No description available.

In this work the structure of the electrochemical metal-liquid interface is determined through use of quantum mechanics, molecular simulation, and experiment. Herein are profiled the molecular dynamics details and results of solid-liquid interfaces at flat non-specific solid surfaces and copper metal electrodes. Ab initio quantum-mechanical calculations are reported and define the interatomic potentials in the simulations. Some of the quantum-mechanical calculations involve small copper clusters interacting with 3-mercaptopropanesulfonic acid (MPSA), sodium, chloride, bisulfate and cuprous ions. In connection with these I develop the electrode charge dynamics (ECD) routine to treat the charge mobility in a metal. ECD bridges the gap between small-scale metal-cluster ab initio calculations and large-scale simulations of metal surfaces of arbitrary geometry. As water is the most abundant surface species in aqueous systems, water determines much of the interfacial dynamics. In contrast to prior simulation work, simulations in this work show the presence of a dense 2D ice-like rhombus structure of water on the surface that is relatively impervious to perturbation by typical electrode charges. I also find that chloride ions are adsorbed at both positive and negative electrode potentials, in agreement with experimental findings. Including internal modes of vibration in the water model enhances the ion contact adsorption at the solid surface. In superconformal filling of copper chip interconnects, organic additives are used to bottom-up fill high-aspect ratio trenches or vias. I use molecular dynamics and rotating-disk-electrode experiments to provide insight into the function of MPSA, one such additive. It is concluded that the thiol head group of MPSA inhibits copper deposition by preferentially occupying the active surface sites. The sulfonate head group participates in binding the copper ions and facilitating their transfer to the surface. Chloride ions reduce the work function of the copper electrode, reduce the binding energy of MPSA to the copper surface, and attenuate the binding of copper ions to the sulfonate head group of MPSA.

The following project presents in silico investigation of axonal damage in Diffuse Axonal Injury (DAI). When axons face a shear force, orientation of the lipids in the axonal membrane gets disrupted. Depending on the value of the force, a tensile strain causes the axons to get partially or fully deformed and in some cases a pore forms in the membrane. Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single bilayer, parallel bilayer and cylindrical bilayer) and similar composition to biological axonal membrane were simulated. This was initially done to investigate the strain rate dependency of the bilayers, and their viscoelastic ability on returning to their original shape from their deformed forms. To achieve this, various deformation velocities were applied to the bilayers reaching 20% strain and relaxing the bilayer after. Additionally, the bilayers were deformed further until they reached a pore. It was found that the bilayers can almost recover from their deformed forms to their original length when they were deformed at 20% strain level. In conjunction, no correlation between the deformation velocity and lipid deformation was observed. Further, it was found that bilayers with different lipid percentage to axonal bilayer has different strain values for water penetration and for pore formation. The strain value for cylindrical bilayer was found very high compared to the strain values found in vitro. The strain for pore formation of parallel and single bilayer was found to be around 80% to 90% and for water penetration was found to be 70% for single bilayer and 50% for parallel bilayer. A slight difference in strain for pore formation between single and parallel bilayer was found which showed the bilayer structure can play a role in simulation results. The effect of the length in the simulations results was also observed where shorter bilayers showed lower strain for pore formation compared to longer bilayers.

No description available.

No description available.

