Le mémoire est consacré à l'étude numérique des phénomènes survenant à l'interface solide-fluide. Trois processus ont été étudiés: auto-organisation de films moléculaires sur un substrat solide, adsorption du gaz moléculaires dans un matériau nanoporeux et la cristallisation à l'interface organique/inorganique. L'étude de l'auto-organisation et des transitions de phase dans des multicouches de l'azote moléculaires adsorbées sur graphite est présentée dans le chapitre III. L'analyse est focalisée sur l'hétérogénéité spatiale du système et son influence sur le mécanisme et température de transitions ordre/désordre et la fusion des couches. Elle complète ainsi l'étude numérique du diagramme de phase de l'azote moléculaire, bien connu pour le matériau massif (3D) et les monocouches (2D) adsorbées sur un substrat. Le chapitre IV présente une étude de cinétique du mélange des gaz (méthane et méthyle-mercaptan) confiné dans les nanopores de carbone (pores en forme de fentes, de dimensions latérales finies et largeur nanométrique). L'étude porte sur la capacité de stockage de pores, la dynamique des composantes du mélange des gaz sous confinement et l'évaluation de la quantité de l'odorant nécessaire pour une détection facile en cas de fuite. Chapitre V résume les résultats de l'étude préliminaire ayant pour but la mise en place des simulations de biomineralization à l'interface organique/inorganique. Les structures secondaires de deux biomolécules, human leucine-rich peptide hLRAP et full length amelogenin, rM179 ont été prédéterminées. Les plus probables configurations ont été optimisées dans un environnement aqueux. / The present work is devoted to computer simulations of phenomena occurring at solid-fluid interfaces. Three processes have been studied in details: auto organization of molecular films at a solid substrate, adsorption of molecular gas in confined geometry and crystal formation at organic-inorganic interface. Two classical simulation methods have been used: stochastic Monte Carlo and deterministic Molecular Dynamics.The study of self-organisation and phase transitions in molecular nitrogen multilayers adsorbed on the basal plane of graphite is presented in chapter III. It focusses on the systems' spatial heterogeneity and its influence on temperatures of order-disorder and melting transitions. This study completes the numerical analysis of molecular nitrogen phase diagram, well described and understood for 3d (bulk) and 2D (monolayer film) systems.The analysis of kinetics of fluid confined in nanopores is presented in chapter IV. The working case consists of methane-methyl mercaptan mixtures confined in slit-shaped carbon nanopores. Simulations focused on both: storage capacity of carbon pores of finite size and nanometric width, and dynamics of gas mixture components under confinement. An evaluation of odorant content necessary for easy gas leak detection is presented.Chapter V gathers the results of calculations performed to set up the simulations of biomineralization at the organic-inorganic interface. The secondary structures of two amelogenins (human leucine-rich peptide, hLRAP, and full length amelogenin, rM179) have been predicted. The most probable structures have been further refined and the chain folding optimized in aqueous environment.

Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure. Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure. Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure. Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions. The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.

In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.

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This thesis uses a simple deterministic model represented by an ordinary di- fferential equation with two equilibrium points - depending on the initial state the illness either vanishes or persists forever. This model is expanded by adding some diffusion coefficients leading to different stochastic differential equations. They are analyzed to show how the choice of diffusion coefficients changes be- havior of the model in proximity of its equilibria and near the boundary of area with biological meaning. The theoretical results are than illustrated by computer simulations. 1

Os conceitos presentes na Física Moderna e Contemporânea (FMC), como aqueles relacionados à estrutura da matéria, rompem com ideias do cotidiano e envolvem fenômenos e entidades que são parte de uma realidade tecnicamente construída e não podem ser percebidos de forma direta pelos sentidos humanos. Seu ensino requer meios representativos, e as simulações computacionais atendem a esta necessidade. Nesta pesquisa, tendo como marco teórico ideias relacionadas ao estudo dos modelos mentais e conceituais, ideias provenientes da epistemologia da ciência de Bachelard, e considerando algumas ideias presentes na teoria das situações didáticas de Brousseau, buscamos identificar obstáculos de aprendizagem que atuam no ensino de conceitos do tópico Estrutura da Matéria em que são utilizadas simulações computacionais. Tendo como pano de fundo um processo iterativo de desenho, implementação e redesenho de um curso sobre a estrutura da matéria e aceleradores de partículas, analisamos a emersão de possíveis obstáculos epistemológicos, e verificamos como obstáculos didático-pedagógicos facilitavam esta emersão. Como resultados, identificamos obstáculos epistemológicos e didático-pedagógicos de diferentes naturezas, entre os quais, alguns relacionados à percepção ingênua de fenômenos do cotidiano, alguns relacionados ao uso de metáforas e imagens, e outros relacionados a um raciocínio limitado e incongruente. Acreditamos que as análises e conclusões desta pesquisa contribuem para uma reflexão sobre o ensino de tópicos de Física Moderna e Contemporânea, e sobre o uso de simulações computacionais como ferramentas pedagógicas. / The concepts of Modern and Contemporary Physics (MCP), such as those related to the structure of matter, break with the everyday ideas and involve phenomena and entities that are part of a reality technically built that cannot be directly perceived by human senses. Its teaching requires representative media, and the computer simulations meet this need. In this research, having as theoretical framework ideas related to the study of mental and conceptual models, ideas from the epistemology of science of Bachelard, and considering some of the ideas present in the theory of didactic situations of Brousseau, we seek to identify learning obstacles who work in teaching concepts of the topic Structure of Matter in which computer simulations are used. Against the backdrop of an iterative process of design, implementing and redesign of a course on the structure of matter and particle accelerators, we analyze the possible emergence of epistemological obstacles, and check how didactic-pedagogical obstacles facilitated this emersion. As a result, we identified epistemological obstacles and didactic-pedagogical obstacles of different nature, including some related to the naive perception of everyday phenomena, some related to the use of metaphors and images, and other related to a limited reasoning and incongruous. We believe that the analysis and conclusions of this research contribute to a reflection on the teaching of Modern and Contemporary Physics topics, and on the use of computer simulations as educational tools.

