L'exploitation des ressources non conventionnelles de roches mères telles que les schistes gazeux contribue de plus en plus au mix énergétique mondial en raison de la raréfaction des ressources conventionnelles. L'exploitabilité de ces réservoirs repose principalement sur la qualité, la teneur et le type de matière organique qu'ils contiennent. En effet, il est admis que plus de la moitié des hydrocarbures présents dans les schistes sont adsorbés dans la matière organique solide, appelée kérogène, dont la structure est microporeuse et amorphe, et qui représente à la fois la source et le réservoir d'hydrocarbures. Le kérogène se trouve sous forme dispersée dans la matière minérale et représente environ 5% de la masse totale de la roche. La compréhension des propriétés de transport des fluides à l'échelle des micropores, en particulier leur dépendance aux conditions thermodynamiques et aux propriétés structurelles du matériau, revêt une importance cruciale pour l'optimisation de la récupération de ces ressources. De ce point de vue, l'objectif principal de cette thèse vise à bien documenter les propriétés de transport des hydrocarbures à travers les kérogènes et améliorer leur description théorique. Pour ce faire, nous avons fait le choix d'étudier les propriétés de transport des fluides à travers ces matériaux en utilisant une approche numérique basée sur des simulations moléculaires de type dynamique moléculaire et Monte Carlo, conduites sur des modèles moléculaires de kérogène mature et sur un système modèle simplifié. Ceci nous a permis d’explorer les mécanismes de transport à une échelle où l'observation expérimentale est difficile, voire impossible, et également de nous situer dans des conditions thermodynamiques supercritiques (haute pression, haute température) caractéristiques des réservoirs de gaz de schiste. La première partie de ce travail a consisté à étudier les propriétés de transport et d'adsorption des fluides purs dans des structures de kérogène mature reconstruites par simulations moléculaires. Ensuite, la dépendance des propriétés de transport aux variations des conditions thermodynamiques (température à gradient de pression fixe) ainsi qu'à la distribution de tailles de pores a été étudiée. Concernant le deuxième objectif, afin de mieux comprendre et modéliser la diffusion des fluides à l'échelle d'une constriction microporeuse entre deux pores, nous avons étudié un système modèle constitué d'une seule fente microporeuse formée dans un solide mono-couche. L'étude a consisté à simuler la diffusion de transport d'un fluide à travers la constriction en variant les paramètres géométriques (rapport d’aspect entre la largeur du pore et la taille des molécules diffusantes) et thermodynamiques (température, chargement en fluide). Ces résultats de simulations ont été comparés aux prédictions d'un modèle théorique, fondé sur la théorie cinétique des gaz et la mécanique statistique classique, qui prend en compte l'effet de la température sur la porosité accessible ainsi que l'effet du chargement en fluide à l'entrée du seuil de pore. Un bon accord a été observé entre les valeurs simulées des coefficients de diffusion et les prédictions du modèle proposé. Ce système a ainsi contribué à la compréhension des phénomènes de tamisage moléculaire survenant lors du franchissement d'une constriction microporeuse, inhérents au transport de fluides dans les matériaux microporeux tels que le kérogène. / The share of unconventional resources in the global energy mix is expected to rise because of the shortage of conventional fossil resources. The major part of these unconventional resources are found in source rocks such as gas shales. The profitability of shale reservoirs strongly depends on the quality, type and content of organic matter contained in the rock. Indeed, it is admitted that more than half of the hydrocarbons stored in the shale are adsorbed in the solid organic matter, the so-called kerogen. The latter exhibits a microporous amorphous structure, and acts as both the source and the reservoir of hydrocarbons. Kerogen is finely dispersed in the mineral matrix and represents about 5% of the total mass of the rock. The understanding of the transport of fluids at the microporous scale is of crucial importance for optimizing the recovery of these resources. More specifically, how the structural properties of the microporous material and thermodynamic conditions influence its transport properties is an open question. In this regard, the main objective of this thesis is to document the transport properties of hydrocarbons through kerogens and to improve their theoretical description. To do so, we opted for a numerical approach based on molecular simulations of molecular dynamics and Monte Carlo codes performed on molecular models of mature kerogen, as well as simplified model systems. We thus explored transport mechanisms at the molecular scale, at which experimental observations are difficult, if not impossible. Supercritical thermodynamic conditions (high pressure, high temperature) were considered, which are characteristic of shale gas reservoirs. The first part of this work has consisted in studying the transport and adsorption properties of pure fluids in mature kerogen structures reconstructed by molecular simulations. We studied the dependence of the transport properties on the variations of the thermodynamic conditions (pressure gradient at a fixed temperature) as well as the influence of the pore size distribution. In order to better understand and describe the diffusion of fluids at the scale of a microporous constriction between two pores, the second objective of this thesis focused on a model system, which consisted of a single-layer solid with a slit aperture of controllable width. We simulated the diffusional transport of simple fluids through the constriction for various geometrical parameters (aspect ratio between the width of the pore and the size of the diffusing molecules) and thermodynamic conditions (temperature, fluid loading). These simulations results have been compared to the predictions of a theoretical model, based on the kinetic theory and classical statistical mechanics, which accounts for the effect of temperature on the accessible porosity and the effect of fluid loading at the entrance of the pore. A good agreement was observed between the simulated values of the diffusion coefficients and the predictions of the proposed model. The investigation of this simplified system helped in understanding the molecular sieving phenomena inherent to the transport of fluids in microporous materials such as kerogen.

