Les Récepteurs Couplés aux Protéines-G forment la plus importante famille de protéines membranaires chez l’homme et sont impliqués dans de nombreux processus de signalisation cellulaire. Aussi, ils forment un vivier très important de cibles thérapeutiques, déjà identifiées ou potentielles. L’activation d’un RCPG est amorcée par la liaison d’un ligand dans sa partie extra-cellulaire, modifiant ainsi ses propriétés dynamiques intrinsèques. Ces changements structuraux vont alors se répercuter le long des domaines trans-membranaires et promouvoir la dissociation de la Protéine-G hétéro-trimérique, de l’autre côté de la membrane, propageant ainsi le signal au compartiment intra-cellulaire. Ce processus peut être modulé par la liaison de nombreux autres partenaires des RCPGs. Malgré de nombreuses données structurales existantes, ces mécanismes restent encore mal connus à l’échelle moléculaire. Ainsi, la dynamique moléculaire s’est révélée être un outil formidable pour mieux comprendre ces mécanismes. Toutefois, les échelles de taille et de temps requises pour discuter de la dynamique de ces systèmes membranaires limitent ces études aux laboratoires ayant accès à une très grande puissance de calcul. L’objectif des travaux présentés dans ce manuscrit a été de prédire et de mieux comprendre la dynamique d’interaction de différents récepteurs de cette famille avec leurs partenaires, en développant un protocole de dynamique moléculaire, peu coûteux en ressources de calcul, combinant le champ de forces gros-grains MARTINI à un protocole de dynamique moléculaire « Replica-Exchange ».Dans un premier temps, nous présentons la validation de notre protocole pour la prédiction de la liaison de peptides à leur récepteur avec l’étude des peptides Neurotensine, agoniste du Récepteur de la Neurotensine-1, et CVX15, antagoniste du Récepteur Chemokine C-X-C de type-4. Nous montrons également que notre protocole est capable de prédire la sélectivité de plusieurs peptides dérivés de la Neurotensine envers plusieurs récepteurs sauvages et mutés, ne présentant qu’un résidu de différence.Dans un second temps, nous nous sommes intéressés à la dynamique de formation d’un hétéro-dimère de RCPGs impliquant le Récepteur de la Ghréline et le récepteur de la Dopamine D2, couplés aux protéines Gq et Gi respectivement. Ce modèle validé au laboratoire par des mesures LRET montre une interface impliquant une forte complémentarité entre les protéines-G. En se basant sur notre modèle, nous avons conçu et synthétisé des peptides inhibiteurs de la formation de cet hétéro-dimère de protéines-G.Enfin, nous présentons d’autres exemples d’applications de notre protocole et comment il peut être utilisé de concert avec l’expérience avec : la prédiction de la liaison de toxines de serpents aux Récepteurs de la Vasopressine-1a et V2 ; la prédiction de la liaison des peptides Ghréline et Leap2 au Récepteur GHSR-1a et la prédiction de la sélectivité de couplage de différents récepteurs aux peptides C-terminaux de la sous-unité α des protéines-G. / G-Protein Coupled Receptors form the largest family of human membrane proteins and are involved in many cellular signaling processes. Thus, they constitute a pool of already identified or potential pharmacological targets. The activation of a GPCR starts with the binding of a ligand in its extra-cellular part, further modifying its intrinsic dynamical properties. These structural rearrangements are then transmitted along the transmembrane domains and promote the dissociation of the G-protein on the other side of the bilayer, thus propagating the signal into the intra-cellular compartment. This activation process can be modulated by the binding of many other partners of GPCRs. Despite many structural data now available, these mechanisms are still badly known at the molecular scale. In agreement, molecular dynamics simulations appear to be a method of choice to get a better description of these mechanisms. Nevertheless, the size and the time scales required for the simulation of these membrane systems limit such studies to laboratories having access to large computational facilities.The objective of this work was to predict and get a dynamical view of the interactions of several GPCRs with their partners, by developing an affordable molecular dynamics protocol that combines the coarse-grained MARTINI force field to Replica-Exchange MD simulations.In a first step, we validated our protocol by showing its ability to predict the dynamical binding of peptides to their receptors, through the study of Neurotensin, an agonist of the Neurotensin-1 receptor and CVX15, an antagonist of the CXCR4 chemokine receptor. We also show that the same protocol is able to predict the selectivity of several Neurotensin derived peptides against several wild-type/mutated receptors differing by a single residue.In a second step, we were concerned by the dynamical assembly of a GPCR heterodimer involving the Ghrelin and the Dopamine D2 receptors, respectively coupled to Gq and Gi proteins. Our model was validated by LRET measurements confirming a large protein:protein interface and a high complementarity between G-proteins. Based on this model, we designed and synthesized some peptides able to inhibit the assembly of this G-proteins heterodimer.Finally, we describe other applications of our protocol and how it can be employed and confronted to experiments to : predict the dynamical binding of toxins from snake’s venom to the Vasopressin-1a and Vasopressin-2 receptors ; predict the binding of the Ghrelin and Leap2 peptides to their GHSR-1a receptor and predict the coupling selectivity of several receptors to peptides mimicking the C-terminus of the α subunit of G-proteins.

