties of CNTs make them ideal candidates for many nanotechnological applications. They can, however, pose a potential risk as toxins. While research into the positive benefits of CNTs continues, very little is known about their basic interactions with cellular components. It is particularly important to understand the interaction of CNTs with biological membranes, which form the primary physical barrier surrounding a cell. Coarse grained molecular dynamics (MD) simulations and atomic force microscopy (AFM) have been used to study the interactions of CNTs and lipid bilayers. They are investigated in a controlled manner using MD simulations, while AFM has allowed the controlled approach-to-contact and insertion of CNTs into bilayers. A number of effects are reported, including lipid creep along the CNT and bilayer thickening upon contact. The robustness of this response is established using different force fields and lipid species. The experimental results show an unusual reaction to mechanical indentation, and are further backed by MD simulations. The lipid bilayer response to multiple CNTs is studied and the effects of CNTs on bilayer conformation and lipid diffusion are reported. CNT internalisation from the solvent is observed in the simulations. Indeed, many of the observed phenomena are reminiscent of those known from the field of membrane protein. This project focuses on understanding the basic molecular interactions of CNTs with lipid bilayers and addresses the gap between experimental and computational work.

A capacidade de prever a estrutura nativa de uma proteína é um problema ainda sem solução. A predição da estrutura final ou nativa de uma proteína -, ou seja, partir da estrutura primária (sequência de aminoácidos linear) de um polipeptídeo tentar prever qual será a estrutura terciária (arranjo de hélices alfa, folhas beta e grampos) - tem sido um desafio para diversos pesquisadores desde o século passado. Atualmente existem diversos modelos que se propõem a executar essa tarefa, mas poucos que de fato partem de princípios físicos básicos para realizá-la. A grande maioria baseia-se em estruturas já conhecidas de proteínas com sequenciamento ou função similares para prever a estrutura terciária. Neste trabalho, no entanto, propõe-se o desenvolvimento de um campo de forças coarse-grained para aplicação em simulações de dinâmica molecular a fim de prever a estrutura de proteínas sem que seja necessária a comparação com estruturas já conhecidas. O fator de forma é um importante indicativo da estrutura de uma molécula em solução. Apesar de se tratar de uma grandeza que fornece informações de baixa resolução, ou seja, não fornece pormenores a respeito da posição dos átomos na estrutura da molécula, é uma estimativa inicial do espaço ocupado pela molécula e também da maneira com a qual ela interage com outras moléculas em solução. Isso é decorrente das operações matemáticas necessárias para que o fator de forma seja acessado a partir de dados de experimentos de espalhamento de raios X. Os resultados mostram que o método consegue prever uma estrutura condizente com os dados de espalhamento de raios X das estruturas cristalográficas e com os dados experimentais utilizados. / The prediction of the final structure of a protein (also called native structure) has been addressed by many research groups since the last century. This problem can be understood as how to predict the tertiary structure that a protein molecule assumes after the folding process from just the primary structure (the sequence of amino acids). Nowadays there are several models aiming at solving this problem, but very few of them are based on physical principles. Most of these models are template-based ones that search for similar amino acids sequences or analogous biological functions to predict the native structure. In the present work, however, we propose the development of a force field predict the form factor of proteins that does not entail the knowledge of any other model or template to do so. The form factor is an important aspect of the structure of a molecule in solution. Despite being a low-resolution method of analysis, in the sense that it does not provide details about the exact positions of the atoms inside the molecular structure (because of the mathematical operations needed to retrieve informations from the scattering data), it is an initial estimative of the volume occupied by this molecule and also a good initial path for uncovering how these molecules interact to each other in solution. The results show that the method presented here can predict a structure that agrees with the scattering data of the crystallographic structure and with available experimental data of x-ray scattering of proteins in solution.

