L’objectif de cette thèse est d’analyser et prédire les conformations d’un système moléculaire en combinant la théorie des graphes et la chimie computationnelle.Dans le cadre des simulations de dynamique moléculaire, une molécule peut avoir une ou plusieurs conformations au cours du temps. Dans les trajectoires de simulation de dynamique moléculaire, on peut avoir des trajectoires n’explorant qu’une seule conformation ou des trajectoires explorant plusieurs conformations, donc plusieurs transitions entre conformations sont observées. L’exploration de ces conformations dépend du temps de la simulation et de l'énergie (température) fixée dans le système. Pour avoir une bonne exploration des conformations d’un système moléculaire, il faut générer et analyser plusieurs trajectoires à différentes énergies. Notre objectif est de proposer un algorithme universel qui permet d’analyser la dynamique conformationnelle de ces trajectoires d’une façon rapide et automatique. Les trajectoires fournissent les positions cartésiennes des atomes du système moléculaire à des intervalles de temps réguliers. Chaque intervalle contenant un ensemble de positions est appelé image. L’algorithme utilise des règles de géométrie (distances, angles, etc.) sur les positions pour trouver les liaisons (liaisons covalentes, liaisons hydrogène et interactions électrostatiques) créées entre les atomes, permettant par la suite d’obtenir le graphe mixte qui modélise une conformation. Nous ne considérons un changement conformationnel que s’il y a un changement dans les liaisons calculées à partir des positions données. L’algorithme permet de donner l’ensemble des conformations explorées sur une ou plusieurs trajectoires, la durée d’exploration de chaque conformation, ainsi que le graphe de transitions qui contient tous les changements conformationnels observés.Les conformations se caractérisent par une énergie appelée énergie potentielle. Cette énergie est représentée par une courbe appelée surface d’énergie potentielle. En chimie théorique et computationnelle, certains s’intéressent à trouver des points particuliers sur cette surface. Il s'agit des minima qui représentent les conformations les plus stables et des maxima ou états de transition qui représentent les points de passage d'une conformation à une autre. En effet, d'une part, la conformation la plus stable est celle de plus basse énergie. D'autres part, pour aller d’une conformation à une autre il faut une énergie supplémentaire, le point maximum représente l'état de transition. Les méthodes développées pour calculer ces points nécessitent une connaissance de l’énergie potentielle ce qui est coûteux en temps et en calculs. Notre objectif est de proposer une méthode alternative en utilisant des mesures ah doc basées sur des propriétés des graphes qu’on a utilisées dans le premier algorithme et sans faire appel à la géométrie ni aux calculs moléculaires. Ces mesures permettent de générer des conformations avec un classement énergétique ainsi de définir le coût énergétique de chaque transition permise. Les conformations possibles avec les transitions représentent respectivement les sommets et les arcs de ce qu’on appelle le “graphe des possibles”. Les hypothèses utilisées dans le modèle proposé est que seules les liaisons hydrogène peuvent changer entre les conformations et que le nombre de liaisons hydrogène présentes dans le système permet de déterminer son coût énergétique.L’algorithme d'analyser des trajectoires a été testé sur trois types de systèmes moléculaires en phase gazeuse de taille et de complexité croissantes. Bien que la complexité théorique de l’algorithme est exponentielle (tests d’isomorphisme) les résultats ont montré que l’algorithme est rapide (quelques secondes). De plus, cet algorithme peut être facilement adapté et appliqué à d’autres systèmes. Pour la prédiction conformationnelle, le modèle proposé a été testé sur des peptides isolés. / This PhD is part of transdisciplinary works, combining graph theory and computational chemistry.In molecular dynamics simulations, a molecular system can adopt different conformations over time. Along a trajectory, one conformation or more can thus be explored. This depends on the simulation time and energy within the system. To get a good exploration of the molecular conformations, one must generate and analyse several trajectories (this can amount to thousands of trajectories). Our objective is to propose an automatic method that provides rapid and efficient analysis of the conformational dynamics explored over these trajectories. The trajectories of interest here are in cartesian coordinates of the atoms that constitute the molecular system, recorded at regular time intervals (time-steps). Each interval containing a set of positions is called a snapshot. At each snapshot, our developed algorithm uses geometric rules (distances, angles, etc.) to compute bonds (covalent bonds, hydrogen bonds and any other kind of intermolecular criterium) formed between atoms in order to get the mixed graph modelling one given conformation. Within our current definitions, a conformational change is characterized by either a change in the hydrogen bonds or in the covalent bonds. One choice or the