La perméabilité aux gaz et aux liquides des matériaux polymères est une propriété qui est mise à profit dans de nombreux domaines industriels. Cette thèse est effectuée dans l'optique de mieux appréhender la problématique de l'étanchéité des conduites flexibles par les polymères. Ainsi, les perméabilités de H2S, CO2 et CH4 dans le polyéthylène (PE) ont fait l'objet d'une étude effectuée dans le contexte de cette thèse. La perméabilité est une propriété qui résulte de la solubilisation des gaz dans le polymère puis de la diffusion de ces produits à travers la matière. La solubilité, qui caractérise l’aptitude d’un gaz à pouvoir s’absorber dans le polymère, est une propriété d’équilibre, qui pourra être étudiée par les techniques de Monte Carlo. La diffusion, qui caractérise l’aptitude d’un gaz à se mouvoir plus ou moins rapidement dans le réseau polymère, sera quant à elle, étudiée par dynamique moléculaire. Au dessous de la température de fusion, le polyéthylène est à l'état semi-cristallin. Cet état est composé de régions contenant des chaînes orientées aléatoirement (régions amorphes) et des régions contenant des chaînes orientées sur un réseau (régions cristallines). La morphologie complexe des polymères semi-cristallins présente des hétérogénéités de dimensions nanométriques, ce qui est difficilement accessible par la simulation moléculaire. A fin d'étudier la solubilité et la diffusion de gaz dans le polyéthylène semi-cristallin, nous modéliserons uniquement la phase amorphe au cours de ce travail. Par contre, l’effet des régions cristallines sur la phase amorphe sera pris en compte dans la simulation par une contrainte ad-hoc. / The gas permeability through the polymers is a property that is exploited in many industrial fields. The objective of this thesis is to better understand the problem of sealing of flexible pipes with polymers. Thus, the permeability of H2S, CO2 and CH4 in polyethylene (PE) was studied during this work. Permeability is a property resulting from the dissolution of gases in the polymer and then diffusion of these products through the material. Solubility, which characterizes the ability of a gas to be absorbed in the polymer, is a property of equilibrium, which can be studied by Monte Carlo techniques. Diffusion coefficient, which characterizes the ability of a gas to move more or less rapidly into the polymer network, will in turn studied by molecular dynamics.Below the melting temperature, polyethylene is in semi-crystalline state. This state is composed of regions containing randomly oriented chains (amorphous regions) and regions containing chains oriented regularly on a network (crystalline regions). The complex morphology of semi-crystalline polymers has nanometric heterogeneities, which is not easily accessible by molecular simulation. In order to study the solubility and diffusion coefficient of gases in semi-crystalline polyethylene, we model only the amorphous phase in this work. However, the effect of crystalline regions on the amorphous phase will be taken into account in the simulation by an ad-hoc constraint.

Les matériaux hybrides de type MOFs sont des solides poreux dans lesquels des centres métalliques sont reliés entre eux par des ligands organiques. Il est possible, non seulement de faire varier la taille et la géométrie de leurs porosités, mais aussi de moduler leurs compositions chimiques en modifiant à la fois la nature de la brique inorganique et des groupements sur le ligand organique. Cette nouvelle famille de matériaux a fait l'objet d'une attention particulière ces dernières années pour des applications potentielles dans différents domaines à fort intérêt socio-économique comme le captage ou la séparation de gaz ou bien encore la catalyse. Au-delà d'une stabilité chimique et thermique, ces matériaux doivent être aussi suffisamment résistants mécaniquement pour s'adapter au mieux aux contraintes de l'application visée (mise en forme de l'échantillon, conditions opératoires….). Il est donc impératif de connaître les propriétés mécaniques de ces nouveaux matériaux, sujet qui n'a fait l'objet à ce jour que de très peu d'études. L'objectif de ce travail est donc de mettre en œuvre des mesures de diffraction des rayons X et neutrons sur grands instruments afin de caractériser dans un premier temps le comportement structural du matériau flexible MIL-53 (MIL pour Matériaux de l'Institut Lavoisier) sous l'application d'une pression mécanique modérée (P~1 GPa) en fonction de la nature du métal (Al,Cr) et de la fonction greffée sur le ligand organique (-H, -Cl, -CH3). Ces données expérimentales sont ensuite discutées à partir de résultats issus de la simulation moléculaire. L'étape suivante consiste à étudier l'effet