"Hydrophobic hydration of non polar molecules is the principal driving force that dictates several interfacial phenomena in nature such as self assembly of surfactant molecules, fate of environmental pollutants, wetting of surfaces, solution behavior of polymers and folding of biological molecules such as proteins. However, the physics associated with hydrophobic interactions on a molecular length scale, which is central to self assembly and protein folding, is different from the macroscopic phenomena of de-mixing of oil and water or wetting of surfaces. This dissertation seeks to understand the implication of hydrophobic interactions to energy and environmental applications using different approaches. The first approach is to examine the behavior of water molecules with hydrophobic moieties at a molecular level using molecular dynamics simulations and evaluate macroscopic thermodynamic properties. The first problem addressed in this dissertation is the enclathration of gas molecules by water molecules in the presence of quaternary ammonium ions. Small polar organic molecules such as quaternary ammonium salts form crystalline inclusion compounds called semi-clathrate hydrates, where these polar molecules occupy a lattice position of the hydrogen bond network of water molecules. These crystalline structures of water are formed at ambient temperature and pressure conditions and can store as much 3%(w/w) of methane, making them potential materials for gas storage. The stability and structure of semi-clathrate hydrates of tetrabutylammonium bromide (TBAB) and methane were investigated using molecular dynamics (MD) simulations. MD simulations were done at varying conditions of temperature and pressure for methane-TBAB ratios of 0, 0.5, 1, 1.5 and 2. Thermo-mechanical properties evaluated using MD simulations were in agreement with experimental data available. Our investigation of this system shows that enclathration of methane in these semi-clathrate hydrates is thermodynamically favorable even at higher temperatures and shows signatures of hydrophobic hydration. Our estimation of free energies associated with successive inclusion of methane molecules in these cavities suggests a Langmuir-type adsorption of methane in these cages. Another problem investigated in this dissertation is the effect of chemical heterogeneity of crystalline cellulose (110) and (100) surfaces on their respective wetting behavior. Understanding the interaction of water with cellulose is important in the view of its role in consumer textiles made from cotton cellulose and potential applications of cellulose as biomaterials and as an energy source. The difference in the wetting behavior of (110) and (100) crystal surfaces is due to the asymmetry in the exposure of the hydroxyl groups by these surfaces. MD simulations were used to evaluate the contact angles of hemi-cylindrical water nanodroplets on crystalline (110) and (100) surfaces of the cellulose Iβ allomorph. While the native crystalline surfaces were completely wetted by water nanodroplets, substituting the primary hydroxyl groups with methyl and methoxy groups results in dewetting. The contact angle of a hemicylidrical water nanodroplet on the hydrophobically-modified (110) surface is greater than on the (100) surface suggesting that the (110) surface has a greater exposure of the primary hydroxyl groups. The solubility of cellulose in aliphatic N-oxides has been of particular interest because of its application in industrial processes such as Lyocell process. However, the mechanisms that dictate the dissolution of cellulose in these selective solvents are not clearly understood. Attempt is made to understand the solvation of cellulose in N-Methylmorpholine oxide (NMMO) and water from a molecular perspective. MD simulations of a model cellohexaose crystallite solvated respectively in pure water, NMMO and in an equimolar mixture suggest that while NMMO molecules preferentially cluster around the primary hydroxyl groups in cellohexaose chains, the role of water is critical in its ability to access the glycosidic oxygen. The second approach is to study the implication of introducing hydrophobicity at molecular level and experimental determination of its implication to addressing interfacial aspects of environmental remediation. Sub-micron size carbon particles derived from hydrothermal decomposition of sucrose are effective in stabilizing water-in-trichloroethylene (TCE) emulsions. Irreversible adsorption of carbon particles at the TCE-water interface resulting in the formation of a monolayer around the water droplet in the emulsion phase is identified as the key reason for emulsion stability. Cryogenic Scanning Electron Microscopy was used to clearly image the assembly of carbon particles at the TCE-water interface and the formation of bilayers at regions of droplet-droplet contact. The results from this study have broad implications to the subsurface injection of carbon submicron particles containing zerovalent iron nanoparticles to treat pools of chlorinated hydrocarbons that are sequestered in fractured bedrock. Interfacial aspects of hydrophobically modified biopolymer and its ability to enhance the stability of crude-oil droplets formed were investigated. Turbidimetric analyses show that emulsions of crude oil in saline water prepared using a combination of the biopolymer and the well-studied chemical dispersant (Corexit 9500A) remain stable for extended periods in comparison to emulsions stabilized by the dispersant alone. The hydrophobic residues attached to the polymer preferentially anchor at the oil-water interface and form a protective layer of the polymer around the droplets. The enhanced stability of the droplets is due to the polymer layer providing an increase in electrostatic and steric repulsions and thereby a large barrier to droplet coalescence. The implication of this study to current remediation methods is significant since the addition of hydrophobically modified chitosan following the application of chemical dispersant to an oil spill can potentially reduce the use of chemical dispersants. Increasing the molecular weight of the biopolymer changes the rheological properties of the oil-in-water emulsion. Emulsions stabilized by using a combination of Corexit 9500A and high molecular weight hydrophobically modified chitosan show characteristics of a weak gel. The ability of the biopolymer to tether the oil droplets in a gel-like matrix has potential applications in the immobilization of surface oil spills for enhanced removal. Carbon microspheres containing magnetite nanoparticles, synthesized using inexpensive precursors such as sucrose and iron chloride, are ferromagnetic and have affinity to the oil phase. We demonstrate that a thin layer of crude oil can be corralled and thickened by the application of nonionic surfactant. Following the application of magnetite-carbon particles, hydrophobically modified chitosan was applied to form a gel-like phase. This gel-like phase of crude oil containing magnetic carbon spheres can be removed as an aggregate using a magnet resulting in enhanced recovery of crude oil. The results from the current study point to developing potential applications for confinement, magnetic tracking and removal of surface oil. " / acase@tulane.edu