Dans cette thèse, nous abordons le contrôle moteur du mouvement du coude à travers deux approches expérimentales : une première étude psychophysique a été effectuée chez les sujets humains, et une seconde implique des enregistrements neurophysiologiques chez le singe. Nous avons recensé plusieurs aspects non résolus jusqu’à présent dans l’apprentissage moteur, particulièrement concernant l’interférence survenant lors de l’adaptation à deux ou plusieurs champs de force anti-corrélés. Nous avons conçu un paradigme où des stimuli de couleur aident les sujets à prédire la nature du champ de force externe actuel avant qu’ils ne l’expérimentent physiquement durant des mouvements d’atteinte. Ces connaissances contextuelles faciliteraient l’adaptation à des champs de forces en diminuant l’interférence. Selon le modèle computationnel de l’apprentissage moteur MOSAIC (MOdular Selection And Identification model for Control), les stimuli de couleur aident les sujets à former « un modèle interne » de chaque champ de forces, à s’en rappeler et à faire la transition entre deux champs de force différents, sans interférence. Dans l’expérience psychophysique, quatre groupes de sujets humains ont exécuté des mouvements de flexion/extension du coude contre deux champs de forces. Chaque force visqueuse était associée à une couleur de l’écran de l’ordinateur et les deux forces étaient anti-corrélées : une force résistante (Vr) a été associée à la couleur rouge de l’écran et l’autre, assistante (Va), à la couleur verte de l’écran. Les deux premiers groupes de sujets étaient des groupes témoins : la couleur de l’écran changeait à chaque bloc de 4 essais, tandis que le champ de force ne changeait pas. Les sujets du groupe témoin Va ne rencontraient que la force assistante Va et les sujets du groupe témoin Vr performaient leurs mouvements uniquement contre une force résistante Vr. Ainsi, dans ces deux groupes témoins, les stimuli de couleur n’étaient pas pertinents pour adapter le mouvement et les sujets ne s’adaptaient qu’à une seule force (Va ou Vr). Dans les deux groupes expérimentaux, cependant, les sujets expérimentaient deux champs de forces différents dans les différents blocs d’essais (4 par bloc), associés à ces couleurs. Dans le premier groupe expérimental (groupe « indice certain », IC), la relation entre le champ de force et le stimulus (couleur de l’écran) était constante. La couleur rouge signalait toujours la force Vr tandis que la force Va était signalée par la couleur verte. L’adaptation aux deux forces anti-corrélées pour le groupe IC s’est avérée significative au cours des 10 jours d’entraînement et leurs mouvements étaient presque aussi bien ajustés que ceux des deux groupes témoins qui n’avaient expérimenté qu’une seule des deux forces. De plus, les sujets du groupe IC ont rapidement démontré des changements adaptatifs prédictifs dans leurs sorties motrices à chaque changement de couleur de l’écran, et ceci même durant leur première journée d’entraînement. Ceci démontre qu’ils pouvaient utiliser les stimuli de couleur afin de se rappeler de la commande motrice adéquate. Dans le deuxième groupe expérimental, la couleur de l’écran changeait régulièrement de vert à rouge à chaque transition de blocs d’essais, mais le changement des champs de forces était randomisé par rapport aux changements de couleur (groupe « indice-incertain », II). Ces sujets ont pris plus de temps à s’adapter aux champs de forces que les 3 autres groupes et ne pouvaient pas utiliser les stimuli de couleurs, qui n’étaient pas fiables puisque non systématiquement reliés aux champs de forces, pour faire des changements prédictifs dans leurs sorties motrices. Toutefois, tous les sujets de ce groupe ont développé une stratégie ingénieuse leur permettant d’émettre une réponse motrice « par défaut » afin de palper ou de sentir le type de la force qu’ils allaient rencontrer dans le premier essai de chaque bloc, à chaque changement de couleur. En effet, ils utilisaient la rétroaction proprioceptive liée à la nature du champ de force afin de prédire la sortie motrice appropriée pour les essais qui suivent, jusqu’au prochain changement de couleur d’écran qui signifiait la possibilité de changement de force. Cette stratégie était efficace puisque la force demeurait la même dans chaque bloc, pendant lequel la couleur de l’écran restait inchangée. Cette étude a démontré que les sujets du groupe II étaient capables d’utiliser les stimuli de couleur pour extraire des informations implicites et explicites nécessaires à la réalisation des mouvements, et qu’ils pouvaient utiliser ces informations pour diminuer l’interférence lors de l’adaptation aux forces anti-corrélées. Les résultats de cette première étude nous ont encouragés à étudier les mécanismes permettant aux sujets de se rappeler d’habiletés motrices multiples jumelées à des stimuli contextuels de couleur. Dans le cadre de notre deuxième étude, nos expériences ont été effectuées au niveau neuronal chez le singe. Notre but était alors d’élucider à quel point les neurones du cortex moteur primaire (M1) peuvent contribuer à la compensation d’un large éventail de différentes forces externes durant un mouvement de flexion/extension du coude. Par cette étude, nous avons testé l’hypothèse liée au modèle MOSAIC, selon laquelle il existe plusieurs modules contrôleurs dans le cervelet qui peuvent prédire chaque contexte et produire un signal de sortie motrice approprié pour un nombre restreint de conditions. Selon ce modèle, les neurones de M1 recevraient des entrées de la part de plusieurs contrôleurs cérébelleux spécialisés et montreraient ensuite une modulation appropriée de la réponse pour une large variété de conditions. Nous avons entraîné deux singes à adapter leurs mouvements de flexion/extension du coude dans le cadre de 5 champs de force différents : un champ nul ne présentant aucune perturbation, deux forces visqueuses anti-corrélées (assistante et résistante) qui dépendaient de la vitesse du mouvement et qui ressemblaient à celles utilisées dans notre étude psychophysique chez l’homme, une force élastique résistante qui dépendait de la position de l’articulation du coude et, finalement, un champ viscoélastique comportant une sommation linéaire de la force élastique et de la force visqueuse. Chaque champ de force était couplé à une couleur d’écran de l’ordinateur, donc nous avions un total de 5 couleurs différentes associées chacune à un champ de force (relation fixe). Les singes étaient bien adaptés aux 5 conditions de champs de forces et utilisaient les stimuli contextuels de couleur pour se rappeler de la sortie motrice appropriée au contexte de forces associé à chaque couleur, prédisant ainsi leur sortie motrice avant de sentir les effets du champ de force. Les enregistrements d’EMG ont permis d’éliminer la possibilité de co-contractions sous-tendant ces adaptations, étant donné que le patron des EMG était approprié pour compenser chaque condition de champ de force. En parallèle, les neurones de M1 ont montré des changements systématiques dans leurs