du confinement de molécules de solvants dans les pores de ce solide sur la transition structurale du réseau hôte. Enfin, deux familles de MOFs rigides, la MIL-125(Ti) et l'UiO-66(Zr) (UiO pour Unversité d'Oslo) sont considérées afin de caractériser non seulement leur domaine de stabilité mécanique en pression (Pmax~ 5 GPa) mais aussi leur compressibilité. Les résultats ainsi obtenus sont comparés aux performances mécaniques des meilleurs MOFs. / Metal Organic Framework (MOF) materials have been the focus of intense research activities over the past 10 years, with the emergence of a wide range of novel architectures, constructed from inorganic clusters linked by organic moieties. In order to maintain their useful functionalities and high performances in the different fields explored so far (gas storage/separation, catalysis, sensors and many others), besides high chemical and thermal stabilities, MOFs must be also stable enough to resist to different mechanical constraints in both processing and applications. Indeed, there is nowadays a growing interest to characterize the mechanical behaviours of this class of materials under moderate and high applied pressure. This work first aimed to probe the pressure dependence of the structural behaviour of the highly flexible MIL-53 system [MIL stands for Materials of Institut Lavoisier] as a function of the nature of (i) the metal center (Al,Cr) and (ii) the functional group grafted on the organic linker (-H,-Cl,-CH3) using a combination of high-pressure x-ray/neutron diffraction and molecular simulations. The same methodology was further applied to probe how the presence of guest molecules affects the structural transition of this class of hybrid porous solids. Finally, the mechanical stability and the compressibility of two families of rigid MOFs, the MIL-125(Ti) and the UiO-66(Zr) [UiO stands for University of Oslo] up to high pressure (P~5 GPa) have been investigated and their properties in terms of bulk modulus were compared with the most resilient MOFs reported so far.

La simulación molecular presenta la ventaja de ofrecer un marco teórico importante para predecir propiedades termodinámicas y de transporte de fluidos con aplicaciones industriales. En este trabajo, se explotó está ventaja para predecir el equilibrio líquido vapor de agua, compuestos aromáticos y sus mezclas a condiciones tanto sub- como supercríticas. Se realizó una comparación de diferentes potenciales intermoleculares conocidos mediante el cálculo de propiedades termodinámicas de sistemas puros que sirvió de punto de partida para llevar a cabo una optimización de parámetros transferibles para un potencial intermolecular de agua y compuestos aromáticos. En el caso de agua, se llevo a cabo el análisis y evaluación de propiedades termodinámicas de un modelo simple de agua. En este modelo, las contribuciones electrostáticas se aproximan mediante interacciones de corto alcance en vez de las típicas fuerzas de Coulomb de largo alcance. En general, se han encontrado grandes desviaciones con respecto a los datos experimentales, tal como un valor de temperatura crítica de 360K, valor 50% alejado del valor experimental. Debido a que estos resultados nos indican la importancia de incluir las fuerzas de Coulomb en el modelo molecular empleado para reproducir correctamente las propiedades de agua, el trabajo de investigación se ha enfocado en la optimización de los parámetros de los potenciales TIP4P y SPC/E. Los resultados obtenidos muestran que es posible encontrar una mejor aproximación al punto crítico experimental a partir de la optimización del modelo SPC/E. Sin embargo, el buen acuerdo con los experimentos del modelo original a condiciones ambiente se pierde usando los parámetros del modelo optimizado. Por otro lado, la estimación de propiedades de compuestos aromáticos esta de acuerdo con los datos experimentales permitiendo la reproducción de la densidad de líquido saturado, presión de saturación y entalpía de vaporización para compuestos puros. Finalmente, en el caso de mezclas se ha aplicado el conjunto de parámetros obtenidos para aromáticos. Las propiedades termodinámicas de la mezcla binaria aromático-aromático y aromático agua son analizadas en un amplio rango de temperaturas y presiones. Las desviaciones encontradas entre los valores calculados y los experimentales sugieren aplicar un mejor método de optimización para sistemas puros o por otro lado, promover un potencial de interacción intermolecular más sofisticado. Las estimaciones a condiciones cercanas al punto crítico están en buen acuerdo con los datos experimentales. / La simulació molecular presenta l'avantatge d'oferir un marc teòric important per a cercar propietats termodinàmiques