Polyethylene oxide polymers are intrinsic to oil spill dispersants used in Macondo well blowout of 2010. We believe that effective thermo-physical modeling of these materials should assist the application of lab-scale results into ocean-scales. Fully defensible molecular scale theory of such materials will be challenging. This thesis is the first step towards that challenge. Molecular dynamics simulations are useful in generating structural and phase behavior data for these versatile polymers. Microstructures of PEO polymers, hydrophobic interactions, direct numerical test of controversial Pratt-Chandler theory, concentration dependence of Flory-Huggins interaction parameter and neutron scattering experiments will be discussed. / acase@tulane.edu

The very large number of distinct structures that are known for metal-organic frameworks (MOFs) and zeolites presents both an opportunity and a challenge for identifying materials with useful properties for targeted separations. In this thesis we propose a three-stage computational methodology for addressing this issue and comprehensively screening all available nanoporous materials. We introduce efficient pore size calculations as a way of discarding large number of materials, which are unsuitable for a specific separation. Materials identified as having desired geometric characteristics can be further analyzed for their infinite dilution adsorption and diffusion properties by calculating the Henry's constants and activation energy barriers for diffusion. This enables us to calculate membrane selectivity in an unprecedented scale and use these values to generate a small set of materials for which the membrane selectivity can be calculated in detail and at finite loading using well-established computational tools. We display the results of using these methods for >500 MOFs and >160 silica zeolites for spherical adsorbates at first and for small linear molecules such as CO₂ later on. In addition we also demonstrate the size of the group of materials this procedure can be applied to, by performing these calculations, for simple adsorbate molecules, for an existing library of >250,000 hypothetical silica zeolites. Finally, efficient methods are introduced for assessing the role of framework flexibility on molecular diffusion in MOFs that do not require defining a classical forcefield for the MOF. These methods combine ab initio MD of the MOF with classical transition state theory and molecular dynamics simulations of the diffusing molecules. The effects of flexibility are shown to be large for CH₄, but not for CO₂ and other small spherical adsorbates, in ZIF-8.