<p>Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure.</p><p>Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure. </p><p>Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure.</p><p>Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions.</p><p>The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.</p>

Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme. Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.

Die vorliegende Dissertation beschäftigt sich mit Wachstum und Aufbau von Fluorapatit-Gelatine-Nanokompositaggregaten. Diese Aggregate werden im sogenannten Doppeldiffusionsversuch biomimetisch erzeugt und ihre äußere Form bzw. Formentwicklung lässt sich anhand eines fraktalen Modells bis ins Detail nachvollziehen. Sie zeigen einen komplexen inneren Aufbau, in dem die Makromoleküle der organischen Komponente einerseits im Zentrum jeder Nanoeinheit und andererseits zu Strängen, den sogenannten Fibrillen, zusammengelagert am Aufbau der Kompositaggregate beteiligt sind. Im Fall des Kompositkeims ist die innere Architektur in hoher Detailstufe verstanden, auch wenn -- insbesondere bezüglich der späteren Wachstumsphasen -- eine Reihe ungeklärter Fragestellungen verbleibt. Ein zentrales Ergebnis der vorliegenden Arbeit bildet die Entdeckung eines weiteren Wachstumstypen, der im Vergleich zu den bekannten, fraktalen Kompositaggregaten grundsätzliche Unterschiede bezüglich des inneren und äußeren Aufbaus zeigt. Der Grund für die andersartige Formentwicklung liegt in der Versteifung der organischen Komponente durch eine vorangegangene Einlagerung von Calciumionen, wie sowohl experimentell als auch mit atomistischen Computersimulationen gezeigt werden konnte. Aufgrund der hohen Komplexität des Systems ist es bislang allerdings nicht möglich, lokale Ionen-Konzentrationen und pH-Werte vor bzw. während Nukleation und Wachstum der Kompositaggregate im Doppeldiffusionsversuch zu bestimmen. Deshalb wurde ein Ersatzversuch -- der sehr ähnlich strukturierte Aggregate erzeugt, sich aber mit rechnerischen Methoden analysieren lässt -- entworfen und untersucht. Anhand dieser Ergebnisse konnte erstmals die &amp;quot;Geschichte&amp;quot; von Fluorapatit-Gelatine-Nanokompositaggregaten detailliert nachvollzogen werden. Da über die Rolle der Gelatine beim Wachstum der Kompositaggregate nur wenig bekannt ist, wurde eine Reihe von Versuchen durchgeführt, in denen Gelatinen mit verschiedenen Molekülmassenverteilungen eingesetzt wurden. Es stellte sich heraus, dass für selbstorganisiertes und insbesondere fraktales Wachstum der Kompositaggregate lange, möglichst wenig gestörte Makromoleküle von zentraler Wichtigkeit sind. Um die Funktion der organischen Komponente für das Kompositwachstum näher zu untersuchen, wurden Oberflächen von Kompositkeimen mit rasterkraftmikroskopischen Methoden studiert. Durch Säuberung der Oberflächen konnten Austrittsstellen der organischen Komponente durch die Oberfläche der Kompositkeime identifiziert werden. Damit konnte gezeigt werden, dass die organische Komponente aus dem Inneren des Festkörpers teilweise durch die Oberfläche dringt und somit während des Wachstums weit in das Gel hineinreichen sollte. Für die mesoskopische Strukturbildung der Kompositaggregate spielen intrinsische elektrische Felder eine essenzielle Rolle. Deshalb wurde bislang eine Wirkung externer elektrischer Felder auf das Wachstum der Kompositaggregate vermutet. Im Rahmen der vorliegenden Arbeit wurde herausgearbeitet, dass es zwar zu keiner direkten Beeinflussung kommen kann, jedoch in den elektrodennahen Bereichen des Gels eine Ordnung der organischen Moleküle durch externe elektrische Felder zu erwarten ist. Dies könnte eine Wirkung auf wachsende Kompositaggregate zeigen. Da diese Effekte auch aufgrund der elektrischen Felder um die dipolaren Kompositaggregate zu erwarten sind, könnte eine ähnliche Strukturierung der Gelatine in der Nähe der wachsenden Kompositaggregate stattfinden. Insgesamt wurden in dieser Arbeit eine Reihe grundlegender Beiträge zur Erforschung der biomimetisch erzeugten Fluorapatit-Gelatine-Nanokompositaggregate geleistet. Es konnten neue Erkenntnisse zur inneren und äußeren Architektur der Kompositaggregate, zu Mechanismen der Morphogenese und deren wichtigsten Einflussgrößen sowie zum Verständnis der chemisch-physikalischen Vorgänge auf atomarer Größenskala gewonnen werden. Als besonders fruchtbar erwies sich die Verbindung von Experimenten mit theoretischen Untersuchungen, so dass dieser Weg auch in Zukunft grundlegende Erkenntnisse bei der Erforschung der Biomineralisation verspricht und weiterhin verfolgt werden sollte.

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