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 37 for “"molecular dynamics (MD) simulation"”.
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Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning
Molecular dynamics (MD) simulation is the workhorse of various scientific domains but is limited by high computational cost. Learning-based force fields have made major progress in accelerating ab-initio MD simulation but are still not fast enough for many real-world applications that require …
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Nanoscale control in biological and synthetic systems
… study. The “computational microscope” of the molecular dynamics (MD) simulation method provides insight into the behavior of systems at the atomic level, enabling the visualization of systems far beyond the limits of any experimental method. Moreover, MD facilitates experimentation with a …
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Study of slow dynamics in supercooled water by molecular dynamics and quasi-elastic neutron scattering
The slow dynamics of supercooled water is studied by modelling the spectrum of test particle fluctuations: intermediate scattering function (ISF). The theoretical models are compared with experimental measurements by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation …
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Development of Thin-Film Composite Membranes Incorporated With Graphene Oxide and Derivatives for Forward Osmosis Processes
… was investigated both experimentally and using molecular dynamics (MD) simulation. GQDs decreased the IP reaction rate by reducing the diffusivities of PA monomers, reduced water permeability by acting as barriers to water molecules when present at a high concentration near the PA surface, and …
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Atomistic Study of Grain Boundary Sliding
… of the threshold stress for sliding. Molecular Dynamics (MD) simulation performed by Qi and Krajewski establish a linear fit to the constitutive response which gives a sliding velocity of the order of km/sec. Their predicted threshold stress is 20 times the yield stress of the …
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Atomistic simulation of strength and deformation of ceramic materials
… and deformation of ceramic materials, utilizing molecular dynamics (MD) simulation that incorporates newly developed theoretical models and computational algorithms to probe the microstructural effects in crystalline, amorphous, and nanocrystalline media. Specific issues of a materials property …
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Molecular Dynamics Simulation of Forsterite and Magnesite Mechanical Properties: Effect of Carbonation on Comminution Energy
… forsterite (Mg2SiO4) and magnesite (MgCO3) using molecular dynamics (MD) simulation. The goal is to understand whether carbonation results in hardness reduction of rock and subsequently comminution energy during the crushing and processing of the ore. We investigated how these materials respond to …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; …
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Molecular understanding of osmosis and a multiscale framework to investigate confined fluid properties
… of osmosis. In this thesis, first, a molecular understanding of osmosis in uncharged and charged semi-permeable membranes is developed using Molecular Dynamics (MD) simulation studies. Specifically, we identify key inter-molecular forces that initiate osmosis in uncharged and charged …
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Computational investigation of membrane proteins across species and functional classes
… In this dissertation, I implement advanced molecular dynamics (MD) simulation workflows to investigate the conformational dynamics, substrate recognition, and lipid-mediated regulatory mechanisms of a diverse set of membrane-associated proteins across species and functional classes, spanning …
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Molecular Dynamics Study of Nano-confinement Effect on Hydrocarbons Fluid Phase Behavior and Composition in Organic Shale
… and challenge conventional macroscale reservoir simulation predictions. Moreover, the unusual high temperatures and pressures have increased the cost as well as the hazardous level for reservoir analyzes by lab experiments. Molecular Dynamics (MD) simulation of reservoirs can be a safe and …
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Hydration Mechanisms in Sulfonated Polysulfones for Desalination Membrane Applications
… the effects of water on these ionic polysulfones molecular dynamics (MD) simulation is used to investigate ion aggregation and hydration at the atomic scale. MD simulations show that the sulfonate and sodium ions are not simply paired. Instead, they form an ionic network. The molecular nature of …
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Effects of water on chemomechanical instabilities in amorphous silica : nanoscale experiments and molecular simulation
… atomic force microscope (AFM) bending tests, (b) molecular dynamics (MD) simulation and (c) molecular orbital (MO) simulation. Bending tests of silica nanowires provide validation for the predictions of the simulations, in which we study the failure of dry silica using MD and define a …
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Probing the conformational dynamics of amyloid oligomers in biologically relevant microenvironments
… microenvironment on amyloid conformational dynamics remains a large confounding factor in our understanding of oligomeric species. Amyloidogenic peptides are typically intrinsically disordered, and their conformational landscape is highly sensitive to aggregation conditions, like the …
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Establishing Faithful Simulation of Polar Surfaces in Contact with the Aqueous Phase
… by adsorbates. In this thesis, we will use molecular dynamics (MD) simulation to investigate the potential of an aqueous phase to stabilise several polar surfaces. Firstly, we address certain finite-size effects by using finite field Hamiltonians developed by Stengel, Spaldin and Vanderbilt …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… by drug applications, are both governed by biomolecular thermodynamics and kinetics. In order to make meaningful and efficient predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of association and dissociation of a protein-ligand …
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Computational Studies of Polyetherimides: Beyond All-Atom Molecular Dynamics Simulations
… properties, and chemical stability. All-atom molecular dynamics (MD) simulation is a useful tool to study polymers, but the accessible length and time scales are limited. In this thesis, we explore several computational methods that go beyond all-atom MD simulations to investigate …
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Developing a new interatomic potential and atomistic study of NiTiHf
… behavior of these HTSMAs. Computational simulations are a very cost-effective and feasible approach for addressing this shortcoming. Among computational methods, molecular dynamics (MD) simulation as an atomistic method offers comprehensive means to explore microstructural phenomena that …
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Multiscale Analysis of Macromolecular Systems
Molecular dynamics (MD) simulation serves as both a supplement to experiments and a predictive tool by revealing details inaccessible to current state-of-the-art experimental techniques. The relevant dynamics in complex macromolecular systems correspond to timescales longer than what can be sampled …
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Computational and Experimental Investigation of Allosteric Communication in the Transcriptional Regulator NikR
… that are involved in allostery, an equilibrium molecular dynamics: MD) simulation is utilized to explore the conformational dynamics of the NikR tetramer. This study includes advances in methods development focused on identifying signatures of allosteric communication in MD simulations. Using …
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