other depends on the underlying physics and chemistry of interest. The proposed algorithm provides all conformations explored along one or several trajectories, the period of time for the existence of each one of these conformations, and also provides the graph of transitions that shows all conformational changes that have been observed during the trajectories. A user-friendly interface has been developed, that can de distributed freely.Our proposed algorithm for analysing the trajectories of molecular dynamics simulations has been tested on three kinds of gas phase molecular systems (peptides, ionic clusters). This model can be easily adapted and applied to any other molecular systems as well as to condensed matter systems, with little effort. Although the theoretical complexity of the algorithm is exponential (isomorphism tests), results have shown that the algorithm is rapid.We have also worked on computationally low cost graph methods that can be applied in order to pre-characterize specific conformations/points on a potential energy surface (it describes the energy of a system in terms of positions of the atoms). These points are the minima on the surface, representing the most stable conformations of a molecular system, and the maxima on that surface, representing transition states between two conformers. Our developed methods and algorithms aim at getting these specific points, without the prerequisite knowledge/calculation of the potential energy surface by quantum chemistry methods (or even by classical representations). By avoiding an explicit calculation of the potential energy surface by quantum chemistry methods, one saves computational time and effort. We have proposed an alternative method using ad doc measures based on properties of the graphs (already used in the first part of the PhD), without any knowledge of energy and/or molecular calculations. These measures allow getting the possible conformations with a realistic energy classification, as well as transition states, at very low computational cost. The algorithm has been tested on gas phase peptides.

No description available.

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

No description available.

A unique mechanism of protein oligomerization is domain swapping. It is a feature found in some proteins wherein a dimer or a higher oligomer is formed by the exchange of identical structural segments between protomers. Domain swapping is thought to have played a key role in the evolution of stable oligomeric proteins and in oligomerization of amyloid proteins. This thesis deals with studies to understand the significance of hinges involved in domain swapping for protein oligomerization and function. The stationary phase survival protein SurE from Salmonella typhimurium (StSurE) and Sesbania mosaic virus (SeMV) coat protein have been used as models for studies on domain swapping. This thesis has been divided into eight chapters. Chapter 1 provides a brief introduction to domain swapping, while Chapters 2 to 6 describes the studies carried out on StSurE protein, Chapter 7 deals with studies on SeMV coat protein. The final Chapter 8 provides brief descriptions of various experimental techniques employed during these investigations. Chapter 1 deals with a brief introduction to domain swapping in proteins. Examples where different domains are exchanged are cited. Then it describes physiological relevance of domain swapping in proteins and probable factors which promote swapping. Finally it also discusses the uncertainties that are inevitable in protein structure prediction and design. Chapter 2 describes the structure of Salmonella typhimurium SurE (StSurE; Pappachan et al., 2008) determined at a higher resolution. The chapter also deals with the sequence and structure based comparison of StSurE with other known SurE homolog structures. A comparative analysis of the relative conservation of N- and C-terminal halves of SurE protomer and variations observed in the quaternary structures of SurE homologs are presented. Then a brief introduction is provided on function of StSurE. The conserved active site of StSurE that might be important for its phosphatase activity is described. A plausible mechanism for the phosphatase activity as proposed by Pappachan et al. (2008) is presented. Crystal structures of StSurE bound with AMP, pNPP and pNP that was determined with the view of better understanding the mechanism of enzyme function is presented. These structures provide structural evidence for the mechanism proposed by Pappachan et al. (2008). Finally a substrate entry channel inferred from these structures is discussed. SurE from Salmonella typhimurium (StSurE) was selected for studies on domain swapping as there is at least one homologous structure (Pyrobaculum aerophilum - PaSurE) in which swapping of the C-terminal helices appears to have been avoided without leading to the loss of oligomeric structure or function. It was of interest to examine if an unswapped dimer of StSurE resembling PaSurE dimer could be constructed by mutagenesis. To achieve this objective, a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was abolished by mutagenesis. These mutants were constructed with the