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À l'approche d'un point critique, la divergence de la longueur de corrélation des fluctuations peut être tronquée par le confinement du système. Cette troncature engendre des effets de taille finie présentant des caractères universels au sein d'un classe de transitions de phases.Nous nous sommes intéressés particulièrement à la classe d'universalité du modèle d'Ising, regroupant notamment les transitions de phase ferro/paramagnétique pour les systèmes magnétiques uniaxiaux, la transition liquide/gaz et encore la démixtion de mélanges binaires. Nous présentons tout d'abord une introduction aux phénomènes critiques, à l'universalité, au « finite-size scaling » et aux simulations Monte Carlo du modèle d'Ising, sur lesquelles se fondent la majeur partie de ce travail.Un effet de taille finie ayant attiré une grande attention durant les dernières dizaines d'années est la force de Casimir critique. Les travaux théoriques et numériques concernant cette force ont, dans leur quasi totalité, été menés dans des systèmes magnétiques modèles, tel que les modèles d'Ising ou XY. Par contre, les approches expérimentales ont toutes été réalisées dans des systèmes fluides, tels que des mélanges binaires ou de l'hélium IV proche de la transition superfluide.Une motivation de ce travail a été de chercher a résoudre cette situation paradoxale en proposant, d'une part, un protocole expérimental pour la mesure de la force de Casimir dans une couche mince magnétique et, d'autre part, une approche numérique dans un mélange binaire de type Lennard-Jones. Cette dernière approche présente l'avantage d'ouvrir la porte à des études des fluctuations de la force de Casimir ou encore hors-équilibre. / Approaching a critical point, the divergence of the correlation length of fluctuations can be cut-off by a confinement of the system. This truncation fosters finite size effects with universal features in a class of continuous phase transitions. We are particularly interested in the Ising universality class, regrouping transitions such as the ferromagnetic/paramagnetic transition for uniaxial magnetic systems, the liquid/gas tran- sition and the demixing of binary mixtures. We will first present an introduction to critical phenomena, universality, finite-size scaling and Monte Carlo simulations of the Ising model, on which a major part of this work relies.A finite size effect that has particularly drawn attention in the past decades is the critical Casimir force. On the one hand, theoretical and numerical works on the subject have almost systematically been performed in magnetic model systems, such as the Ising or XY models. On the other hand, experimental approaches were all realized in fluid systems, such as binary mixtures or helium IV close to the superfluid transition.A motivation of this work was to bridge this gap by proposing, firstly, an experimental protocol for measuring the critical Casimir force in a magnetic layer and, secondly, a numerical approach in a Lennard-Jones binary mixture. The latter is of particular interest as it could lead the way to studying fluctuations of the Casimir force or out-of-equilibrium phenomena.

The thesis involves computer simulation and theoretical studies of phase transition in soft-condensed matter systems and theoretical understanding of enzyme kinetics along with kinetic proofreading of tRNA-aminoacylation in biological systems. Based on the system and phenomena of interest, the work has be classified into the following four major parts: I. Surface phenomena and surface energy of vapor-liquid interface. II. Condensation of vapor in two and three dimensions. III. Liquid-solid phase transition in polydisperse systems. IV. Enzyme catalysis and kinetic proofreading in biosynthesis. Above mentioned four parts have further been divided into thirteen chapters. In the following we provide a brief chapter-wise outline of the thesis. Part I deals with surface tension and interfacial properties of vapor-liquid interface for Lennard-Jones (LJ) fluid in both two and three dimensions. In Chapter 1, we provide a brief overview of vapor-liquid interface and existing theoretical and computer simulation studies of surface/line tension. In this chapter we also discuss about the existing experimental studies. In Chapter 2, we present computer simulation studies of surface tension in two dimensional Lennard-Jones system. The sensitivity of line tension on range (potential cut-off) of interparticle interaction is discussed in this chapter. We present Density Functional Theory (DFT) of line tension of vapor-liquid interface based on Weeks-Chandler-Anderson (WCA) and Barker-Hendersen (BH) perturbation techniques. We compare the DFT prediction with the computer simulation results. In general, WCA approach has been found to be successful for 3D system in predicting the surface tension. In 2D, however, it does not give good agreement either for phase diagram or for the line tension. In fact, BH also does not give accurate values of the coexistence parameters, however, it predicts better line