i de transport de fluids amb aplicacions industrials. En aquest treball es va explotar aquesta avantatge per predir l'equilibri líquid vapor d'aigua, components aromàtics i les seves mescles, tant a condicions sub com supercrítiques. Es va realitzar una comparació de diferents potencials intermoleculars, coneguts mitjançant el càlcul de propietats termodinàmiques de sistemes purs, que ha servit de punt de sortida per portar a terme una optimització de paràmetres transferibles per a un potencial intermolecular de propietats termodinàmiques d'un model simple d'aigua. En aquest model, les contribucions electrostàtiques s'aproximen mitjançant interaccions de curt abast en lloc de les típiques forces de Coulomb de llarg abast. En general, s'ha trobat grans desviacions respecte a les dades experimentals, tal com un valor de temperatura crítica de 360K, valor 50% allunyat del valor experimental. Degut a que aquests resultats ens indiquen la importància d'incloure les forces de Coulomb en el model molecular emprat per reproduir correctament les propietats d'aigua, el treball d'investigació s'ha enfocat en l'optimització dels paràmetres dels potencials TIP4P i SPC/E. Els resultats obtinguts mostren que és possible trobar una millor aproximació al punt crític experimental a partir de l'optimització del model SPC/E. No obstant, el bon acord amb els experiments del model original a condicions ambientals es perden usant els paràmetres del model optimitzat. Per altre banda, l'estimació de propietats de compostos aromàtics esta d'acord amb les dades experimentals permetent la reproducció de la densitat de líquid saturat, pressió de saturació i entalpia de vaporització per a compostos purs mitjançant el potencial AUA-Aromátics proposat. Finalment, en el cas de mescles s'ha aplicat el conjunt de paràmetres obtinguts per aromàtics. Les propietats termodinàmiques de la mescla binària aromàtic-aromàtic i aromàtic-aigua són analitzades en un ample rang de temperatures i pressions. Les desviacions trobades entre els valors calculats i els experimentals suggereixen aplicar un millor mètode d'optimització per a sistemes purs o, per altre banda, promoure un potencial d'interacció intermolecular més sofisticat. Les estimacions en condicions properes al punt crític tenen un bon acord amb les dades experimentals. / Molecular simulation presents the advantage of providing a unified theoretical framework to model fluid properties for industrial applications. In this work we exploit this advantage to predict thermodynamic properties of pure water and aromatics and their mixtures at sub- and supercritical conditions. A comprehensive comparison of different intermolecular potentials has been carried out in order to analyze model predictions for pure component properties. In addition, an optimization of transferable parameters has been performed for an intermolecular potential for aromatics and water. In the case of water, an analysis and evaluation of the thermodynamic properties of a simple model has been performed. In this model, the electrostatic contributions are approximated by short-range interactions instead of the typical long-range Coulombic forces. On the whole, we found huge deviations with experimental data, such as a critical temperature value of 360K, 50% far away from the experimental value. Since, these calculations indicate the importance of including the electrostatic contribution in order to correctly model water, we also focus on reproducing critical properties from an optimization of the well known TIP4P and SPC/E water model parameters. Results obtained show that a better approximation to the critical point prediction is possible from the optimization of the SPC/E parameters, however, the good agreement with experiments for the original model at room conditions vanishes using the optimized parameters. On the other hand, thermodynamic property estimations of aromatic molecules are in good agreement with experimental data and we are able to reproduce saturation liquid densities, saturation pressures, vaporization enthalpies and liquid structure for pure compounds. Finally, in the case of mixtures, we applied the optimized set of parameters obtained for aromatics. The thermodynamic properties of binary aromatic-aromatic and aromatic water mixtures are analyzed over a wide range of temperatures and pressures. Deviations between the predicted and experimental values are found at low temperatures and high densities suggesting that a better optimization process needs to be performed for the pure systems or a more sophisticated intermolecular interaction potential is needed. Nevertheless, the estimations close to critical conditions are in good agreement with experimental data.