intention of increasing the flexibility of the hinge which might bring the C-terminal helices closer to the respective protomer as in PaSurE. Chapter 3 presents a comparative analysis of the hinges involved in C-terminal helix swapping in PaSurE and StSurE. Based on the comparison of structure and sequence, crucial residues important for C-terminal helix swapping in StSurE were identified as D230 and H234. The chapter describes the construction of mutants obtained by substituting D230 and H234 by alanine and their biophysical characterization. Finally it describes structural studies carried out on these mutants. The mutation H234A and D230A/H234A resulted in highly distorted dimers, although helix swapping was not avoided. Comparative analysis of the X-ray crystal structures of native StSurE and mutants H234A and D230A/H234A reveal large structural changes in the mutants relative to the native structure. However the crystal structures do not provide information on the changes in dynamics of the protein resulting from these mutations. To gain better insights into the dynamics involved in the native and mutants H234A and D230A/H234A, MD simulations were carried on using GROMACS 4.0.7. Chapter 4 deals with a brief description of the theory of molecular dynamics, followed by results of simulation studies carried out on monomeric and dimeric forms of StSurE and dimeric forms of its mutants H234A and D230A/H234A. The conformational changes and dynamics of different swapped segments are discussed. Crystal structures of H234A and D230A/H234A mutants reveal that they form highly distorted dimers with altered dimeric interfaces. Chapter 5 focuses on comparison of dimeric interfaces of the native StSurE and hinge mutants H234A and D230A/H234A. Based on the analysis, three sets of interactions were selected to investigate the importance of the interface formed by swapped segments in StSurE mutants H234A and D230A/H234A. One of the selected sites corresponds to a novel interaction involving tetramerization loop in the hinge mutants H234A and D230A/H234A resulting in a salt bridge between E112 – R179’ and E112’ – H180 (prime denotes residue from the other chain of the dimeric protein). This salt bridge seems to stabilize the distorted dimer. It is shown by structural studies that the loss of this salt bridge due to targeted mutation restores symmetry and dimeric organization of the mutants. Loss of a crucial hydrogen bond in the hinge region involved in C-terminal helix swapping in SurE not only leads to large structural changes but also alters the conformation of a loop near the active site. It is of interest to understand functional consequences of these structural changes. StSurE is a phosphatase, and its activity could be conveniently monitored using the synthetic substrate para nitrophenyl phosphate (pNPP) at pH 7 and 25 ºC. Chapter 6 deals with the functional studies carried out with various StSurE mutants. The studies suggest that there is a drastic loss in phosphatase activity in hinge mutants D230A, H234A and D230A/H234A, while in the salt bridge mutants the function seems to have been restored. Few of these mutants also exhibit positive cooperativity, which could probably be due to altered dynamics of domains. Sesbania mosaic virus (SeMV) is a plant virus, belonging to genus sobemovirus. SeMV is a T=3 icosahedral virus (532 symmetry) made up of 180 coat protein (CP) subunits enclosing a positive-sense RNA genome. The asymmetric unit of the icosahedral capsid is composed of chemically identical A, B and C subunits occupying quasi-equivalent environments. Residues 48 – 59 of the N-terminal arms of the C subunits interact at the nearby icosahedral three-fold axes through a network of hydrogen bonds to form a structure called the “β-annulus”. Residues 60 – 73 form the “βA-arm” that connects the N-terminal β-annulus to the rest of the protomer. Various studies on SeMV-CP suggest that different lengths of the N-terminal segments affect the assembly of virus. It might be possible to exploit this flexibility of the N-terminus in SeMV-CP to introduce swapping of this segment between two 2-fold related C subunits as is found in Rice yellow mottle virus (RYMV), another sobemovirus, with which SeMV shares significant sequence similarity. Chapter 7 focuses on attempts made to examine the mutational effects planned to introduce domain swapping. The strategy used for introducing swapping in SeMV-CP was based on the sequence of the βA-arm or the hinge involved in swapping of β-annulus in RYMV. TEM images of the mutant virus like particles obtained suggest that they are heterogeneous. These mutants could not be crystallized, probably due to the heterogeneity. However, the assembly of the expressed proteins to virus like particles was profoundly influenced by the mutations. Chapter 8 discusses various crystallographic, biophysical and biochemical techniques used during these investigations. Finally the thesis concludes with Conclusions and Future perspectives of the various studies reported in the thesis. In summary, I have addressed the importance of amino acid residues and interactions of hinges involved in domain swapping for the quaternary structure and function of proteins.

