Interaction potentials for the double-perovskite cryolite, Na3AlF6, have been developed for use in classical Molecular Dynamics (MD) simulations using a method whereby ionic configurations are generated with empirical pair potentials, the multipoles and forces on the ions and the stress tensor of the cell are extracted from ab initio single-point DFT calculations, and then the multipoles, forces and stresses from the MD simulations are ‘fit’ to the ab initio quantities in a series of steps in which the potential parameters are optimized, for models of varying complexity. Previously, interaction potentials have been developed empirically by tuning the parameters to reproduce experimentally-derived properties such as structure factors and densities, and so the testing and development of the newer method is necessary in order to standardize a way of obtaining potentials from first principle considerations. A fitted potential was then used to characterize the ion dynamics in crystalline cryolite: a monoclinic to orthorhombic phase transition and the low-temperature-phase tilt-domain structure of the AlF3− 6 , the dominant structural features, are reproduced. The motional processes, which have been studied indirectly in NMR, conductivity and diffraction experiments, include oscillation of the AlF3− 6 and sodium ion diffusion - it has been suggested that these occur at a remarkably fast rate. The nature of the AlF3− 6 oscillatory motion is studied in more depth than accessible to experiment, and its connection with diffusion is investigated. Given the intrinsically defective nature of cryolite and the absence of diffusion in the initial simulations, defects are introduced to observe their effect on the dynamics: they are shown to be necessary for diffusion. This work has been written up in an article accepted for publication in the Journal of Physical Chemistry. The ab initio potentials developed as above involve representing a system with formally charged monatomic ions. We extended the scope of the method significantly with technical developments to allow for the inclusion of molecular ions, such as the hydroxide ion, the sulphate ion or the uranyl ion, where the intraionic bonding has significant covalent character. The appropriate modifications of the MD code were made and a modified force-fitting procedure was developed. The new method was applied to Mg(OH)2 which is an important mineral (brucite) and to the melts of uranyl chloride which are of interest in nuclear waste reprocessing. Although we found good potentials were harder to obtain for these compounds, we found this arose from their layered structure rather than the molecular nature of the ions, and that our method could achieve a level of success approaching that used in the cryolite work on further iterations of the fitting process.

Una de les àrees més prometedores en recerca biomèdica i farmacèutica és el disseny molecular computacional, que intenta establir relacions entre propietats físico-químiques i activitat biològica. L'èxit d'aquestes tècniques depen críticament de la qualitat de la descripció molecular. En aquest sentit, metodologies basades en potencials d'interacció molecular (MIP) són eines útils per la comparació de compostos que presenten comportaments biològics semblants. Aquest projecte desenvolupa eines per comparar molècules basades en la caracterització de llurs MIPs. El programa de similaritat molecular MIPsim ha estat desenvolupat i aplicat a diferents problemes biològics. Aquesta tesi consisteix en quatre estudis científics que mostren l'ús del MIPSim en aliniament molecular, catalisi enzimàtica, en acoratge de molècules dins el lligand i en estudis 3D-QSAR. / One of the most promising areas in biomedical and pharmaceutical research is computer assisted molecular design, which tries to stablish relationships between physicochemical properties and biological activity. The success of these techniques depends critically on the quality of the molecular description. In this sense, methodologies based on molecular interaction potentials (MIP) are useful tools for the comparison of compounds displaying related biological behaviours. This project aims to develop tools to compare 'molecules based on the characterization 'of their MIPs. To this end, the molecular similarity program MIPSim has been further developed and applied to different biological problems. This thesis consists on four scientific studies showing the use of MIPSim for molecular alignment, enzymatic catalysis, ligand-protein docking and 3D-QSAR analyses.

Les propriétés de transport à haute température dans les gaz et/ou dans les plasmas ont une importance capitale dans différents domaines, à savoir dans le domaine de technologie de coupure à arc, plasmas de coupure, de soudure ou de gravure. La connaissance des coefficients de transport est nécessaire pour toute modélisation faisant intervenir les équations hydrodynamiques. Dans le cadre de la théorie cinétique des gaz dilués, une solution approchée de l’équation intégro-différentielle de Boltzmann régissant les fonctions de distribution a été proposée par Chapman-Enskog. Les coefficients de transport sont calculés classiquement par la méthode de Chapman-Enskog via les intégrales de collision. Dans le cadre de notre étude nous avons développé, dans un premier temps, un code numérique permettant l’obtention de ces intégrales de collision en tenant compte des singularités qui peuvent apparaître dans le calcul des sections efficaces relatives aux interactions entre les particules constituant les gaz et/ou les plasmas. Dans un second temps nous avons étudié l’influence du choix des paramètres des potentiels d’interaction sur les coefficients de transport. Par la suite, nous avons utilisé le code numérique ainsi développé pour évaluer les coefficients de transport du plasma d’hélium en étudiant l’influence du choix de la méthode de calcul de composition chimique sur ces coefficients. Enfin, un modèle simplifié d’une interaction entre une onde électromagnétique et un plasma d’hélium a été proposé comme une application directe des coefficients de transport. / Transport properties at high temperature in gases and/or in plasmas are of very importance in various fields, namely in the field of breaking technology in arc, cutting plasma, welding or burning. Knowledge of transport coefficients is necessary for any modeling involving hydrodynamic equations. As part of the kinetic theory of diluted gas, an approximate solution of the integro-differential Boltzmann equation governing distribution functions was proposed by Chapman-Enskog. Transport coefficients are classically computed using the method of Chapman-Enskog through the collision integrals. In our study we have developed, initially, a numerical code to obtain these collision integral taking into account the singularities that may occur in the calculation of the cross sections relating to interactions between particles forming the gas and/or plasmas. Secondly, we have studied the influence of the choice of parameters of interaction potentials on transport coefficients. Subsequently, we have used the numerical code developed for evaluating and helium plasma transport coefficients by studying the influence of the choice of method for calculating chemical composition on these coefficients. Finally, a simplified model of an interaction between an electromagnetic wave and a helium plasma has been proposed as a direct application of the transport coefficients.