activités, sur le plan unitaire et populationnel, dans chaque condition de champ de force, signalant les changements requis dans la direction, l’amplitude et le décours temporel de la sortie de force musculaire nécessaire pour compenser les 5 conditions de champs de force. Les changements dans le patron de réponse pour chaque champ de force étaient assez cohérents entre les divers neurones de M1, ce qui suggère que la plupart des neurones de M1 contribuent à la compensation de toutes les conditions de champs de force, conformément aux prédictions du modèle MOSAIC. Aussi, cette modulation de l’activité neuronale ne supporte pas l’hypothèse d’une organisation fortement modulaire de M1. / In this thesis, we addressed motor control by two experimental approaches: psychophysical studies in human subjects and neurophysiological recordings in non-human primates. We identified unresolved issues concerning interference in motor learning during adaptation of subjects to two or more anti-correlated force fields. We designed paradigms in which arbitrary color stimuli provided contextual cues that allowed subjects to predict the nature of impending external force fields before encountering them physically during arm movements. This contextual knowledge helped to facilitate adaptation to the force fields by reducing this interference. According to one computational model of motor learning (MOdular Selection And Identification model for Control; MOSAIC), the color context cues made it easier for subjects to build “internal models” of each force field, to recall them and to switch between them with minimal interference. In our first experiment, four groups of human subjects performed elbow flexion/extension movements against two anti-correlated viscous force fields. We combined two different colors for the computer monitor background with two forces: resistive (Vr) and assistive (Va). The first two groups were control subjects. In those subjects, the color of the computer monitor changed at regular intervals but the force field remained constant; Vr was presented to the first group while the second group only experienced Va. As a result, the color cues were irrelevant in the two control groups. All control subjects adapted well to the single experienced force field (Vr or Va). In the two experimental groups, in contrast, the anti-correlated force fields and the monitor colors changed repeatedly between short blocks of trials. In the first experimental group (Reliable-cue subjects), there was a consistent relationship between the force and the stimulus (color of the monitor) - the red colour always signalled the resistive force while the green colour always signalled the assistive force. Adaptation to the two anti-correlated forces for the Reliable-cue group was significant during 10 days of training and almost as good as in the Irrelevant-cue groups who only experienced one of the two force fields. Furthermore, the Reliable-cue subjects quickly demonstrated predictive adaptive changes in their motor output whenever the monitor color changed, even during their first day of training, showing that they could use the reliable color context cues to recall the appropriate motor skills. In contrast, the monitor color also changed regularly between red and green in the second experimental group, but the force fields were not consistently associated with the color cue (Unreliable-cue group). These subjects took longer to adapt to the two force fields than the other three groups, and could not use the unreliable color cue change to make predictive changes to their motor output. Nevertheless, all Unreliable-cue subjects developed an ingenious strategy of making a specific “default” arm movement to probe the type of force field they would encounter in the first trial after the monitor color changed and used the proprioceptive feedback about the nature of the field to make appropriate predictive changes to their motor output for the next few trials, until the monitor color changed again, signifying the possibility of a change in force fields. This strategy was effective since the force remained constant in each short block of trials while the monitor color remained unchanged. This showed that the Unreliable-cue subjects were able to extract implicit and explicit information about the structure of the task from the color stimuli and use that knowledge to reduce interference when adapting to anti-correlated forces. The results of this first study encouraged us to advance our understanding of how subjects can recall multiple motor skills coupled to color context stimuli can be recalled, and how this phenomenon can be reflected by the neuronal activity in monkeys. Our aim was to elucidate how neurons of primary motor cortex (M1) can contribute to adaptive compensation for a wide range of different external forces during single-joint elbow flexion/extension movements. At the same time, we aimed to test the hypothesis evoked in the MOSAIC model, whereby multiple controller modules located in the cerebellum may predict each context and produce appropriate adaptive output signals for a small range of task conditions. Also, according to this hypothesis, M1 neurons may receive inputs from many specialized cerebellar controllers and show appropriate response modulations for a wide range of task conditions. We trained two monkeys to adapt their flexion/extension elbow movements against 5 different force-field conditions: null field without any external force disturbance, two anti-correlated viscous forces (assistive and resistive), which depended on movement speed and resembled that used in the human psychophysical study, a resistive elastic force which depended on elbow-joint position and finally, a visco-elastic field that was the linear sum of the elastic and viscous forces field. Each force field was reliably coupled to 5 different computer monitor background colors. The monkeys properly adapted to the 5 different force-field conditions and used the color context cues to recall the corresponding motor skill for the force field associated with each color, so that they could make predictive changes to their motor output before they physically encountered the force fields. EMG recordings eliminated the possibility that a co-contraction strategy was used by the monkeys to adapt to the force fields, since the EMG patterns were appropriate to compensate for each force-field condition. In parallel, M1 neurons showed systematic changes in their activity at the single-neuron and population level in each force-field condition that could signal the required changes in the direction, magnitude and time course of muscle force output required to compensate for the 5 force-field conditions. The patterns of response changes in each force field were consistent enough across M1 neurons to suggest that most M1 neurons contributed to the compensation for all force field conditions, in line with the predictions of the MOSAIC model. Also, these response changes do not support a strongly modular organization for M1.