Cette thèse comporte quatre fichiers vidéo. This thesis comes with four video files. / L'industrie chimique mondiale est en pleine mutation, cherchant des solutions pour rendre la synthèse organique classique plus durable. Une telle solution consiste à passer de la catalyse chimique classique à la biocatalyse. Bien que les avantages des enzymes incluent leur stéréo, régio et chimiosélectivité, cette sélectivité réduit souvent leur promiscuité. Les efforts requis pour adapter la fonction enzymatique aux réactions désirées se sont révélés d'une efficacité modérée, de sorte que des méthodes rapides et rentables sont nécessaires pour générer des biocatalyseurs qui rendront la production chimique plus efficace. Dans l’ère de la bioinformatique et des outils de calcul pour soutenir l'ingénierie des enzymes, le développement rapide de nouvelles fonctions enzymatiques devient une réalité. Cette thèse commence par un examen des développements récents sur les outils de calcul pour l’ingénierie des enzymes. Ceci est suivi par un exemple de l’ingénierie des enzymes purement expérimental ainsi que de l’évolution des protéines. Nous avons exploré l’espace mutationnel d'une enzyme primitive, la dihydrofolate réductase R67 (DHFR R67), en utilisant l’ingénierie semi-rationnelle des protéines. La conception rationnelle d’une librarie de mutants, ou «Smart library design», impliquait l’association covalente de monomères de l’homotétramère DHFR R67 en dimères afin d’augmenter la diversité de la librairie d’enzymes mutées. Le criblage par activité enzymatique a révélé un fort biais pour le maintien de la séquence native dans un des protomères tout en tolérant une variation de séquence élevée pour le deuxième. Il est plausible que les protomères natifs procurent l’activité observée, de sorte que nos efforts pour modifier le site actif de la DHFR R67 peuvent n’avoir été que modérément fructueux. Les limites des méthodes expérimentales sont ensuite abordées par le développement d’outils qui facilitent la prédiction des points chauds mutationnels, c’est-à-dire les sites privilégiés à muter afin de moduler la fonction. Le développement de ces techniques est intensif en termes de calcul, car les protéines sont de grandes molécules complexes dans un environnement à base d’eau, l’un des solvants les plus difficiles à modéliser. Nous présentons l’identification rapide des points chauds mutationnels spécifiques au substrat en utilisant l'exemple d’une enzyme cytochrome P450 industriellement pertinente, la CYP102A1. En appliquant la technique de simulation de la dynamique moléculaire par la force de polarisation adaptative, ou «ABF», nous confirmons les points chauds mutationnels connus pour l’hydroxylation des acides gras tout en identifiant de nouveaux points chauds mutationnels. Nous prédisons également la conformation du substrat naturel, l’acide palmitique, dans le site actif et nous appliquons ces connaissances pour effectuer un criblage virtuel d'autres substrats de cette enzyme. Nous effectuons ensuite des simulations de dynamique moléculaire pour traiter l’impact potentiel de la dynamique des protéines sur la catalyse enzymatique, qui est le sujet de discussions animées entre les experts du domaine. Avec la disponibilité accrue de structures cristallines dans la banque de données de protéines (PDB), il devient clair qu’une seule structure de protéine n’est pas suffisante pour élucider la fonction enzymatique. Nous le démontrons en analysant quatre structures cristallines que nous avons obtenues d’une enzyme β-lactamase, parmi lesquelles un réarrangement important des résidus clés du site actif est observable. Nous avons réalisé de longues simulations de dynamique moléculaire pour générer un ensemble de structures suggérant que les structures cristallines ne reflètent pas nécessairement la conformation de plus basse énergie. Enfin, nous étudions la nécessité de compléter de manière informatisée un hémisphère où l’expérimental n’est actuellement pas possible, à savoir la prédiction de la migration des gaz dans les enzymes. À titre d'exemple, la réactivité des enzymes cytochrome P450 dépend de la disponibilité des molécules d’oxygène envers l’hème du site actif. Par le biais de simulations de la dynamique moléculaire de type Simulation Implicite du Ligand (ILS), nous dérivons le paysage de l’énergie