tension compared to WCA. In Chapter 3 we present both theoretical and computer simulation studies of gas-liquid surface tension for three dimensional Lennard-Jones fluid. We perform non-equilibrium computer simulation study following Transition Matrix Monte Carlo (TMMC) method to obtain surface tension for various ranges of potential and introduce a new scaling relation of surface tension in order to capture both the temperature and interparticle interaction range dependence. The scaling shows excellent agreement with the simulation result and it can also predict the critical temperature with sufficient accuracy. The width of the gas-liquid interface is found to be insensitive to the range of the potential, whereas the density separation of the bulk vapor and liquid phases increases with increasing range of potential. Thus, the major contribution comes from the increasing density separation of the bulk vapor and liquid phases. Part II consists of four chapters, where we focus on the age old problem of nucleation, from the perspective of thermodynamics and kinetics. We account for the rich history of the problem in the introductory Chapter 4. In this chapter we describe various types and examples of the nucleation phenomena, and a brief account of the major theoretical approaches used so far. We begin with the most successful Classical Nucleation Theory (CNT), and then move on to more recent applications of Density Functional Theory (DFT) and other mean-field types of models. We present various experimental techniques used in the literature to obtain rate of nucleation. We conclude with a comparison between the experiments, theories and computational studies. In the next chapter (Chapter 5) we attempt to understand the mechanism of the gas-liquid nucleation in three dimension at large metastability from microscopic point of view. Here we study the nature of sequential growth of all liquid-like clusters (not just the largest cluster) at different degrees of metastability. Therefore, we have ordered the clusters according to their decreasing sizes and identified them in terms of kth largest cluster where, k = 1 denotes the largest cluster in the system, k = 2 represents the second largest and k = 3 is the third largest and so on. We have studied both the free energies and the trajectories of the liquid-like clusters in this extended set of order parameters. We further define Fkl(n) as the free energy of the kth largest cluster with size n. Classical nucleation theory provides an expression of unconditional free energy of a single cluster, F (n) (the free energy of formation of a cluster of size n), which is an intensive property of the system. The study of our conditional free energy surfaces, Fkl(n), reveals a more detailed, microscopic picture of the system’s cluster size distribution that is necessary to understand the kinetics of nucleation and growth at large metastability. The rate of nucleation shows a cross over at kinetic spinodal (the limit of metastability, ∆F1 l = 0). Below kinetic spinodal only one (largest) cluster crosses the critical size through activation whereas above this point more than one cluster grow simultaneously through barrierless diffusion. We present a theoretical analysis of the free energy of kth largest cluster based on order statistics. The theoretical predictions are in excellent agreement with computer simulation results for the range of supersaturation we studied. While the previous chapter focuses on relatively well-studied nucleation mechanism in 3dimensional (3D) LJ system at large metastability, in Chapter 6 we present our studies on the characteristics of the nucleation phenomena in two dimensional Lennard-Jones fluid for different ranges of interparticle interaction. Using various Monte Carlo (MC) methods, we calculate the free energy barrier of nucleation and bulk densities of equilibrium liquid and vapor phases, and also investigate the size and shape of the critical nuclei. We find an interesting interplay between the range of interaction potential and the extent of metastability. The free energy barrier of nucleation strongly depends on the range of interaction potential. The study is carried out at an intermediate level of supersaturation (away from the kinetic spinodal limit). A surprisingly large cutoff (rc � 7.0�, where � is the diameter of LJ particles) in the truncation of the LJ potential is required to obtain converged results. A lower cutoff leads to a substantial deviation in the values of the nucleation barrier, and characteristics of the critical cluster (with respect to full range of interaction). We observe that in 2D system CNT fails to provide a reliable estimate of the free energy barrier. While it is known to slightly overestimate the nucleation barrier in 3D, it underestimates the barrier by � 50% at the saturation ratio S =1.1 (defined as S = P/Pc, where Pc is the coexistence pressure) and at the reduced temperature T � =0.427 (defined as T � = kBT/�, where � is the depth of the potential well). The reason for the marked inadequacy of the CNT in 2D can be attributed to the