One of the main challenges to transform highly useful Direct Methanol Fuel Cells (DMFC) into a commercially viable technology has been to develop a low cost polymer electrolyte membrane (PEM) with high proton conductivity, high stability and low methanol crossover under operating conditions desirably including high temperatures. Nafion, the widely used PEM, fails to meet all of these criteria simultaneously. Recently developed acid-base polymer blend membranes constitute a promising class of PEMs alternative to Nafion on above criteria. Even though some of these membranes produce better performance than Nafion, they still present numerous opportunities for maximizing high temperature proton conductivity and dimensional stability with concomitant minimization of methanol crossover. Our contribution embarks on the fundamental study of one such novel class of blend membranes viz., sulfonated poly (ether ether ketone) (SPEEK)(95 % by weight) blended with polysulfone tethered with base (5 % by weight) such as 2-aminobenzimidazole (ABIm), 5-amino-benzotriazole (BTraz) and 1H-perimidine (PImd), developed by Manthiram group at The University of Texas at Austin. In this work, we report extensive all-atom classical as well as ab-initio molecular dynamics (MD) simulations of such water-methanol solvated blend membranes (as well as pure SPEEK and Nafion) the first time. Our approach consists of three steps: (1) Predict dynamical properties such as diffusivities of water, methanol and proton in such membranes (2) Validate against experiments (3) Develop understanding on the interplay between basic chemistry, structure and properties, the knowledge that can potentially be used to develop better candidate membranes. In particular, we elucidate the impact of simple, fundamental physiochemical features of the polymeric membranes such as hydrophilicity, hydrophobicity, structure or the size of the base on the structural manifestations on the bigger scale such as nanophase segregation, hydrogen bonding or pore sizes, which ultimately affect the permeant transport through such systems. / text

This work concerns the interrelationship between thermodynamic, kinetic and structural aspects of crystal polymorphism. It is both experimental and theoretical, and limited with respect to compounds to substituted monocyclic aromatics. Two polymorphs of the compound m-aminobenzoic acid have been experimentally isolated and characterized by ATR-FTIR spectroscopy, X-ray powder diffraction and optical microscopy. In addition, two polymorphs of the compound m-hydroxybenzoic acid have been isolated and characterized by ATR-FTIR spectroscopy, high-temperature XRPD, confocal Raman, hot-stage and scanning electron microscopy. For all polymorphs, melting properties and specific heat capacity have been determined calorimetrically, and the solubility in several pure solvents measured at different temperatures with a gravimetric method. The solid-state activity (ideal solubility), and the free energy, enthalpy and entropy of fusion have been determined as functions of temperature for all solid phases through a thermodynamic analysis of multiple experimental data. It is shown that m-aminobenzoic acid is an enantiotropic system, with a stability transition point determined to be located at approximately 156°C, and that the difference in free energy at room temperature between the polymorphs is considerable. It is further shown that m-hydroxybenzoic acid is a monotropic system, with minor differences in free energy, enthalpy and entropy. 1393 primary nucleation experiments have been carried out for both compounds in different series of repeatability experiments, differing with respect to solvent, cooling rate, saturation temperature and solution preparation and pre-treatment. It is found that in the vast majority of experiments, either the stable or the metastable polymorph is obtained in the pure form, and only for a few evaluated experimental conditions does one polymorph crystallize in all experiments. The fact that the polymorphic outcome of a crystallization is the result of the interplay between relative thermodynamic stability and nucleation kinetics, and that it is vital to perform multiple experiments under identical conditions when studying nucleation of polymorphic compounds, is strongly emphasized by the results of this work. The main experimental variable which in this work has been found to affect which polymorph will preferentially crystallize is the solvent. For m-aminobenzoic acid, it is shown how a significantly metastable polymorph can be obtained by choosing a solvent in which nucleation of the stable form is sufficiently obstructed. For m-hydroxybenzoic acid, nucleation of the stable polymorph is promoted in solvents where the solubility is high. It is shown how this partly can be rationalized by analysing solubility data with respect to temperature dependence. By crystallizing solutions differing only with respect to pre-treatment and which polymorph was dissolved, it is found that the immediate thermal and structural history of a solution can have a significant effect on nucleation, affecting the predisposition for overall nucleation as well as which polymorph will preferentially crystallize. A set of polymorphic crystal structures has been compiled from the Cambridge Structural Database. It is found that statistically, about 50% crystallize in the crystallographic space group P21/c. Furthermore, it is found that crystal structures of polymorphs tend to differ significantly with respect to either hydrogen bond network or molecular conformation. Molecular mechanics based Monte Carlo simulated annealing has been used to sample different potential crystal structures corresponding to minima in potential energy with respect to structural degrees of freedom, restricted to one space group, for each of the polymorphic compounds. It is found that all simulations result in very large numbers of predicted structures. About 15% of the predicted structures have excess relative lattice energies of <=10% compared to the most stable predicted structure; a limit verified to reflect maximum lattice energy differences between