En ingénierie mécanique, la rupture des matériaux est un risque qu'il convient d'anticiper et qui reste aujourd'hui une menace pour les structures. La rupture des systèmes pré-fissurés a lieu quand l'énergie libérée par la propagation de la fissure préexistante excède un seuil critique (taux de restitution d'énergie) qui représente une propriété du matériau. Au contraire, la rupture de systèmes sans défauts préexistants survient lorsque la contrainte appliquée atteint la résistance, également propriété du matériau. L'existence de deux critères pour la rupture semble indiquer des mécanismes d'amorçage différents, ce qui soulève la question des cas réels intermédiaires qui présentent des concentrations de contrainte modérées. Différentes approches existantes sont cohérentes avec les deux situations limites mais il n'y a pas de consensus clair dans la communauté scientifique. Dans cette thèse, nous étudions les mécanismes de la rupture fragile à l'échelle atomique afin d'en comprendre l'origine physique pour différentes concentrations de contraintes. La rupture provient de la rupture des liaisons à l'échelle atomique. Nous utilisons donc des techniques de simulation moléculaire pour étudier la physique élémentaire de l'initiation de la rupture fragile. Dans ce but, on étudie deux types de structure atomique. Le premier est un matériau modèle à maille triangulaire, dont le potentiel permet d'interpréter analytiquement, et avec précision, les résultats des simulations moléculaires. L'étude est étendue à un système plus réel : le graphène. Ce matériau, qui présente une résistance élevée au regard de sa faible ténacité, a l'une des plus petites tailles de zone d'élaboration par rapport aux autres matériaux fragiles, ce qui permet d'appliquer numériquement les concepts de la rupture fragile jusqu'à l'échelle nanométrique de la simulation moléculaire. On s'intéresse dans un premier temps à la rupture des matériaux à 0K. À cette température, un système atomique est en équilibre statique. La rupture peut donc être traitée comme une instabilité. L'analyse du profil énergétique du système atomique fournit un moyen d'identifier les mécanismes de rupture. Nous montrons qu'on peut identifier la rupture en cherchant les valeurs propres nulles ou négative de la matrice hessienne. Les vecteurs propres correspondants indiquent les modes de rupture et montrent l'apparition de bandes de transition entre mouvements de groupes d'atomes pour des systèmes intacts, dont la largeur rappelle la longueur d'élaboration, généralement introduite dans des théories macroscopiques d'initiation de la rupture. On étudie aussi l'effet de la présence de défauts sur les modes d'instabilité et leur dégénérescence. Cette étude fournit une technique générale pour identifier les mécanismes d'initiation de rupture quelle que soit la concentration de contrainte dans la structure. On s'intéresse ensuite aux températures non nulles. On étudie les effets combinés de la température, de la taille du système et du taux de chargement. En partant de la théorie cinétique, nous montrons qu'il existe des lois d'échelle générales fournissant une équivalence taille-vitesse de chargement-température et permettant de relier résistance et ténacité à la limite à 0K. La différence entre la loi d'échelle en résistance et celle en ténacité réside dans le fait que la rupture ne soit pas sensible à la taille du système pré-fissuré mais au nombre de pointes de fissure. Cela indique une différence statistique essentielle entre la rupture en résistance et la fracture ce qui permet de mieux comprendre la transition de l'une à l'autre. Dans l'esprit de mieux comprendre la transition entre les deux types de rupture, on traite le cas de trous elliptiques à différents rapports d'aspects et on analyse en même temps l'effet de cette transition sur les modes d'instabilité. On étudie en dernière partie, l'effet des surfaces libres et les différents paramètres caractérisant cette situation / In mechanical engineering, failure is a risk that must be anticipated and is still a threat for structures. The failure of pre-cracked systems occurs when the energy released by the propagation of the pre-existing crack exceeds a critical threshold (Griffith's energy release rate) which represents a property of the material. On the contrary, the failure of systems without pre-existing defects occurs when the applied stress reaches the strength, also property of the material. The existence of two criteria for failure suggests different driving mechanisms, which raises the question of intermediate cases with moderate stress concentrations. Different existing approaches are consistent with the two limit cases but there is no clear consensus in the scientific community.In this work, we study the mechanisms of brittle failure on the atomic scale in order to understand the underlying physical mechanisms. Macroscopic failure comes from the breaking of bonds at the atomic scale. We therefore use molecular simulation techniques to study the elementary physics of brittle failure initiation. Two types of atomic structure are studied. The first one is a triangular lattice toy model whose simplicity allows precise analytical interpretation of the molecular simulation results. The study is extended to a more realistic system: graphene. This material, which has a high strength and a rather low toughness in comparison, has one of the smallest process zones compared to other brittle materials, which makes it possible to apply the concepts of brittle failure up to the nanometric scale of molecular simulation. We first investigate the failure of materials at 0K. At this temperature, an atomic system is in static equilibrium. The breaking of bonds can be treated as instability. The analysis of the energy profile of the atomic system provides a means of identifying the mechanisms of failure. We show that we can identify failure initiation by looking for negative or zero eigenvalues of the Hessian matrix. The corresponding eigenvectors indicate the modes of failure and show the appearance of transition bands between motions of groups of atoms for intact systems, whose width recalls the size of the process zone, generally introduced in macroscopic theories of failure initiation. We also study the effect of defects on the instability modes and their degeneracy. This study provides a general technique to capture fracture initiation mechanisms irrespective of the stress concentration in the structure. We focus afterwards on finite temperatures. We study the combined effects of temperature, system size and loading rate. Starting from the kinetic theory, we identify general scaling laws providing a size-loading rate-temperature equivalence and relating the strength and toughness to the limit at 0K. The difference between the scaling law of strength and that of toughness lies in the fact that failure is not sensitive to the size of the pre-cracked system but to the number of crack tips. This indicates an essential statistical difference between strength and fracture failures which makes it possible to better understand the transition from one to the other.In order to better understand the transition between the two types of failure, we treat the case of elliptic holes with different aspect ratios and we focus at the same time on the effect of this transition on instability modes. We study in the last part the case of non-periodic structures with free surfaces. We determine the various parameters characterizing this situation and the effect of the presence of surface phenomena on instability modes