non-circular nature of the critical clusters. Although the shape becomes increasingly circular and the clusters become more compact with increase in cutoff radius, an appreciable non-circular nature remains even for full potential (without truncation) to make the predictions of CNT inaccurate. In Chapter 7 we report the computer simulation study of nucleation in three dimensional LJ system. At a fixed supersaturation the free energy barrier of nucleation increases with increasing range of interparticle interaction. On increasing range of intermolecular interaction, the kinetic spinodal where the mechanism of nucleation changes from activated barrier crossing to barrierless diffusion, shifts towards the deep metastable region. Both the critical cluster size and pre-critical minimum in the free energy surface of kth largest cluster shift towards the smaller size at their respective kinetic spinodal as we increase the range of potential. We find only a weak non-trivial (other than supersaturation and surface tension) contribution to the free energy barrier of nucleation. Part III consists of two chapters and focuses on the liquid-solid phase transition of polydisperse fluid. In Chapter 8 we introduce polydisperse systems and their classification based on different identities. We describe the importance and abundance of polydisperse system in nature. The theoretical modeling of different polydisperse systems and their extent of applicability have also been presented. We have discussed about the various factors which control the phase diagram and various phenomena related to the structure and phase transition. In Chapter 9 we present computer simulation study on freezing/melting of Lennard-Jones (LJ) fluid at different polydispersities. The freezing/melting of polydisperse LJ fluids presents an interesting case study, because, as the polydispersity increases the energy-entropy balance becomes increasingly unfavorable for the solid to exist as a stable phase. The energy of the solid increases due to build up of strain energy because of increasing mismatch in size of the neighbors, while the entropy of the liquid increases. These two factors lead to the existence of a terminal polydispersity. We find beyond the terminal ploydispersity, δ. 0.11system remains in the disorder state even at very high pressure and low temperature. The terminal polydispersity obtained in the present study is close to the experimental value (δt. ≈ 12%). Interestingly, contrary to hard sphere polydisperse fluid, LJ fluid does not exhibit reentrant melting. The last part (Part IV) of the thesis consists of three chapters that deal with the enzyme catalysis and kinetic proofreading of tRNA-aminoacyl synthetases. In Chapter 10 we describe protein synthesis process in biological system and corresponding two processes: aminoacylation of tRNA and translation of amino acid in ribosome. Our interest is to understand the enzyme catalysis involved in aminoacylation of tRNA in the process of protein synthesis. We present the classification of 20 aminoacyl-tRNA synthetases into two classes based on their structure and mode of binding to ATP and tRNA. We discuss all the steps involved in whole tRNA-aminoacylation process. Then we introduce kinetic proofreading during aminoacylation reaction. In Chapter 11 we theoretically analyze the single turn over and steady state reaction mechanism of two classes of aminoacyl-tRNA synthetases. Class I enzymes not only differ in their structure but they also differ with respect to the pre-steady kinetics compared to class II enzymes. We find that the strong binding of product to class I enzymes causes the product release step to be rate limiting step leading to the burst of product formation in pre-steady reaction. On the other hand class II enzymes do not show any burst kinetics. The present study based on time dependent probability statistics is successful in explaining all the experimental results quantitatively. In Chapter 12 we present an augmented kinetic scheme and then employ methods of time dependent probability statistics to understand the mechanism of kinetic proofreading of isoleucyl-tRNA synthetase (IRS) which belongs to class I. We investigate that the enhanced hydrolysis of wrong substrate (Val) enables IRS to discriminate the correct substrate (Ile) and wrong substrate (Val) efficiently. It has been observed that an extra CP1 editing domain serves as an activating domain towards enhanced hydrolysis of Val. The present study is able to explain most of the existing experimental observations. In the concluding note, Chapter 13 lists a few relevant problems that may prove worthwhile to be addressed in future. In the Appendices, we present two of the techniques used in our present computer simulation and theoretical studies. Appendix A describes Grand Canonical Transition Matrix Monte Carlo (GC-TMMC) method which is employed in computer simulation studies of nucleation and surface tension. In Appendix B we present the probabilistic method of waiting time distribution computation used in enzyme catalysis and kinetic proofreading.

