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 324 for “"MD simulations"”.
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Molecular dynamics modeling of normal shock waves in monatomic and polyatomic gas mixtures.
Large-scale molecular dynamics (MD) simulations using the Lennard-Jones potential are performed to study the structure of normal shock waves in dilute Nitrogen and mixtures of Helium-Argon and Helium-Xenon. The use of realistic MD simulations of normal shock waves promises to provide a more …
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Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations
… we use a combination of molecular dynamics (MD) simulations and experiments to gain insights into the hidden complexities of ESI-MS. The structure and reactivity of electrosprayed protein ions is governed by their net charge. In Chapter 2, we sought to uncover the mechanistic basis of …
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Nanoscale control in biological and synthetic systems
… 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 virtually unlimited …
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Combined computational and neutron scattering studies of hydrocarbons confined in mesoporous materials
Molecular Dynamics (MD) simulations and Quasi Elastic Neutron Scattering (QENS) experiments are used to investigate the dynamics of industrially relevant catalysis reactions. Despite the widespread industrial applications of mesoporous materials there is often little understanding of the dynamical …
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Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations
… biophysics where molecular dynamics (MD) simulations provide microscopic resolution details of how biomolecules move, fold, and assemble into intricate complexes that perform biological functions. However, it still remains a challenge to accurately perform MD simulations of …
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Molecular modeling of water and aqueous electrolytes under electric field: thermal, dielectric, and transport properties
… behavior remains a challenge in MD simulations. This study combines machine learning, and MD simulations to provide a computational study of water and electrolyte systems. To increase the predictive accuracy of the TIP4P water model, a machine learning-guided reparameterization …
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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 dynamic simulation of xenon bubble re-solution in uranium dioxide
… bubble re-solution in UO2 by molecular dynamics (MD) simulations: homogeneous re-solution and heterogeneous re-solution. For the homogeneous mechanism, a hybrid approach is employed whereby Monte Carlo (MC) simulations are used to obtain the full recoil energy spectrum of fission gas atoms, and MD …
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Computer simulations of Fréchet dendrimers in solutions
… through nanosecond atomistic Molecular Dynamics (MD) simulations of explicitly solvated Fréchet dendrimers, generations G1 to G5. The properties of these dendrimers are investigated in four solvent invironments: vacuum and water (representatives of poor solvents), and tetrahydrofuran (THF) and …
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Towards exact molecular dynamics simulations with invariant machine-learned models
Molecular dynamics (MD) simulations constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, one of the widely recognized and increasingly pressing issues in MD simulations is the lack of accuracy of underlying classical interatomic …
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Protein and RNA folding: from bulk towards high throughput single molecule experiments
… using experiments and molecular dynamics (MD) simulations. Firstly, the folding of an RNA hairpin has been looked at with the fluorescent probe 2-aminopurine. The effect of stem and loop dynamics have been separately analyzed. Motivated by MD simulations, a global four state energy …
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Effects of Background Ions on Polyethersulfone (Pes) Membrane Fouling by Natural Organic Matter (Nom)
… of supramolecular NOM clusters. Large-scale MD simulations with multiple NOM molecules were then performed to probe possible formation of supramolecular NOM structures or aggregates. The MD simulations revealed two different mechanisms of NOM aggregation. Calcium ions connect NOM molecules by …
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Molecular modeling and simulation of bacterial chemosensory arrays
… work, specifically all-atom molecular dynamics (MD) simulation and Molecular Dynamics Flexible Fitting (MDFF). In addition, two of the primary techniques used to analyze the MD simulations presented in this dissertation are sketched out, namely structural clustering based on root- mean-square …
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Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly
… organism. Computational molecular dynamics (MD) simulations can characterize biomolecules at a microscopic level. These indispensable tools use classical mechanical approaches to describe biomolecular dynamics, folding, and binding mechanisms. Although there are many different types of MD …
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GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations
Molecular Dynamics (MD) simulations provide a molecular-resolution picture of
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ASSESSING MUTATIONS IN A ZINC FINGER DOMAIN OF NF-κB ESSENTIAL MODULATOR (NEMO) USING MOLECULAR DYNAMICS SIMULATIONS
Molecular dynamics (MD) simulations permit the probing of biomolecular systems in
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Using molecular dynamics to probe protein conformational transition mechanisms at the membrane surface
… presented herein leverages molecular dynamics (MD) simulations as a method to explore and characterize the dynamics of both peripheral and integral membrane proteins in the context of the membrane. While MD simulations have unrivaled spatiotemporal resolution, the timescales accessible to MD …
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Molecular dynamics simulations and neural network solutions for applications in biophysics
… computational methods is molecular dynamics (MD) simulations. On the contrary, deep learning is a newly emerging family of methods that have only recently found success in the biophysics community. In this dissertation, I present several contributions to biophysics by employing both MD …
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Finite Opening of Propagating Shear Cracks
Molecular Dynamics (MD) simulations of shear-dominated crack propagation by Abraham and Gao (2000) showed that there was finite crack opening when the crack propagated at a sub-Rayleigh speed while the crack opening became negligible when the crack propagated faster than the shear wave speed. On …
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Computational Modeling of Claudin-15 Paracellular Channels
… This dissertation employs molecular dynamics (MD) simulations, reduced computational modeling, and cryo-electron tomography (cryo-ET) to address these gaps. Atomistic MD simulations of Cldn-15 strands in opposing plasma membranes demonstrated that lateral flexibility emerges from multiple …
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