experimentally observed polymorphs of similar compounds. The number of predicted structures is found to correlate to molecular weight and to the number of rotatable covalent bonds. A close study of two compounds has shown that predicted structures tend to belong to different groups defined by unique hydrogen bond networks, located in well-defined regions in energy/packing space according to the close-packing principle. It is hypothesized that kinetic effects in combination with this structural segregation might affect the number of potential structures that can be realized experimentally. The experimentally determined crystal structures of several compounds have been geometry-optimized (relaxed) to the nearest potential energy minimum using ten different combinations of common potential energy functions (force fields) and techniques for assigning nucleus-centred point charges used in the electrostatic description of the energy. Changes in structural coordinates upon relaxation have been quantified, crystal lattice energies calculated and compared with experimentally determined enthalpies of sublimation, and the energy difference before and after relaxation computed and analysed. It is found that certain combinations of force fields and charge assignment techniques work reasonably well for modelling crystal structures of small aromatics, provided that proper attention is paid to electrostatic description and to how the force field was parameterized. A comparison of energy differences for randomly packed as well as experimentally determined crystal structures before and after relaxation suggests that the potential energy function for the solid state of a small organic molecule is highly undulating with many deep, narrow and steep minima. / QC 20110527

Professional nurses comprise the largest number of health care professionals in South Africa. High turnover rates contribute to shortages of nurses in South Africa, aggravated by the emigration of nurses, inadequate recruitment of student nurses, and the expected retirement of many baby boomer nurses by 2016. This study addressed factors influencing the retention of professional nurses in the Gauteng Province of South Africa. In phase 1, postal questionnaires were completed by 101 registered nurses while semi-structured interviews were conducted with 21 nurse managers in phase 2. Personal, organisational and managerial factors influenced the retention potential of the professional nurses. In terms of Maslow' Hierarchy of Needs Theory, most factors influencing nurses' retention operated on the lowest (physiological) level and concerned remuneration. Safety needs were compromised by the lack of equipment and supplies, the shortage of nurses and unsafe working places. Esteem needs included respect from doctors, managers and colleagues as well as recognition for outstanding performance. In terms of Vogt et al's Theory of Nurse Retention Theory, the constrictions caused by inadequate remuneration and safety aspects should be addressed. Lewin's Force-Field Analysis Theory recommends that the factors that influence nurses' retention negatively should be unfrozen, changed and refrozen, including communication. Based on these results guidelines were compiled for enhancing the retention rates of professional nurses (Annexure G). / Health Studies / D.Litt. et Phil. (Health Studies)

Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.

FKBP12 est une protéine ubiquitaire, principalement cytosolique, qui est au carrefour de plusieurs voies signalétiques. Son abondance naturelle dans les tissus nerveux peut être reliée à son implication dans les maladies neurodégénératives telles que les maladies d'Alzheimer et de Parkinson ainsi que dans les neuropathies périphériques et diabétiques ou dans des blessures des cordons spinaux. De nombreuses études ont montré que des molécules exogènes (ligands) venant se fixer sur cette protéine permettent la régénération d'un grand nombre de connexions neuronales endommagées. Une difficulté provient cependant du fait que, pour un ligand donné, il n'existe aucune relation claire entre sa structure et sa capacité de liaison à FKBP12. Notre étude vise ainsi à rationaliser la relation entre la structure d'un ligand et son affinité pour cette protéine. Deux complexes modèles, formés entre FKBP12 et chacun des deux ligands 8 et 308, ont été utilisés. Ces deux ligands de haute affinité ont des structures différentes. Notre travail s'est appuyé sur des simulations de dynamique moléculaire pour caractériser l'état intermédiaire qui est formé transitoirement lors du processus de complexation entre la protéine et son ligand. Dans cet état particulier, l'identification des interactions naissantes entre les partenaires a permis (i) de comprendre l'implication des différentes parties du ligand dans le mécanisme de reconnaissance avec FKBP12 et (ii) de rationaliser les affinités de certains ligands apparentés. / FKBP12 is an ubiquitous, mostly cytosolic, protein found at the crossroads of several signaling pathways. Its natural abundance in the nervous tissues can be related to its implication in neurodegenerative diseases like Alzheimer's and Parkinson's as well as in peripheral neuropathies and diabetes or in injuries of the spinal cords. Several studies have demonstrated that exogenous molecules (ligands) that can bind to FKBP12 allow the regeneration of many damaged neuron connections. However, there is no clear relationship between the structure of a ligand and its ability to bind to FKBP12. Our study aims at rationalizing the relationship between the structure of a ligand and its affinity to FKBP12. Two model complexes, formed between FKBP12 and each of the two high-affinity ligands 8 and 308, were studied. These two ligands are structurally different. We used molecular dynamics simulations to characterize the intermediate state that is transiently formed during the binding process between the protein and its ligand. In this state, the analysis of the nascent interactions allowed (i) to unravel the role played by the various ligand moieties in the recognition process with FKBP12 and (ii) to rationalize the affinities of related ligands.