libre de petites molécules neutres de gaz pour cartographier les canaux potentiels empruntés par les gaz dans les cytochromes P450 : CYP102A1 et CYP102A5. La comparaison pour les gaz CO, N2 et O2 suggère que ces enzymes évoluent vers l’exclusion du CO inhibiteur. De plus, nous prédisons que les canaux empruntés par les gaz sont distincts des canaux empruntés par le substrat connu et que ces canaux peuvent donc être modifiés indépendamment les uns des autres. / The chemical industry worldwide is at a turning point, seeking solutions to make classical organic synthesis more sustainable. One such solution is to shift from classical catalysis to biocatalysis. Although the advantages of enzymes include their stereo-, regio-, and chemoselectivity, their selectivity often reduces versatility. Past efforts to tailor enzymatic function towards desired reactions have met with moderate effectiveness, such that fast and cost-effective methods are in demand to generate biocatalysts that will render the production of fine and bulk chemical production more benign. In the wake of bioinformatics and computational tools to support enzyme engineering, the fast development of new enzyme functions is becoming a reality. This thesis begins with a review of recent developments on computational tools for enzyme engineering. This is followed by an example of purely experimental enzyme engineering and protein evolution. We explored the mutational space of a primitive enzyme, the R67 dihydrofolate reductase (DHFR), using semi-rational protein engineering. ‘Smart library design’ involved fusing monomers of the homotetrameric R67 DHFR into dimers, to increase the diversity in the resulting mutated enzyme libraries. Activity-based screening revealed a strong bias for maintenance of the native sequence in one protomer with tolerance for high sequence variation in the second. It is plausible that the native protomers procure the observed activity, such that our efforts to modify the enzyme active site may have been only moderately fruitful. The limitations of experimental methods are then addressed by developing tools that facilitate computational mutational hotspot prediction. Developing these techniques is computationally intensive, as proteins are large molecular objects and work in aqueous media, one of the most complex solvents to model. We present the rapid, substrate-specific identification of mutational hotspots using the example of the industrially relevant P450 cytochrome CYP102A1. Applying the adaptive biasing force (ABF) molecular dynamics simulation technique, we confirm the known mutational hotspots for fatty acid hydroxylation and identify a new one. We also predict a catalytic binding pose for the natural substrate, palmitic acid, and apply that knowledge to perform virtual screening for further substrates for this enzyme. We then perform molecular dynamics simulations to address the potential impact of protein dynamics on enzyme catalysis, which is the topic of heated discussions among experts in the field. With the availability of more crystal structures in the Protein Data Bank, it is becoming clear that a single protein structure is not sufficient to elucidate enzyme function. We demonstrate this by analyzing four crystal structures we obtained of a β-lactamase enzyme, among which a striking rearrangement of key active site residues was observed. We performed long molecular dynamics simulations to generate a structural ensemble that suggests that crystal structures do not necessarily reflect the conformation of lowest energy. Finally, we address the need to computationally complement an area where experimentation is not currently possible, namely the prediction of gas migration into enzymes. As an example, the reactivity of P450 cytochrome enzymes depends on the availability of molecular oxygen at the active-site heme. Using the Implicit Ligand Sampling (ILS) molecular dynamics simulation technique, we derive the free energy landscape of small neutral gas molecules to map potential gas channels in cytochrome P450 CYP102A1 and CYP102A5. Comparison of CO, N2 and O2 suggests that those enzymes evolved towards exclusion of the inhibiting CO. In addition, we predict that gas channels are distinct from known substrate channels and therefore can be engineered independently from one another.