The potential applications of dispersed and self-assembled nanoparticles depend critically on accurate control and prediction of their phase behavior. The chemical potential is essential in describing the equilibrium distribution of all components present in every phase of a system and is useful as a building block for constructing phase diagrams. Furthermore, the chemical potential is a sensitive indicator of the local environment of a molecule or particle and is defined in a mathematically rigorous manner in both classical and statistical thermodynamics. The goal of this research is to use simulations and experiments to understand how particle size and composition affect the particle chemical potential of attractive nanoparticle-polymer mixtures. The expanded ensemble Monte Carlo (EEMC) simulation method for the calculation of the particle chemical potential for a nanocolloid in a freely adsorbing polymer solution is extended to concentrated polymer mixtures. The dependence of the particle chemical potential and polymer adsorption on the polymer concentration and particle diameter are presented. The perturbed Lennard-Jones chain (PLJC) equation of state (EOS) for polymer chains1 is adapted to calculate the particle chemical potential of nanocolloid-polymer mixtures. The adapted PLJC equation is able to predict the EEMC simulation results of the particle chemical potential by introducing an additional parameter that reduces the effects of polymer adsorption and the effective size of the colloidal particle. Osmotic pressure measurements are used to calculate the chemical potential of nanocolloidal silica in an aqueous poly(ethylene oxide) (PEO) solution at different silica and PEO concentrations. The experimental data was compared with results calculated from Expanded Ensemble Monte Carlo (EEMC) simulations. The results agree qualitatively with the experimentally observed chemical potential trends and illustrate the experimentally-observed dependence of the chemical potential on the composition. Furthermore, as is the case with the EEMC simulations, polymer adsorption was found to play the most significant role in determining the chemical potential trends. The simulation and experimental results illustrate the relative importance of the particles size and composition as well as the polymer concentration on the particle chemical potential. Furthermore, a method for using osmometry to measure chemical potential of nanoparticles in a nanocolloid-mixture is presented that could be combined with simulation and theoretical efforts to develop accurate equations of state and phase behavior predictions. Finally, an equation of state originally developed for polymer liquid-liquid equilibria (LLE) was demonstrated to be effective in predicting nanoparticle chemical potential behavior observed in the EEMC simulations of particle-polymer mixtures.

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Ce travail propose une nouvelle approche de la description des phénomènes physiques qui interviennent dans le cadre de la modélisation de l'interaction plasma-isolant. Pour cela un code de calcul de dynamique moléculaire à été réalisé pour décrire les mécanismes fondamentaux qui régissent cette interaction à l'échelle microscopique.<br />Une étude fondamentale de la dynamique moléculaire, basée sur l'utilisation des méthodes numériques particulières comme les intégrateurs symplétiques et l'exploitation des différents potentiels d'interactions existants (Morse, Lennard-Jones...), a abouti à deux modèles de polymère : le polyéthylène ou PE (CH2)n. Le premier modèle dit simplifié consiste à considérer un groupement CH2 comme un atome fictif de masse molaire 14g, tandis que le second plus complet traite la dynamique de l'atome d'hydrogène au sein de la macromolécule. Ces deux modèles sont utilsés, dans le cadre de ce travail, pour diverses interactions.<br />Par ailleurs, des mesures expérimentales de perte de masse des matériaux polymères qui interagissent avec un plasma, créé par l'explosion d'un fil de cuivre, sont exposées. Ces résultats sont corrélés par des calculs théoriques de thermodynamique qui montrent une différence de comportement des deux polymères testés : le polyéthylène et le polyoxyméthylène, POM ou Delrin (CH2O)n.