Siliziumnanodrähte (SiNWs) bieten eine aussichtsreiche Grundlage zur Entwicklung neuartiger nanoelektronischer Bauelemente, wie Feldeffekttransistoren oder Sensoren. Dabei ist insbesondere die Oxidation der Drähte interessant, weil diese weitreichenden Einfluss auf die elektronischen Eigenschaften der Bauelemente hat, die aus den SiNWs gefertigt werden. Die Größe der untersuchten Strukturen erfordert eine atomistische Analyse des Oxidationsprozesses. In der vorliegenden Arbeit wird der bisher wenig verstandene Beginn der Oxidation dünner Drähte molekulardynamisch simuliert, wobei als Potential ein reaktives Kraftfeld dient. Dabei wird sich intensiv mit dem Transfer elektrischer Ladungen zwischen Atomen unterschiedlicher Elektronegativitäten während der Simulationen auseinandergesetzt. Desweiteren werden Strukturen, die während der Oxidation von SiNWs der Orientierungen <100> und <110> bei Temperaturen von 300 K und 1200 K entstehen, untersucht. Ein Fokuspunkt dieser Untersuchungen ist die Analyse der Anzahl am Draht adsorbierter Sauerstoffatome während der frühen Oxidationsphase. Darüber hinaus wird die Dichte der entstehenden Strukturen beleuchtet. Dies geschieht mit einer hohen radialen Auflösung und erstmalig während der gesamten Simulation. Hierbei zeigt sich, dass während des Übergangs von kristallinem Silizium zu amorphem Siliziumdioxid zwischen den Siliziumatomen Sauerstoff eingelagert wird, die Kristallstruktur des Siliziums sich zunächst jedoch noch nicht auflöst. Dadurch entsteht ein charakteristisches Muster hoher und niedriger Dichten, das von der ursprünglichen Kristallstruktur des SiNW abhängt.:Abbildungsverzeichnis Abkürzungsverzeichnis Symbolverzeichnis 1 Einleitung 2 Einführung zu Siliziumnanodrähten 2.1 Kristallstuktur von Silizium 2.2 Ideale Siliziumnanodrähte 2.3 Herstellung von Siliziumnanodrähten 3 Grundlagen der Molekulardynamik 3.1 Newtonsche Axiome 3.2 Einige grundlegende Begriffe der statistischen Physik 3.3 Molekulardynamik 3.4 Reaktives Kraftfeld 3.5 Methoden zur Beschreibung des Ladungstransfers 3.6 Thermostat und Barostat 3.7 Large-scale Atomic/Molecular Massively Parallel Simulator 4 Entwicklung des Modellsystems 4.1 Ausgangsstruktur 4.2 Vorrelaxation 4.3 Ablauf der Oxidation 4.4 Verwendeter ReaxFF-Parametersatz 4.5 Optimierung der Zeitschrittweite 4.5.1 Modellsystem, Relaxation und Oxidation 4.5.2 Festlegung der Zeitschrittweite 4.6 Optimierung der Systemlänge 4.6.1 Modellsystem, Relaxation und Oxidation 4.6.2 Festlegung der Systemlänge 4.7 Einfluss des globalen, instantanen Ladungstransfers auf die Simulation 4.7.1 Festlegung des Einsetzabstands 4.7.2 Vergleich mit Daten von Khalilov et al. 5 Variation von System- und Einsetztemperatur sowie Drahtorientierung 5.1 Variation von System- und Einsetztemperatur 5.1.1 Untersuchung des Oxidationsgrads 5.1.2 Untersuchung von Dichten und Grenzflächenpositionen 5.2 Variation der Drahtorientierung 5.2.1 Untersuchung des Oxidationsgrads 5.2.2 Untersuchung von Dichten und Grenzflächenpositionen 6 Zusammenfassung und Ausblick 6.1 Zusammenfassung 6.2 Ausblick Literaturverzeichnis

Siliziumnanodrähte (SiNWs) bieten aufgrund ihrer exzellenten elektrostatischen Kontrollierbarkeit eine gute Grundlage für die Entwicklung neuartiger Bauelemente, wie rekonfigurierbarer Feldeffekttransistoren (RFETs). Da SiNWs durch die Oxidation gezielt verzerrt werden können und diese Verzerrung die Bandstruktur des Siliziums verändert, bietet der Oxidationsprozess eine Möglichkeit, die Leitungseigenschaften der RFETs zu modulieren und eine symmetrische Transfercharakteristik zu erhalten. Die Untersuchung von SiNWs mit Durchmessern im einstelligen Nanometerbereich bedarf eines atomistischen Ansatzes. In der vorliegenden Arbeit wird mit einem reaktiven Kraftfeld die initiale Phase der Oxidation dünner SiNWs molekulardynamisch simuliert. Gegenstand der Untersuchungen sind die Temperaturabhängigkeit der Oxidation von <110>-SiNWs mit Anfangsradien von 10.2 Å sowie das Oxidationsverhalten von <110>- und <100>-SiNWs mit Anfangsradien von 5.1 Å. Dabei wird neben dem Sauerstoffanteil im Simulationssystem und der radial aufgelösten Dichte auch das radial aufgelöste Verhältnis zwischen Sauerstoff- und Siliziumatomen während der gesamten Simulationsdauer untersucht und ein Zusammenhang zur Dichte festgestellt. Darüber hinaus wird bei 300 K erstmals eine Analyse der Verzerrungsentwicklung während der initialen Oxidationsphase durchgeführt, bei der sich sowohl für <110>-SiNWs als auch für <100>-SiNWs eine tensile Verzerrung im unoxidierten Drahtkern einstellt. Wie eine Analyse der