Large amount of data is generated by applications used in basic-science research and development applications. The size of data introduces great challenges in storage, analysis and preserving privacy. This dissertation proposes novel techniques to efficiently analyze the data and reduce storage space requirements through a data compression technique while preserving privacy and providing data security. We present an efficient technique to compute an analytical query called spatial distance histogram (SDH) using spatiotemporal properties of the data. Special spatiotemporal properties present in the data are exploited to process SDH efficiently on the fly. General purpose graphics processing units (GPGPU or just GPU) are employed to further boost the performance of the algorithm. Size of the data generated in scientific applications poses problems of disk space requirements, input/output (I/O) delays and data transfer bandwidth requirements. These problems are addressed by applying proposed compression technique. We also address the issue of preserving privacy and security in scientific data by proposing a security model. The security model monitors user queries input to the database that stores and manages scientific data. Outputs of user queries are also inspected to detect privacy breach. Privacy policies are enforced by the monitor to allow only those queries and results that satisfy data owner specified policies.

Biological molecules often undergo large structural changes to perform their function. Computational methods can provide a fine-grained description at the atomistic scale. Without sufficient approximations to accelerate the simulations, however, the time-scale on which functional motions often occur is out of reach for many traditional methods. Natural Move Monte Carlo belongs to a class of methods that were introduced to bridge this gap. I present three novel applications for Natural Move Monte Carlo, two on proteins and one on DNA epigenetics. In the second part of this thesis I introduce a new protocol for the testing of hypotheses regarding the functional motions of biological systems, named customised Natural Move Monte Carlo. Two different case studies are presented aimed at demonstrating the feasibility of customised Natural Move Monte Carlo.

Les simulations moléculaires sont devenues un outil essentiel en biologie, chimie et physique. Malheureusement, elles restent très coûteuses. Dans cette thèse, nous proposons des algorithmes qui accélèrent les simulations moléculaires en regroupant des particules en plusieurs objets rigides. Nous étudions d’abord plusieurs algorithmes de recherche de voisins dans le cas des grands objets rigides, et démontrons que les algorithmes hiérarchiques permettent d’obtenir des accélérations importantes. En conséquence, nous proposons une technique pour construire une représentation hiérarchique d’un graphe moléculaire arbitraire. Nous démontrons l’usage de cette technique pour la mécanique adaptative en angles de torsion, une méthode de simulation qui décrit les molécules comme des objets rigides articulés. Enfin, nous introduisons ARPS – Adaptively Restrained Particle Simulations (“Simulations de particules restreintes de façon adaptative”) – une méthode mathématiquement fondée capable d’activer et de désactiver les degrés de liberté en position. Nous proposons deux stratégies d’adaptation, et illustrons les avantages de ARPS sur plusieurs exemples. En particulier, nous démontrons comment ARPS permet de choisir finement le compromis entre précision et vitesse, ainsi que de calculer rapidement des proprietésstatiques d’équilibre sur les systèmes moléculaires. / Molecular simulations have become an essential tool in biology, chemistry and physics. Unfortunately, they still remain computationally challenging. In this dissertation, we propose algorithms that accelerate molecular simulations by clustering particles into rigid bodies.We first study several neighbor-search algorithms for large rigid bodies, and show that hierarchy-based algorithms may provide significant speedups. Accordingly, we propose a technique to build a hierarchical representation of an arbitrary molecular graph. We show how this technique can be used in adaptive torsion-angle mechanics, a simulation method that describes molecules as articulated rigid bodies. Finally, we introduce ARPS – Adaptively Restrained Particle Simulations – a mathematically-grounded method able to switch positional degrees of freedom on and off. We propose two switching strategies, and illustrate the advantages of ARPS on various examples. In particular, we show how ARPS allow us to smoothly trade between precision and speed, and to efficiently compute correct static equilibrium properties on molecular systems.