Durante la última década y paralelamente al incremento de la velocidad de computación, las técnicas de simulación molecular se han erigido como una importante herramienta para la predicción de propiedades físicas de sistemas de interés industrial. Estas propiedades resultan esenciales en las industrias química y petroquímica a la hora de diseñar, optimizar, simular o controlar procesos. El actual coste moderado de computadoras potentes hace que la simulación molecular se convierta en una excelente opción para proporcionar predicciones de dichas propiedades. En particular, la capacidad predictiva de estas técnicas resulta muy importante cuando en los sistemas de interés toman parte compuestos tóxicos o condiciones extremas de temperatura o presión debido a la dificultad que entraña la experimentación a dichas condiciones. La simulación molecular proporciona una alternativa a los modelos termofísicos utilizados habitualmente en la industria como es el caso de las ecuaciones de estado, modelos de coeficientes de actividad o teorías de estados correspondientes, que resultan inadecuados al intentar reproducir propiedades complejas de fluidos como es el caso de las de fluidos que presentan enlaces de hidrógeno, polímeros, etc. En particular, los métodos de Monte Carlo (MC) constituyen, junto a la dinámica molecular, una de las técnicas de simulación molecular más adecuadas para el cálculo de propiedades termofísicas. Aunque, por contra del caso de la dinámica molecular, los métodos de Monte Carlo no proporcionan información acerca del proceso molecular o las trayectorias moleculares, éstos se centran en el estudio de propiedades de equilibrio y constituyen una herramienta, en general, más eficiente para el cálculo del equilibrio de fases o la consideración de sistemas que presenten elevados tiempos de relajación debido a su bajos coeficientes de difusión y altas viscosidades. Los objetivos de esta tesis se centran en el desarrollo y la mejora tanto de algoritmos de simulación como de potenciales intermoleculares, factor considerado clave para el desarrollo de las técnicas de simulación de Monte Carlo. En particular, en cuanto a los algoritmos de simulación, la localización de puntos críticos de una manera precisa ha constituido un problema para los métodos habitualmente utilizados en el cálculo de equlibrio de fases, como es el método del colectivo de GIBBS. La aparición de fuertes fluctuaciones de densidad en la región crítica hace imposible obtener datos de simulación en dicha región, debido al hecho de que las simulaciones son llevadas a cabo en una caja de simulación de longitud finita que es superada por la longitud de correlación. Con el fin de proporcionar una ruta adecuada para la localización de puntos críticos tanto de componentes puros como mezclas binarias, la primera parte de esta tesis está dedicada al desarrollo y aplicación de métodos adecuados que permitan superar las dificultades encontradas en el caso de los métodos convencionales. Con este fin se combinan estudios de escalado del tamaño de sitema con técnicas de "Histogram Reweighting" (HR). La aplicación de estos métodos se ha mostrado recientemente como mucho mejor fundamentada y precisa para el cálculo de puntos críticos de sistemas sencillos como es el caso del fluido de LennardJones (LJ). En esta tesis, estas técnicas han sido combinadas con el objetivo de extender su aplicación a mezclas reales de interés industrial. Previamente a su aplicación a dichas mezclas reales, el fluido de LennardJones, capaz de reproducir el comportamiento de fluidos sencillos como es el caso de argón o metano, ha sido tomado como referencia en un paso preliminar. A partir de simulaciones realizadas en el colectivo gran canónico y recombinadas mediante la mencionada técnica de "Histogram Reweighting" se han obtenido los diagramas de fases tanto de fluidos puros como de mezclas binarias. A su vez se han localizado con una gran precisión los puntos críticos de dichos sistemas mediante las técnicas de escalado del tamaño de sistema. Con el fin de extender la aplicación de dichas técnicas a sistemas multicomponente, se han introducido modificaciones a los métodos de HR evitando la construcción de histogramas y el consecuente uso de recursos de memoria. Además, se ha introducido una metodología alternativa, conocida como el cálculo del cumulante de cuarto orden o parámetro de Binder, con el fin de hacer más directa la localización del punto crítico. En particular, se proponen dos posibilidades, en primer lugar la intersección del parámetro de Binder para dos tamaños de sistema diferentes, o la intersección del parámetro de Binder con el valor conocido de la correspondiente clase de universalidad combinado con estudios de escalado. Por otro lado, y en un segundo frente, la segunda parte de esta tesis está dedicada al desarrollo de potenciales intermoleculares capaces de describir las energías inter e intramoleculares de las moléculas involucradas en las simulaciones. En la última década se han desarrolldo diferentes modelos de potenciales para una gran variedad de compuestos. Uno de los más comunmente utilizados para representar hidrocarburos y otras moléculas flexibles es el de átomos unidos, donde cada grupo químico es representado por un potencial del tipo de LennardJones. El uso de este tipo de potencial