Crystallographically solids with well defined crystal structures are normally assumed to be highly ordered. However, it is not uncommon to find considerable degree of disorder amongst many of these crystalline substances. Disorder among crystalline substances often arise from the rotational motion which leads to the well known class of plastic crystalline substances. Typically, globular molecules such as methane, carbon tetrachloride or adamantane exhibit plastic crystalline phase with significant amount of orientational disorder. In many other substances, disorder arises from torsional motion as in the case of biphenyl, p- or o-terphenyls, stilbene or azobenzenes. In case of molecules with flexible segment, such as alkanes or surfactants, motion of the terminal methyl group or terminal ethyl group is responsible for the observed disorder. Chapter 1 discusses various aspects of disorder in crystals. A new pressure induced solid phase of biphenyl is reported at room temperature. Isothermal-isobaric ensemble variable shape simulation cell Monte Carlo calculations are reported on biphenyl at 300K as a function of pressure between 0-4 GPa. The potential proposed by Williams for inter-molecular and Benkert-Heine-Simmons(BHS) for intramolecular interactions have been employed. Different properties indicating changes in the crystal structure, molecular structure, distributions of inter- and intra-molecular energy are reported as a function of pressure. With increase in pressure beyond 0.8 GPa, the dihedral angle distribution undergoes a change from a bimodal to an unimodal distribution. The changes in IR and Raman spectra across the transition computed from ab initio calculations are in agreement with the experimental measurements. It is shown that at pressures larger than 0.8 GPa, competition between inter-molecular interactions with intra-molecular terms v/z., conjugation energy and the ortho-ortho repulsion favors a planar biphenyl due to better packing and consequently a predominant inter-molecular term. The exact value of the transition pressure will depend on the accuracy of the inter- and intra-molecular potentials employed here. p-terphenyl has been modeled at 300K and atmospheric pressure with different potential models. Modified Fihppini parameters for mtermolecular interactions and BHS potential for inter-ring torsion predict the structure of p-terphenyl reasonably well. Pressure variation calculations are carried out with this combination of inter- and intra-molecular potential. The structure as a function of pressure upto 5 GPa has been compared with experimental structure provided by Puschnig et al. The transformation of functional form of the potential energy curve (associated with the inter-ring flipping) from W-shaped to [/-shaped form as a function of pressure has been observed. This is in excellent agreement with previous studies of polyphenyls including biphenyl and p-hexaphenyl. The complete planarization of molecules occurs when the pressure range is 1.0 GPa-1.5 GPa. Molecular simulation of solid stilbene in the isothermal-isobaric ensemble with variable shape simulation are reported. Structure has been characterized by means of lattice parameters and radial distribution functions. Simulations show existence of pedal-like motion at higher temperatures in agreement with the recent X-ray diffraction measurements by Ogawa and co-workers and several others previously. Difference in energy between the major and minor conformers, barrier to conformational change at both the crystallographic sites have been calculated. Temperature dependence of the equilibrium constant between the two conformers as well as the rate of conversion between the con-formers at the two sites have been calculated. These are in agreement with the recent analysis by Harada and Ogawa of non-equilibrium states obtained by rapid cooling of stilbene. Volume and total intermolecular energy suggest existence of two transitions in agreement with previous Raman phonon spectroscopic and calorimetric studies. They seem to be associated with change from order to disorder at the two sites. Ab initio calculations coupled with simulations suggest that the disorder accounts for only a small part of the observed shortening in ethylene bond ength. A Monte Carlo simulation with variable shape simulation cell has been carried out on stilbene. The study attempts to investigate the disorder at various pressures upto 4 GPa. It is seen that the population of minor conformers at sites 1 and 2 decrease with increase in pressure. Population of minor conformers at site 2 decreases to zero by 1.5 GPa. In contrast, the population of minor conformers at site 1 remains finite for the runs reported here. It is seen that the population of minor conformers at site 1 is higher than at site 2 at room temperature which is to be expected on the basis of the activation energies. Associated changes in the unit cell as well as molecular conformation are discussed. Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been earned out with variable shape simulation cell. Low temperature crystalline phase and the room temperature plastic crystalline phases have been studied employing the Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low temperature ordered tetragonal phase of adamantane. The high pressure ordered phase appears to be characterized by a slightly larger shift of the first peak towards lower value of r in C-C, C-H and H-H rdfs as compared to the low temperature tetragonal phase. Co-existence curve between the crystalline and plastic crystalline phase has been obtained approximately upto a pressure of 4 GPa. We investigate the equation of state, variation of lattice parameters and the distortion of molecular geometry of low temperature phase of adamantane upto 26 GPa pressure. A rigid and a flexible model of adamantane have been studied using variable shape simulation within the isothermal-isobaric ensemble. Including six low frequency modes obtained from density functional theory carried out on a single-molecule has incorporated the flexibility. These calculations used Becke 3-parameter method and Lee-Yang-Parr electron correlation functional with 6-31G(d) basis set. The simulated equation of state and variation of c/a ratio as a function of pressure are compared with the experimental results. The results are in good agreement with high pressure experiments. Nature of distortion in molecular geometry obtained from the calculation are also in good agreement with the experiment.