partiellen radialen Verteilungsfunktion zeigt, kommt es zu dieser Verzerrung, weil während der Oxidation die Grundstruktur des Siliziums im Oxid erhalten bleibt, durch die Einlagerung des Sauerstoffs allerdings der Bindungsabstand erhöht wird. Dieser erhöhte Bindungsabstand wird durch Bindungen zu Siliziumatomen im Oxid auch Siliziumatomen im unoxidierten Kern aufgezwungen.:Inhaltsverzeichnis Abbildungsverzeichnis Tabellenverzeichnis Abkürzungsverzeichnis Symbolverzeichnis 1. Einleitung 2. Theoretische Grundlagen 2.1. Molekulardynamik 2.2. Siliziumnanodrähte 2.3. Verzerrung und Verspannung 3. Modellsystem 3.1. Ausgangsstruktur 3.2. Vorrelaxation 3.3. Ablauf der Oxidation 4. Untersuchungsmethoden 4.1. Sauerstofffluenz, Oxidationsgrad und Oxidationsrate 4.2. Massendichte und Siliziumanteil 4.3. Radiale Verteilungsfunktion 4.4. Verzerrung 4.4.1. <110>-Draht 4.4.2. <100>-Draht 5. Ergebnisse und Diskussion 5.1. Festlegung des Einsetzintervalls 5.2. Temperaturvariation 5.2.1. Oxidationsgrad 5.2.2. Siliziumanteil 5.2.3. Massendichte 5.2.4. Radiale Verteilungsfunktion 5.3. Radius- und Orientierungsvariation 5.4. Verzerrung 6. Zusammenfassung und Ausblick 6.1. Zusammenfassung 6.2. Ausblick A. Festlegung des Einsetzintervalls Literaturverzeichnis

The present Doctoral Thesis focuses on the investigation, characterization and influence of polyacrylic materials in different scientific and technological disciplines via a detailed computer simulation using the Molecular Dynamics (MD) technique, in conjunction with the very accurate, all-atom Dreiding force-field. The main research concepts and objectives are discussed and analyzed in three separate parts. In the first part, atomistic configurations of two model pressure-sensitive acrylic adhesives (PSAs), the atactic homopolymer poly(n-BA) [poly(n-butyl acrylate)] and the atactic copolymer poly(n-BA-co-AA) [poly(n-butyl acrylate-co-acrylic acid)] in the bulk phase or confined between two selected substrates, glassy silica (SiO2) and metallic α-ferrite (α-Fe), were built and simulated by MD in the NPT statistical ensemble. First, an equilibration cycle consisting of temperature annealings and coolings was followed, in order to generate well-equilibrated configurations of the PSA systems. Detailed results from the atomistic simulations are presented concerning their volumetric behavior, glass transition temperature, conformational, structural, viscoelastic and dynamic properties. Particular emphasis was given to the analysis and characterization of the hydrogen bonds that form in the poly(n-BA-co-AA) system. By analyzing the MD trajectories, poly(n-BA-co-AA) was found to exhibit a higher density than poly(n-BA) by about 7% at all temperatures, to be characterized by smaller-size chains for a given molecular weight (MW), to exhibit significantly slower terminal and segmental dynamics properties, and to be characterized by a glass transition temperature that was approximately 40% higher than that of poly(n-BA). We also examined the type and degree of adsorption of the two acrylic systems on the selected substrates by analyzing the MD results for the local mass density as a function of distance from the solid plane and the distribution of adsorbed chain segments in train, loop, and tail conformations, and by computing the work of adhesion at the two substrates. The results revealed a stronger adsorption for both acrylics on the SiO2 surface due to highly attractive interactions between polymer molecules and substrate atoms, and as a consequence a higher value for the work of adhesion compared to that on the α-Fe surface. Furthermore, we have developed a generalized non-equilibrium molecular dynamics (NEMD) algorithm to simulate the mechanical response of the two adhesives under a uniaxial stretching deformation. In the second part of the Thesis, results have been obtained from a hierarchical simulation methodology that led to the prediction of the thermodynamic, conformational, structural, dynamic and mechanical properties of two polymer nanocomposites based on syndiotactic poly(methyl methacrylate) or sPMMA. The first was reinforced with uniformly dispersed graphene sheets and the second with fullerene particles. How graphene functionalization affects the elastic constants of the resulting nanocomposite has also been examined. The phase behavior of the nanocomposite (in particular as we varied the relative size between the sPMMA chains and the diameter of fullerene molecules) has also been studied as a function of fullerene volume fraction. The simulation strategy entailed three steps: 1) Generation of an initial structure, which was then subjected to potential energy minimization and detailed molecular dynamics (MD) simulations at T = 500K and P = 1atm to obtain well relaxed melt configurations of the nanocomposite. 