resulta en una significativa disminución del tiempo de cálculo cuando se compara con modelos que consideran la presencia explícita de la totalidad de los átomos. En particular, el trabajo realizado en esta tesis se centra en el desarrollo de potenciales de átomos unidos anisotrópicos (AUA), que se caracterizan por la inclusión de un desplazamiento de los centros de LennardJones en dirección a los hidrógenos de cada grupo, de manera que esta distancia se convierte en un tercer parámetro ajustable junto a los dos del potencial de LennardJones.En la segunda parte de esta tesis se han desarrollado potenciales del tipo AUA4 para diferentes familias de compuesto que resultan de interés industrial como son los tiofenos, alcanoles y éteres. En el caso de los tiofenos este interés es debido a las cada vez más exigentes restricciones medioambientales que obligan a eliminar los compuestos con presencia de azufre. De aquí la creciente de necesidad de propiedades termodinámicas para esta familia de compuestos para la cual solo existe una cantidad de datos termodinámicos experimentales limitada. Con el fin de hacer posible la obtención de dichos datos a través de la simulación molecular hemos extendido el potencial intermolecular AUA4 a esta familia de compuestos. En segundo lugar, el uso de los compuestos oxigenados en el campo de los biocombustibles ha despertado un importante interés en la industria petroquímica por estos compuestos. En particular, los alcoholes más utilizados en la elaboración de los biocombustibles son el metanol y el etanol. Como en el caso de los tiofenos, hemos extendido el potencial AUA4 a esta familia de compuestos mediante la parametrización del grupo hidroxil y la inclusión de un grupo de cargas electrostáticas optimizadas de manera que reproduzcan de la mejor manera posible el potencial electrostático creado por una molecula de referencia en el vacío. Finalmente, y de manera análoga al caso de los alcanoles, el último capítulo de esta tesis la atención se centra en el desarrollo de un potencial AUA4 capaz de reproducir cuantitativamente las propiedades de coexistencia de la familia de los éteres, compuestos que son ampliamente utilizados como solventes. / Parallel with the increase of computer speed, in the last decade, molecular simulation techniques have emerged as important tools to predict physical properties of systems of industrial interest. These properties are essential in the chemical and petrochemical industries in order to perform process design, optimization, simulation and process control. The actual moderate cost of powerful computers converts molecular simulation into an excellent tool to provide predictions of such properties. In particular, the predictive capability of molecular simulation techniques becomes very important when dealing with extreme conditions of temperature and pressure as well as when toxic compounds are involved in the systems to be studied due to the fact that experimentation at such extreme conditions is difficult and expensive.Consequently, alternative processes must be considered in order to obtain the required properties. Chemical and petrochemical industries have made intensive use of thermophysical models including equations of state, activity coefficients models and corresponding state theories. These predictions present the advantage of providing good approximations with minimal computational needs. However, these models are often inadequate when only a limited amount of information is available to determine the necesary parameters, or when trying to reproduce complex fluid properties such as that of molecules which exhibit hydrogen bonding, polymers, etc. In addition, there is no way for dynamical properties to be estimated in a consistent manner.In this thesis, the HR and FSS techniques are combined with the main goal of extending the application of these methodologies to the calculation of the vaporliquid equilibrium and critical point of real mixtures. Before applying the methodologies to the real mixtures of industrial interest, the LennardJones fluid has been taken as a reference model and as a preliminary step. In this case, the predictions are affected only by the omnipresent statistical errors, but not by the accuracy of the model chosen to reproduce the behavior of the real molecules or the interatomic potential used to calculate the configurational energy of the system.The simulations have been performed in the grand canonical ensemble (GCMC)using the GIBBS code. Liquidvapor coexistences curves have been obtained from HR techniques for pure fluids and binary mixtures, while critical parameters were obtained from FSS in order to close the phase envelope of the phase diagrams. In order to extend the calculations to multicomponent systems modifications to the conventional HR techniques have been introduced in order to avoid the construction of histograms and the consequent need for large memory resources. In addition an alternative methodology known as the fourth order cumulant calculation, also known as the Binder parameter, has been implemented to make the location of the critical point more straightforward. In particular, we propose the use of the fourth order cumulant calculation considering two different possibilities: either the intersection of the Binder parameter