Molecular simulations have become an important tool within the last few decades to understand physical processes in the microscale and customize processes in the macroscale according to the understanding developed at the molecular level. We present results from molecular simulations we performed to study the adsorption of hazardous organics in nanoporous materials. Adsorption of water in silicalite, a hydrophobic material, and the effect of defects were investigated by Monte Carlo simulations. Silanol nests were found to have a big impact on the hydrophobicity of silicalite. Even the presence of one silanol nest per unit cell caused a significant amount of water adsorption. We also investigated the effect of four different cations, H+, Li+, Na+, and Cs+. Their presence in silicalite increased the amount of water adsorbed. Monte Carlo and molecular dynamics simulations of MTBE adsorption in silicalite, mordenite, and zeolite beta with different Na+ cation loadings were carried out. The results revealed the importance of the pore structure on the adsorption of MTBE. Although these three zeolites have similar pore volumes, zeolite beta, with its pore structure which is mostly accessible to MTBE molecules, is predicted to adsorb significantly more MTBE than silicalite and mordenite. The Na+ cation loading, up to four cations does not have a significant effect on the adsorption capacity of the zeolites studied here, however, for silicalite and zeolite beta increasing the Na+ content increases the amount adsorbed at very low pressures. A new force field was developed by Monte Carlo simulations for 1,4-Dioxane, an important industrial solvent which has emerged as a potentially significant threat to human health. The objective was to develop reliable atom-atom interaction parameters to use in the simulations of the adsorption of 1,4-Dioxane in different adsorbent materials. Predictions of critical point data, liquid and vapour densities, heats of vaporization with our new force field were in good agreement with experimental data and outperformed predictions from simulations with other force field parameters available in literature. To obtain the isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite Monte Carlo simulations were performed. First we optimized the interaction parameters between the atoms of silicalite and the atoms of MTBE and 1,4-Dioxane. Using these optimized parameters we simulated the adsorption of MTBE and 1,4-Dioxane from water in silicalite. Despite the agreement of simulated and experimental isotherms of pure components, simulated isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite did not yield satisfactory results. Monte Carlo simulations were performed to investigate the affinity between two hazardous materials, PFOA and 1,1-DCE; and four different zeolites. Binding energies and Henry's constants were computed. For both PFOA and 1,1-DCE zeolite-beta had the highest affinity. The affinity between activated carbon with polar surface groups and water, and 1,4-Dioxane were investigated to shed light on why activated carbon is ineffective to remove 1,4-Dioxane from water. Results showed that presence of polar surface groups increased the affinity between water and activated carbon, while the affinity between 1,4-Dioxane and activated carbon was not effected by the presence of polar surface groups.

A capacidade de prever a estrutura nativa de uma proteína é um problema ainda sem solução. A predição da estrutura final ou nativa de uma proteína -, ou seja, partir da estrutura primária (sequência de aminoácidos linear) de um polipeptídeo tentar prever qual será a estrutura terciária (arranjo de hélices alfa, folhas beta e grampos) - tem sido um desafio para diversos pesquisadores desde o século passado. Atualmente existem diversos modelos que se propõem a executar essa tarefa, mas poucos que de fato partem de princípios físicos básicos para realizá-la. A grande maioria baseia-se em estruturas já conhecidas de proteínas com sequenciamento ou função similares para prever a estrutura terciária. Neste trabalho, no entanto, propõe-se o desenvolvimento de um campo de forças coarse-grained para aplicação em simulações de dinâmica molecular a fim de prever a estrutura de proteínas sem que seja necessária a comparação com estruturas já conhecidas. O fator de forma é um importante indicativo da estrutura de uma molécula em solução. Apesar de se tratar de uma grandeza que fornece informações de baixa resolução, ou seja, não fornece pormenores a respeito da posição dos átomos na estrutura da molécula, é uma estimativa inicial do espaço ocupado pela molécula e também da maneira com a qual ela interage com outras moléculas em solução. Isso é decorrente das operações matemáticas necessárias para que o fator de forma seja acessado a partir de dados de experimentos de espalhamento de raios X. Os resultados mostram que o método consegue prever uma estrutura condizente com os dados de espalhamento de raios X das estruturas cristalográficas e com os dados experimentais utilizados. / The prediction of the final structure of a protein (also called native structure) has been addressed by many research groups since the last century. This problem can be understood as how to predict the tertiary structure that a protein molecule assumes after the folding process from just the primary structure (the sequence of amino acids). Nowadays there are several models aiming at solving this problem, but very few of them are based on physical principles. Most of these models are template-based ones that search for similar amino acids sequences or analogous biological functions to predict the native structure. In the present work, however, we propose the development of a force field predict the form factor of proteins that does not entail the knowledge of any other model or template to do so. The form factor is an important aspect of the structure of a molecule in solution. Despite being a low-resolution method of analysis, in the sense that it does not provide details about the exact positions of the atoms inside the molecular structure (because of the mathematical operations needed to retrieve informations from the scattering data), it is an initial estimative of the volume occupied by this molecule and also a good initial path for uncovering how these molecules interact to each other in solution. The results show that the method presented here can predict a structure that agrees with the scattering data of the crystallographic structure and with available experimental data of x-ray scattering of proteins in solution.