2) Gradual cooling of selected configurations down to room temperature to obtain a good number of structures representative of the glassy phase of the polymer nanocomposite. 3) Molecular mechanics (MM) calculations of its mechanical properties following the method originally proposed by Theodorou and Suter. By analyzing the results under constant temperature and pressure, all nanocomposite systems were found to exhibit slower terminal and segmental relaxation dynamics than the pure polymer matrices. The addition of a small fraction of graphene sheets led in all cases to the enhancement of the elastic constants; this was significantly more pronounced in the case of functionalized graphene sheets. We further mention that, for all polymer/fullerene nanocomposites addressed here, no phase separation or variation of polymer chain dimensions was observed as a function of fullerene size and/or fullerene volume fraction. In the third part of the Thesis, and motivated by the use of acrylic polymers for the design of membranes with aligned carbon nanotubes (CNTs) for several separation technologies (such as water desalination and wastewater treatment), we report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall CNTs (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for water molecule were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed in the Thesis include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on carbon nanotube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the (phenolic) molecules simulated in this Thesis, the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This has been attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable structures inside the nanotube, especially under strong confinement. The interaction, in particular, of the methyl group (present in tyrosol, vanillic acid, and p-coumaric acid) with the CNT walls seems to play a key role in all these compounds causing them to remain practically immobile inside nanotubes characterized by diameters smaller than about 26 Å. It was only for larger-diameter CNTs that tyrosol, vanillic acid, and p-coumaric acid were observed to demonstrate appreciable mobility. / Η παρούσα Διδακτορική Διατριβή εστιάζει στη μελέτη της σχέσης μεταξύ δομής και μακροσκοπικών φυσικών ιδιοτήτων υλικών από πολυακρυλικά μέσω μίας λεπτομερούς προσομοίωσης στον υπολογιστή με τη μέθοδο της Μοριακής Δυναμικής (ΜΔ), σε συνδυασμό με ένα πολύ επακριβές πεδίο δυνάμεων (το Dreiding) σε ατομιστική λεπτομέρεια. Οι κύριες ερευνητικές έννοιες καθώς και οι στόχοι συζητιούνται και αναλύονται σε τρία ξεχωριστά μέρη. Στο πρώτο μέρος, ατομιστικές απεικονίσεις δύο προτύπων πίεσο-ευαίσθητων συγκολλητικών υλικών (acrylic pressure sensitive adhesives ή PSAs), του ατακτικού πολυ-βουτυλικού-ακρυλικού εστέρα (poly(n-BA)) και του συμπολυμερούς του με ακρυλικό οξύ (poly(n-BA-co-AA)), τόσο μακριά όσο και κοντά σε υποστρώματα σίλικας (SiO2) και α-φερρίτη (α-Fe), μελετήθηκαν στη βάση ενός φάσματος ιδιοτήτων (θερμοδυναμικές, δομικές, ιξωδοελαστικές, δυναμικές, και συγκολλητικές), όπως και η μηχανική τους απόκριση υπό συνθήκες μονοαξονικής εκτατικής παραμόρφωσης. Στο δεύτερο μέρος παρουσιάζονται τα αποτελέσματα που εξήχθησαν από μία ιεραρχική μεθοδολογία προσομοίωσης που οδήγησε στην πρόβλεψη της φασικής συμπεριφοράς και των μηχανικών ιδιοτήτων νανοσύνθετων πολυμερικών υλικών (polymer nanocomposites ή PNCs) βασισμένων στο συνδιοτατκτικό πολυ-μεθακρυλικό μεθυλεστέρα (syndiotactic poly(methyl methacrylate) ή sPMMA), ενισχυμένο με ομοιόμορφα διεσπαρμένα φύλλα γραφενίου (graphene sheets) ή σωματίδια φουλερενίου (fullerene particles). Στο τρίτο μέρος, υποκινούμενοι από τη χρήση των ακρυλικών πολυμερών στο σχεδιασμό μεμβρανών με ενσωματωμένους ευθυγραμμισμένους νανοσωλήνες άνθρακα (ΝΑ, carbon nanotubes ή CNTs) σε διάφορες τεχνολογίες διαχωρισμού μορίων (με έμφαση στον καθαρισμό του νερού), παρουσιάζουμε αποτελέσματα από προσομοιώσεις, για τη νανο-ρόφηση και την κινητικότητα τεσσάρων διαφορετικών μικρών μορίων (water, tyrosol, vanilic acid, και p-coumaric acid) στο εσωτερικό λείων μονο-στρωματικών ΝΑ (single-wall CNTs ή SWCNTs). Τα θέματα που εξετάζονται περιλαμβάνουν τη μοριακή διευθέτηση και τη διάταξη στο εσωτερικό Ν.Α. των τεσσάρων μορίων, το μέσο χρόνο παραμονής τους, καθώς και τους αξονικούς συντελεστές διάχυσής του, συναρτήσει της διαμέτρου και του μήκους των ΝΑ.