La perméabilité aux gaz et aux liquides des matériaux polymères est une propriété qui est mise à profit dans de nombreux domaines industriels. Cette thèse est effectuée dans l'optique de mieux appréhender la problématique de l'étanchéité des conduites flexibles par les polymères. Ainsi, les perméabilités de H2S, CO2 et CH4 dans le polyéthylène (PE) ont fait l'objet d'une étude effectuée dans le contexte de cette thèse. La perméabilité est une propriété qui résulte de la solubilisation des gaz dans le polymère puis de la diffusion de ces produits à travers la matière. La solubilité, qui caractérise l’aptitude d’un gaz à pouvoir s’absorber dans le polymère, est une propriété d’équilibre, qui pourra être étudiée par les techniques de Monte Carlo. La diffusion, qui caractérise l’aptitude d’un gaz à se mouvoir plus ou moins rapidement dans le réseau polymère, sera quant à elle, étudiée par dynamique moléculaire. Au dessous de la température de fusion, le polyéthylène est à l'état semi-cristallin. Cet état est composé de régions contenant des chaînes orientées aléatoirement (régions amorphes) et des régions contenant des chaînes orientées sur un réseau (régions cristallines). La morphologie complexe des polymères semi-cristallins présente des hétérogénéités de dimensions nanométriques, ce qui est difficilement accessible par la simulation moléculaire. A fin d'étudier la solubilité et la diffusion de gaz dans le polyéthylène semi-cristallin, nous modéliserons uniquement la phase amorphe au cours de ce travail. Par contre, l’effet des régions cristallines sur la phase amorphe sera pris en compte dans la simulation par une contrainte ad-hoc. / The gas permeability through the polymers is a property that is exploited in many industrial fields. The objective of this thesis is to better understand the problem of sealing of flexible pipes with polymers. Thus, the permeability of H2S, CO2 and CH4 in polyethylene (PE) was studied during this work. Permeability is a property resulting from the dissolution of gases in the polymer and then diffusion of these products through the material. Solubility, which characterizes the ability of a gas to be absorbed in the polymer, is a property of equilibrium, which can be studied by Monte Carlo techniques. Diffusion coefficient, which characterizes the ability of a gas to move more or less rapidly into the polymer network, will in turn studied by molecular dynamics.Below the melting temperature, polyethylene is in semi-crystalline state. This state is composed of regions containing randomly oriented chains (amorphous regions) and regions containing chains oriented regularly on a network (crystalline regions). The complex morphology of semi-crystalline polymers has nanometric heterogeneities, which is not easily accessible by molecular simulation. In order to study the solubility and diffusion coefficient of gases in semi-crystalline polyethylene, we model only the amorphous phase in this work. However, the effect of crystalline regions on the amorphous phase will be taken into account in the simulation by an ad-hoc constraint.