for two different system sizes or the intersection of the Binder parameter with the known value for the system universality class combined with a FSS study. The development of transferable potential models able to describe the inter and intramolecular energies of the molecules involved in the simulations constitutes an important field in the improvement of Monte Carlo techniques. In the last decade, potential models, also referred to as force fields, have been developed for a wide range of compounds. One of the most common approaches for modeling hydrocarbons and other flexible molecules is the use of the unitedatoms model, where each chemical group is represented by one LennardJones center. This scheme results in a significant reduction of the computational time as compared to allatoms models since the number of pair interactions goes as the square of the number of sites. Improvements on the standard unitedatoms model, where typically a 612 LennardJones center of force is placed on top of the most significant atom, have been proposed. For instance, the AUA model consists of a displacement of the LennardJones centers of force towards the hydrogen atoms, converting the distance of displacement into a third adjustable parameter. In this thesis we have developed AUA 4 intermolecular potentials for three different families of compounds. The family of ethers is of great importance due to their applications as solvents. The other two families, thiophenes and alkanols, play an important roles in the oil and gas industry. Thiophene due to current and future environmental restrictions and alkanols due ever higher importance and presence of biofuels in this industry.

The thesis involves computer simulation and theoretical studies of dynamics of water under confinement and structural transformation in different complex systems. Based on the systems and phenomena of interest, the work has been classified in to three major parts: I. Dynamics of water under confinement II. Dynamics of water in presence of amphiphilic solutes III. Structural transformation in complex systems The three parts have further been divided into nine chapters. Brief chapter wise outline of the thesis is discussed below. Part I deals with the dynamics of water in confined systems. In Chapter I.1, we provide a brief introduction of water dynamics inc on fined systems. We also give a brief outline of relevant experimental and theoretical techniques used to study the water dynamics under confinement. Chapter I.2 describes a model based analytical study of dynamical correlation in confined systems. Here, we introduce a novel one dimensional Ising model to investigate the propagation and annihilation of dynamical correlations in confined systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles (RMs).In our model, the two spins located at the two end cells are oriented in the opposite directions to mimic the surface effects present in the real systems. These produce opposing polarizations which propagate from the surface to the center, thus producing bulk like condition at the center. This model can be solved analytically for short chains. For long chains, we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm).We show that the model satisfactorily reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is non-exponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of the relaxation of spins undergoes a change with the emergence of homogeneous dynamics, where the decay is predominantly exponential. In Chapter I.3, layer-wise distance dependent orientation relaxation of water confined in reverse micelle s(RM)is studied using theoretical and computational tools. We use both a newly constructed spins on a ring (SOR) Ising-type model with modified Shore-Zwanzig rotational dynamics and atomistic simulations with explicit water. Our study explores the size effect of RMs and the role of intermolecular correlations, compromised by the presence of a highly polar surface, on the distance (from the surface) dependence of water relaxation. The SOR model can capture some aspects of distance dependent orientation relaxation, such as acceleration of orientation relaxation at intermediate layers. In atomistic simulations, layer-wise decomposition of hydrogen bond (H-bond) formation pattern clearly reveal that the H-bond arrangement of water at a certain distance away from the surface can remain frustrated due to interaction with the polar surface head groups. We show that this layer-wise analysis also reveals the presence of a non-monotonic, slow relaxation component which can be attributed to the frustration effect and is accentuated in small to intermediate size RMs. For larger RMs, the long-time component decreases monotonically from the interface to the interior of the RMs with slowest relaxation observed at the interface. In ChapterI.4, we present theoretical two dimensional infrared spectroscopic (2D-IR) studies of water confined within RMs of various sizes. Here we focus again mainly on the altered dynamics of confined water by performing a layer-wise decomposition of water. We aim to quantify the relative contributions to the calculated 2D-IR spectra by water molecules located in different layers. The spectra of 0-1 transition clearly show substantial elongation along the diagonal, due to in