151 research outputs found

    Molecular simulation of biomaterials and biomolecules at the solid-liquid interface

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    Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008.Includes bibliographical references (p. 141-153).Biomaterials and biomineralization have been successfully utilized in a broad variety of technical applications. Properties of natural biopolymers, such as the ability to control the nucleation, growth, and organization of crystals, have been extended to a much wider array of technologically applicable materials through combinatorial selection techniques. However, detailed mechanisms of peptide adsorption on inorganic surfaces have largely escaped characterization. This knowledge would open new routes for the rational design of nanostructures and composite biomaterials. The development of accurate and computationally efficient methods for the simulation of biopolymer-inorganic surface adsorption could provide a more detailed understanding of adsorption mechanisms. While simple models involving reduced solvent representations and polymer flexibility have found some success in limited applications, robust performance for systems of varying size and composition can generally be expected only through accurate inclusion of these key details. Fully atomistic representations of biopolymer and surface are necessary for detailed molecular recognition, while polymer flexibility is required to capture structural rearrangement and the resulting free energy contributions. Finally, electrostatic interactions between the adsorbing biopolymer and inorganic surface, as well as interactions of the polymer and surface with the surrounding solvent environment will play a dominant role in the adsorption process, and an accurate representation of the solvated system is inherently necessary. Computational efficiency can be increased through the application of implicit solvent models, which replace the numerous solvent molecules with a continuum dielectric, and seek to capture the average effects of the statistical solvent environment. The Poisson-Boltzmann model represents the most rigorous treatment of implicit solvent.(cont.) This model, however, requires the relatively expensive solution of a second order elliptical differential equation over the space of the system. Here, a method is presented which reduces the scale at which the Poisson-Boltzmann equation must be solved. However, even when combined with an efficient multi-grid solver, the Poisson-Boltzmann model represents a significant computational cost. The modified Generalized Born model, GBr6, based on an approximation to the Poisson-Boltzmann model, offers a computationally efficient alternative. Generalized Born models, however, are often inaccurate in the case of charges positioned near an extended dielectric interface, which is precisely the system we wish to investigate. Here, an analytical integration of the approximate electric displacement is used to calculate Born radii, and tested in application to surface adsorption studies. Replica-exchange Monte Carlo simulations with modified Generalized Born implicit solvent environment is then used to study the adsorption mechanism of a set of rationally designed sapphire-binding peptides. Modulation of binding affinity is predicted to depend on multiple interactions between basic amino acids and the negatively charged sapphire surface. The proximity of charged residues to one another as well as the conformational ability of each peptide to present functional groups towards the surface are shown to control the relative binding affinities.by Stephen Thomas Kottmann.Ph.D

    Towards modelling physical and chemical effects during wettability alteration in carbonates at pore and continuum scales

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    Understanding what controls the enhanced oil recovery during waterflooding of carbonate rocks is essential as the majority of the world’s remaining hydrocarbon reserves are contained in carbonate rocks. To further this understanding, in this thesis we develop a pore-scale simulator that allows us to look at the fundamental physics of fluid flow and reactive solute transport within the porous media. The simulator is based on the combined finite element – finite volume method, it incorporates efficient discretization schemes and can hence be applied to porous domains with hundreds of pores. Our simulator includes the rule-based method of accounting for the presence of the second immiscibly trapped fluid phase. Provided that we know what chemical conditions initiate enhanced oil recovery, our simulator allows us to analyse whether these conditions occur, where they occur and how they are influenced by the flow of the aqueous phase at the pore scale. To establish the nature of chemical interactions between the injected brines and the carbonate rocks, we analyze the available experimental data on the single-phase coreflooding of carbonate rocks. We then build a continuum scale simulation that incorporates various chemical reactions, such as ions adsorption and mineral dissolution and precipitation. We match the output of the continuum scale model with the experimental data to identify what chemical interactions the ions dissolved in seawater are involved in

    Computational Multiscale Methods

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    Computational Multiscale Methods play an important role in many modern computer simulations in material sciences with different time scales and different scales in space. Besides various computational challenges, the meeting brought together various applications from many disciplines and scientists from various scientific communities

    Lattice Boltzmann simulations of multiphase flows

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    This thesis is a comprehensive account of my experiences implementing the Lattice Boltzmann Method (LBM) for the purpose of simulating multiphase flows relevant to Air Conditioning and Refrigeration Center (ACRC) applications. Other methodologies have been used to simulate multiphase flow including finite volume based Navier-Stokes solvers. These methods have found reasonable success in simulating multiphase flows. LBM was chosen because of its ability to capture multi-fluid physics including phase-change and interfacial dynamics with relative ease. In addition, the LBM algorithm can be easily parallelized. This allows larger problems to be simulated quicker. Among the multiphase LBM algorithms, we have implemented the Shan-Chen method, the He-Chen method, and an extension to the He-Chen method. We carefully document our methodology and discuss relevant kinetic theory and fluid dynamics. We present results for a number of fundamental flow problems including droplet impingement on solid and liquid surfaces as well as multiphase flow in complex micro-channels. In addition, we examine in great detail the problem of axial droplet migration and deformation in a square-duct at moderate Reynolds number. Our results suggest that the LBM algorithm is capable of simulating a wide range of flows and can accurately capture flow physics provided the density ratio among fluid phases is not large. Because ACRC equipment often harbor high density ratio flows, the standard LBM procedures require modification to accommodate higher density ratio problems. We investigate one such modification to the He-Chen algorithm by introducing a pressure Poisson equation (PPE) to reduce density variation related to compressibility effects

    Teaching and Learning of Fluid Mechanics

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    This book contains research on the pedagogical aspects of fluid mechanics and includes case studies, lesson plans, articles on historical aspects of fluid mechanics, and novel and interesting experiments and theoretical calculations that convey complex ideas in creative ways. The current volume showcases the teaching practices of fluid dynamicists from different disciplines, ranging from mathematics, physics, mechanical engineering, and environmental engineering to chemical engineering. The suitability of these articles ranges from early undergraduate to graduate level courses and can be read by faculty and students alike. We hope this collection will encourage cross-disciplinary pedagogical practices and give students a glimpse of the wide range of applications of fluid dynamics
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