Adsorption in porous materials is a promising technology for CO2 capture and storage. Particularly important applications are adsorption separation of streams associated with the fossil fuel power plants operation, as well as natural gas sweetening. High surface area activated carbons are a promising family of materials for these applications, especially in the high pressure regimes. As the streams under consideration are generally multi-component mixtures, development and optimization of adsorption processes for their separation would substantially benefit from predictive simulation models. In this project we combine experimental data and molecular simulations to systematically develop a model for a high surface area carbon material, taking activated carbon Maxsorb MSC-30 as a reference. Our study starts from the application of the well-established slit pore model, and then evolves through the development of a more realistic model, based on a random packing of small graphitic fragments. In the construction of the model, we introduce a number of constraints, such as the value of the accessible surface area, concentration of the surface groups and pore volume, to bring the properties of the model structure close to the reference porous material. Once a plausible model is developed, its properties are further tuned through comparison between simulated and experimental results for carbon dioxide and methane. The model is then validated by predictions for the same species at different conditions and by prediction of other species involved in the carbon capture processes. The model is applied to simulate the separations involved in pre and post combustion capture processes and sweetening of sour natural gas, using realistic conditions and compositions for the multicomponent mixtures. Finally, it is used to explore the effect of water in pre and post combustion separations.

This thesis investigate the structure of cadmium sulfide (CdS) nanoparticles and its stabilization by a surfactant - cetyltrimethylamonnium cation CTA+ and further describe interactions among stabilized CdS nanoparticles and the surface of the layered clay mineral - montmorillonite with using the molecular simulation methods. Initial models of the CdS nanoparticles were build for both crystal structures (Greenockit (G) and Hawleyit (H)). The preferred orientations of the molecules of CTA+ for both crystal types of CdS nanoparticles were found with respect to minimum energy. Prefered orientation is monolayer for Greenockite and bilayer for Hawleyite. Models with the preferred orientation of the molecules of CTA+ were placed on the surface of montmorillonite and after optimization, adsorption energy of CdS nanoparticles with its envelope and montmorillonite surface was calculated. All results and used procedures were compiled in the form of practice for the subject Computational experiments in the theory of molecules I - NBCM100 taught at MFF UK in Prague.

Orientador: Maurice de Koning / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-27T17:09:46Z (GMT). No. of bitstreams: 1 Leite_RodolfoPaula_M.pdf: 4064445 bytes, checksum: 15e944e3607ec0d3b8cb66d00b6ea4f3 (MD5) Previous issue date: 2015 / Resumo: Neste trabalho, apresentamos um estudo a respeito do modelo de Uhlenbeck-Ford como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, utilizando metodos de simulacao molecular. Este sistema artificial, que e caracterizado por um potencial puramente repulsivo e que diverge rapidamente, foi originalmente proposto como um modelo para o estudo teorico de gases imperfeitos. Este modelo foi motivado pelo fato de que todas as integrais de muitos corpos, envolvidas no calculo dos coeficientes viriais, podem ser facilmente calculadas analiticamente. Entretanto apenas oito coeficientes eram conhecidos. Dois novos coeficientes (..10 e ..11) foram determinados para o modelo neste trabalho, alem de uma expressao essencialmente exata para a equacao de estado e energia livre de Helmholtz em funcao de um parametro adimensional. Este nos permitira reunir todas as informacoes a respeito da energia livre do sistema em uma unica expressao, independentemente da escolha de parametros do potencial. Por fim, exploraremos a aplicabilidade deste modelo como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, usando tecnicas de simulacao molecular a partir de processos fora de equilibrio. Nossos resultados para o fluido de Lennard-Jones e para o silicio liquido, descrito pelo potencial de Stillinger-Weber, demonstraram que o modelo de Uhlenbeck-Ford servira como um sistema de referencia para o calculo de energia livre de sistemas na fase fluida / Abstract: In this work, we present a study of the Uhlenbeck-Ford model as a reference system for freeenergy calculations of fluid-phase systems by molecular simulation methods. This artificial system, which is characterized by a rapidly-decaying purely repulsive potential, was originally proposed as a model for the theoretical study of imperfect gases, enabled by the fact that all the many-center integrals involved in the virial coefficients can be easily computed analytically. Although only eight coefficients were known. Two new coefficients (..10 e ..11) were determined for the model in this work, in addition to an essentially accurate expression to the equation of state and Helmholtz free-energy as a function of a dimensionless parameter. This will allow us to gather all information regarding the system of free-energy in a single expression, regardless of the choice of potential parameters. In the end, we explore the applicability of this model as a reference system for free-energy calculations of fluid-phase systems, using non equilibrium process with molecular simulation techniques. Our results for thevLennard-Jones fluid and liquid silicon, described by Stillinger-Weber potential, demonstrate that the Uhlenbeck-Ford model can be used as a reference system for free-energy calculations of fluid-phase systems / Mestrado / Física / Mestre em Física