This thesis deals with several aspects of the structure and dynamics of water molecules confined in nanoscopic pores. Water molecules confined in hydrophobic nanocavities exhibit unusual structural and dynamic properties. Confining walls of single-wall carbon nanotubes (SWCNTs) promote strong inter-water hydrogen bonding which in turn leads to several novel structural, dynamic and thermodynamic features not found in bulk water. Confined water molecules form ordered hydrogen-bonded networks, exhibit exceptionally high flow rates as compared to conventional flow in pipes, allow fast proton conduction and exhibit various other anomalous properties. Proteins are known to exploit some of the properties of confined water to perform certain physiological functions. Various properties of confined water can also be exploited in the design of nanofludic devices such as those for desalination and flow sensors. In addition, water molecules confined in SWCNTs and near graphene sheets serve as model systems to study various effects of confinement on the properties of liquids. In this thesis, we present the results of detailed molecular dynamics simulation studies of confined water molecules. In chapter 1, we summarize the findings of existing simulations and experimental studies of bulk and confined water molecules. We also highlight the significance of studying the structure and dynamics of confined water molecules in biological and biotechnological applications. Chapter 2 provides a brief ac-count of the methods and techniques used to perform the simulations described in subsequent chapters of the thesis. We also present a brief overview of the methods used to extract physical properties of water molecules from simulation data, with emphasis on the Two Phase Thermodynamics (2PT) method which we have used to compute the entropy of confined and bulk water molecules. In chapter 3, we discuss the thermodynamics of water entry in SWCNTs of various diameters. Experiments and computer simulations demonstrate that water spontaneously fills the interior of a carbon nanotube. Given the hydrophobic nature of the interior of carbon nanotubes and the strong confinement produced by narrow nanotubes, the spontaneous entry of water molecules in the pores of such nanotubes is surprising. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of water molecules confined in SWCNTs and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with those of bulk water shows significant shifts in the positions of spectral peaks that are directly related to the tube radius. These peaks are experimentally accessible and can be used to characterize water dynamics from spectroscopy experiments. We have also computed the free-energy transfer when a bulk water molecule enters a SWCNT for various temperatures and carbon-water interactions. We show that for reduced carbon-oxygen interaction, the free energy transfer is unfavourable and the SWCNT remains unoccupied for significant periods of time. As the temperature is increased, the free energy of confined water becomes unfavourable and reduced occupancy of water is observed. Bulk water exhibits many anomalous properties. No single water model is able to reproduce all properties of bulk water. Different empirical water models have been developed to reproduce different properties of water. In chapter 4, a comparative study of the structure, dynamics and thermodynamic proper-ties of water molecules confined in narrow SWCNTs, obtained from simulations using several water models including polarizable ones, is presented. We show that the inclusion of polarizability quantitatively affects the nature of hydro-gen bonding which governs different properties of water molecules. The SPC/E water model is shown to reproduce results in close agreement with those from polarizable water models with much less computational cost. In chapter 5, we report results obtained from simulations of the properties of water confined in the space between two planar surfaces. We consider three cases: two graphene surfaces, two Boron Nitride (BN) surfaces and one graphene and one BN surface. This is the first detailed study of the behaviour of water near extended BN surfaces. We show that the hydrophilic nature of the BN surface leads to several interesting effects on the dynamics of water molecules near it. We have observed a change in the activation energy, extracted from the temperature dependence of the translational and rotational dynamics, near 280K. This change in activation energy coincides with a change in the structure of the confined sheet of water, indicated by a sudden change in energy. We have also found signatures of glassy dynamics at low temperatures for all three cases, the glassy effects being the strongest for water molecules confined between two BN sheets. These results are similar to those of earlier studies in which novel phases of water have been found for water molecules confined between other surfaces at high pressure. In chapter 6, we have described our observation of a novel phenomenon exhibited by water molecules flowing through a SWCNT under a pressure gradient. We have shown that the flow induces changes in the orientation of the water molecules flowing through the nanotube. In particular, the dipole moments of the water molecules inside the nanotube get aligned along the axis of the nanotube under the effect of the flow. With increasing flow velocities, the net dipole moment first increases and eventually saturates to a constant value. This behaviour is similar to the Langevin theory of paramagnetism with the flow velocity acting as an effective aligning field. Preferential entry of water molecules with dipole moments pointing inward is shown to be the main cause of this effect. This observation provides a way to control the dipolar alignment of water molecules inside nano-channels, with possible applications in nanofluidic devices. Chapter 7 contains a summary of our main results and a few concluding re-marks.

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.