homogeneous broadening and incomplete spectral diffusion, in the surface water layer of different size of RMs studied in this work. Our study reveals that the motion of the surface water molecules is sub-diffusive, establishing the constrained nature of their dynamics. This is further supported by the two peak nature of the angular analogue of the van Hove correlation function. With increasing system size the motion of water molecules becomes more diffusive in nature and the structural diffusion is observed to be almost completed in the central layer of larger RMs. Comparisons between experiment and simulation help establishing the correspondence between the spectral decomposition available in experimental 2D-IR with the spatial decomposition of simulated 2D-IR. Simulations also allow a quantitative exploration of the relative role of water, sodium ions and sulfonate head groups in irrational dephasing. Interestingly, the negative cross correlation between forces on oxygen and hydrogen of O-H bond in bulk water significantly decreases in the surface layer of different RMs. This negative cross correlation gradually increases in the central layer with increasing size of the RMs and this is found to be partly responsible for the faster relaxation rate of water in the central layer. Part II consists of two chapters and focuses on the dynamics of water in presence of amphiphilic solutes. In Chapter II.1, we present a brief introduction of water – DMSO binary mixture and various anomalous properties of the same. In Chapter II.2, we present theoretical IR study of water dynamics in water–DMSO binary mixtures of different compositions. We show that with increasing DMSO concentration, the IR absorption peak maxima show the presence of structural transformation in similar concentration range, observed in earlier studies. Analysis of H-bonded network near hydrophilic and hydrophobic part of DMSO also suggests that average number of hydrogen bonds near the hydrophobic parts possess maxima at the same concentration range. We also show that with increasing DMSO concentration water dynamics becomes very slow. This has been supported by the diagonal elongation of the 2D-IR spectra and also the slow decay of frequency fluctuation correlation n function (FFCF) and the orientation time correlation function (OTCF). The decoupling of the OTCF establishes that water-DMSOH-bond is much stronger than that of water-water. The last part (Part III) consists of three chapters that deal with structural transformation in various complex systems. In Chapter III.1, we introduce polydisperse systems and present existing theoretical, computer simulation and experimental studies. It also contains the importance and diversity of polydisperse system in nature. In Chapter III.2, we present computer simulation study of melting of polydisperse Lennard-Jones (LJ) system with Gaussian polydispersity in size. The phase diagram reproduces the existence of an early temperature in variant terminal polydispersity (δt0.11), with no signature of re-entrant melting. The absence of re-entrant melting can be attributed to the influence of attractive part of the potential on melting. We find that at terminal polydispersity the fractional density change approaches zero that seems to arise from vanishingly small compressibility of the disordered phase. At constant temperature and volume fraction system undergoes a sharp transition from crystalline solid to disordered state with increasing polydispersity. This has been quantified by second and third order rotational invariant bond orientational orders as well as by the average inherent structure energy. The translational order parameter also indicates similar structural change The free energy calculation further supports the nature of the transition. The third order bond orientational order shows that with increasing polydispersity, local cluster favors more icosahedral-like arrangements and thus the system loses its crystalline symmetry. In Chapter III.3, we present study of phase transition and effect of confinement on it in SOR model. This system is similar to our SOR model discussed in Chapter I.3. The spins execute continuous rotation under a modified XY Hamiltonian. In order to understand the nature of phase transition in such confined spin systems we have performed extensive Monte Carlo simulations. The system size dependence of Binders cumulant, specific heat, order parameter and finite size scaling of order parameter universally suggest the existence of a phase transition. The absence of hysteresis and Scaling of Binders energy cumulant minimum confirm the continuous nature of the transition. The finite size scaling analyses give rise to the mean field nature of the transition. Plausible applications of the proposed model in modeling dipolar liquids in confined systems are also discussed. In Appendix A, we discuss a preliminary study of front propagation in a non-equilibrium system. The model system analogous to the super cooled liquid shows non-Avrami domain growth during rejuvenation. The origin of the non-Avrami nature of the domain growth and the presence of cross over are also discussed. In Appendix B, we discuss umbrella a sampling technique and WHAM analysis which is used in ChapterIII.2 to get the free energy of polydisperse LJ system.