Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 34 for “"potential of mean force"”.
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Elastic properties and failure behavior of disordered porous solids : a potential-of-mean-force-based lattice element approach
The effective mechanical properties of multiphase materials not only depend on the volume fraction and chemical composition of their constituents but also on details of their local texture. Yet, most homogenization methods do not take this texture effect into account. Understanding how local …
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Theoretical Studies of Particle/Polymer Mixtures
This thesis reports a theoretical study of polymers in the presence of particles. An analytical theory is used to describe the potential of mean force between spheres for the case where the polymer molecular weight dispersity is described by the Schulz-Flory distribution. Exact results are derived …
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
This thesis explores the issue of calculating potentials of mean force (an equilibrium property) from steered molecular dynamics simulations (a nonequilibrium process). Recently discovered Jarzynski's equality provides the theoretical basis. Derivations of Jarzynski's equality are reviewed and …
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Simulations of carbohydrate conformational dynamics and thermodynamics
… employed to establish the conformation freedom of selected carbohydrates. The focus is on the biologically important (1-4)-linked glucans, although the α(1-1) α and α(1-6) linkages are also investigated. Two principal types of potential of mean force (PMF) caltulation are used: free energy …
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
The machinery of life is composed of molecules such as DNA and proteins. Technology has brought us today to the stage where one can investigate biomolecules at the single-molecule level. Atomistic simulations and experimental techniques such as atomic force microscopy and optical tweezer have …
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Theoretical and computational studies of bio-molecular systems : structure and dynamics
… in this thesis is relevant for the study of structure, function and dynamics of complex bio-molecular systems. The thesis contains two parts related to (1) protein structure prediction, and (2) free energy profile calculations in nano-scale systems. The new contributions reported in this …
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Computational and experimental studies of collagen and related diseases
… that model both cleavage and noncleavage sites of collagen type III to study the stability and degradation of collagen as a function of amino acid sequence variation. Molecular Dynamics is used to compute the potential of mean force of these collagen-like peptides and predict their triple …
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Molecular-thermodynamic and simulation-assisted modeling of interfacial energetics
… at material interfaces control the efficiency of chemical engineering processes as diverse as adsorption, emulsification, heat exchange, and froth flotation. In particular, the process of colloidal self-assembly harnesses the rich tapestry of interactions that operate at several length scales, …
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Fluctuations and Instantons in Complex Landscapes: From Ligand Unbinding to Proton Transfer
… dominated by fluctuations on a hierarchy of timescales. These properties confound simulation of ligand binding and catalysis, inflating the scale of the problem to one tractable only with a considerable outlay of resources. In an attempt to ameliorate this restriction, several techniques …
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Interaction of amphiphilic nanoparticles with structurally perturbed lipid membranes
… simulations to demonstrate that the introduction of area asymmetry to a bilayer membrane significantly decreases the insertion latency of amphiphilic gold nanoparticles into both the densely and sparsely packed leaflets. We further demonstrate using transition state analysis that the dominant …
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Non-equilibrium Dynamics of Nanoscale Soft Matter Deformation
Life is soft. From the fluid-like structure of lipid bilayers to the flexible folding of proteins, the realm of nanoscale soft matter is a complex and vibrant area of research. The lure of personalized medicine, advanced sensing technology, and understanding life at a fundamental level pushes …
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Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens
In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes …
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Validation of the charge equilibration lipid force field for simulations of phospholipid membranes with an application to the study of the free energetics of methyl guanidinium permeation across a DPPC bilayer
… group focused on the development and refinement of po-larizable charge equilibration (CHEQ) force fields for use in molecular dynamics (MD) simulations of phospholipid bilayers. We present results to further validate these force fields by extending to simulations of a model DPPC-water monolayer. …
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Ion Pairing in Aqueous Metal Sulfates and Platinum Group Metal Ammonium Solutions
The structure and dynamics of ions and ion pairs in solution play an integral part in several biological and chemical processes. Historically the calculation of ion pair association constants from computer simulations has been complicated due to the difficulty in validating metal ion force fields …
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Electronic and solvent effects on monosaccharide conformations
The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, …
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Fragmentation of Charged Binary Clusters
Fragmentation of binary mesoscopic clusters composed of H2O/CH3OH and charged with ions (Na+, K+, Cs+,F^, Cl-, I-) of similar sign are studied by molecular simulation. The fragmentation involves the departure of a cluster containing one or more ions from the parent droplet by a break-down of the …
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Fast reverse osmosis through nanotube-based membranes: molecular dynamics study
"Development of nanotechnology had led to novel and advanced methods in various fields of science and engineering, and its influence extended to the progress of water purification process. Development of novel membranes and modification of existing membranes for efficient water filtration can be …
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Statistical mechanical theory of structure and miscibility of polymer nanocomposites: Effects of density, filler shape, and chemical heterogeneity
Motivated by increasing interest in various types of nanoparticles or fillers added to polymers to enhance the material properties, the Polymer Reference Site Interaction Model (PRISM) theory is applied to study the structure and miscibility of polymer nanocomposites (PNCs). Spherical fillers are …
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Electronic and solvent effects on monosaccharide conformations
The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, …
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Molecular Dynamics of Interfacial Phenomena at Air/ice, Air/water, and Air/salt Water Interfaces
The purpose of this research is to investigate the adsorption of organic contaminants, namely polycyclic aromatic hydrocarbons (PAHs) and green leaf volatiles (GLVs), as well as their interactions with reactive oxygen species (ROSs) on atmospheric air/water and air/ice interfaces. In another series …
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