<p>Thorium dioxide (ThO₂) and metallic uranium (alpha-U) represent important alternative nuclear fuels. Investigating the behavior of defects introduced into these materials in an irradiation environment is critical for understanding microstructure evolution and property changes. The objective of this dissertation is to investigate the clustering of point defects in ThO₂ and alpha-U under irradiation, into voids and prismatic dislocation loops as a function of irradiation dose rate and temperature. To achieve this, we have developed a mean-field cluster dynamics (CD) model based on reaction rate theory to predict the evolution of self-interstitial atom (SIA) and vacancy loops in neutron-irradiated alpha-U. Detailed atomistic simulations have been carried out using molecular dynamics (MD) to study the configuration of such loops and compute their energetics, which are essential parameters of the CD model. Bond-boost hyper-MD simulations have been performed to compute the diffusivity of uranium SIA and vacancies, which govern the kinetics of the clustering phenomenon. Another CD model has been demonstrated for proton-irradiated ThO₂, considering the clustering of Th and O SIA and vacancies into SIA loops and voids, respectively, with varying sizes and stoichiometry. The compositions of all SIA loops and voids dictated by crystallography of ThO₂ in its fluorite structure have been presented in their respective cluster composition space (CCS). The CD model solves the density evolution of off-stoichiometric loops and voids, with irradiation, in their respective CCS. MD simulations have been performed to compute the energetics of different clusters in their CCS, as parameters of the CD model. Temperature-accelerated MD simulations have been performed to compute the diffusivity of Th and O point defects, that dictates the kinetics of defect clustering on irradiation. In alpha-U, the CD predictions show an accumulation of small sized vacancy loops and the growth of SIA loops with irradiation dose, which closely fits the reported size distribution of loops in neutron-irradiated alpha-U by Hudson and coworkers. The CD predicted density of defect clusters in proton-irradiated ThO₂, shows the evolution of near-stoichiometric SIA loops in their CCS. The size distribution of SIA loops at high irradiation doses closely corresponds to the transmission electron microscopy (TEM) observations reported in the literature. Also, the CD model did not predict the growth of voids and vacancy clusters, which is consistent with findings in literature. The model was further used to predict the density of sub-nanometric defect clusters and point defects, on low-dose irradiation, that significantly impairs the thermal conductivity of ThO₂. An extensive TEM and CD investigation has also been carried out to study the growth and coarsening of SIA loop and voids during post-irradiation isochronal annealing of ThO₂ at high temperatures.</p>

Ligand-gated ion channels play an important role in electrochemical signal transduction across diverse organisms, yet their structural and functional intricacies are not fully understood. Particularly lacking is the knowledge of their response to variations in pH, an aspect necessary for understanding their physiological relevance and potential therapeutic targeting in neurological diseases. In this thesis project, I have investigated the mechanistic response of sTeLIC, a recently reported prokaryotic member of the pentameric ligand-gated ion channel family, to different environmental conditions. Using molecular dynamics simulations, a total of 16 different environmental conditions have been explored including variations in pH (neutral and alkaline), the presence and absence of calcium, and the inclusion of an electric field acting as an external driving force on charged atoms. The results reveal a comprehensive pH-sensing and gating mechanism involving key residues, notably E106 (on the β6 strand) and E160 (on loop F), and their local microenvironments. Additionally, an inhibitory mechanism for calcium is proposed, with E160 playing an important role. The simulations including an electric field has provided support for a non-conventional ion pathway through the pore. Collectively, these results offer insights into a mechanistic framework that may extend to other physiologically relevant systems, providing a foundation for further investigations and potential future therapeutic intervention. / pLGICs har en viktig roll i det elektrokemiska signalsystemet i många organismer, men detaljerna i deras struktur och framför allt funktion är fortfarande inte helt klargjorda. Särskilt är detaljerna kring deras reaktion på ändringar i pH-värde relativt okända, vilket är en viktig del i att förstå kanalernas fysiologiska roll och för att potentiellt hitta läkemedel mot neurologiska sjukdomar där dessa är inblandade. I det här arbetet har jag undersökt hur sTeLIC, som är ett nyligen publicerat bakteriellt protein i familjen pLGICs, reagerar på olika ändringar i miljön. Jag har använt molekyldynamiksimuleringar för att unders öka 16 olika miljöer med två olika pH-värden (neutralt och alkaliskt), med eller utan kalcium samt med eller utan en extern drivkraft över membranet i form av ett elektrisk fält. Arbetet har resulterat i en föreslagen mekanism förhur sTeLIC känner av pH och hur öppningen av kanalen går till. Denna mekanism involverar aminosyrorna E106, som finns på β6-strängen, och E160, som finns på F-loopen, samt deras omgivning. Dessutom har en modulatorisk mekanism föreslagits för en kalciuminhiberande effekt på sTeLIC som också involverar E160. Simuleringarna med en drivkraft över membranet har gett stöd för en ny väg för joner genom kanalen. Tillsammans ger dessa resultat insikt i en mekanism som eventuellt kan appliceras p ̊a andra system. Detta har lagt grunden för fortsatt undersökning som potentiellt kan leda till framtida läkemedelsutveckling inom området.