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 196 for “"molecular dynamics (MD) simulations"”.
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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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Theoretical Studies of the Solvation, Dynamics, and Photochemistry of Ethylene, Retinal Protonated Schiff Base, Oligocellulose, and Gd(III) Clusters
The solution dynamics of an anomerically pure series of cellulose oligomers have been studied by 13C NMR relaxation techniques and compared to molecular dynamics (MD) simulations. We found evidence of anisotropic motion across the series, with experimentally determined order parameters (S 2) …
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Computer simulations of Fréchet dendrimers in solutions
The structure and dynamics of dendrimers in solution are studied 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 …
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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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Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly
A major goal in molecular biophysics is to understand how biomolecules fold into specific structures to carry out cellular processes to result in a functioning organism. Computational molecular dynamics (MD) simulations can characterize biomolecules at a microscopic level. These indispensable …
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Molecular dynamics simulation of mechanical behavior of nanoporous copper foams
… behavior of nanoporous copper was simulated. Molecular dynamics (MD) simulations were performed at room temperature using the Mishin potential on tetrakaidecahedron foam structures. In closed-celled foams close agreement is observed between simulated Young's moduli and constitutive theory. …
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Atomistic engineering of fluid Structure at the fluid-solid interface
… scale is comparable to the fluid's internal (molecular) length scale. Elucidating the physical principles governing nanoconfined fluids is critical for many pursuits in nanoscale engineering. In this thesis, we present several theoretical and computational results on the structure and …
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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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Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations
… leading fields is computational 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 …
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From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation
Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake …
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Graphene/Oxide Interactions with Polymer Networks Modeled Using Molecular Dynamics
… with most polymeric networks. This work used Molecular Dynamics (MD) simulations to demonstrate dispersion of graphene platelets within PMCs is inhibited by molecular surface charge potentials. Further simulations were conducted to demonstrate functionalized forms of graphene, specifically …
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Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations
… In this thesis, 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 …
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The Kinetics of Ni/Al Reactive Intermetallic Composites
Molecular dynamics (MD) simulations have been used to study the underlying physics and atomistic mechanisms of the reaction progression in Ni/Al reactive intermetallic composites. Preparation of these composites, either through deposition techniques or through the process of mechanical ball …
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Correlated long-distance dynamics modulate monoclonal antibody binding resistance in flaviviral envelope pretein domain-3: A molecular dynamics simulations study
… are characterized by perturbation of residue dynamics at the binding interface and at regions physically far from the binding site. Based on above I hypothesized that mutations leading to resistance from antibody binding would perturb dynamics associated with binding at the interface and …
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Atomic-level characterization of protein-lipid interactions using molecular dynamics simulations
… of these systems remains a challenging task. Molecular dynamics (MD) simulations offer a suitable approach to study protein–lipid interactions with high spatial and temporal resolution. Here, we present a summary of recent applications of MD simulations to study the interaction of different …
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Investigation of Distribution and Transport of CO2 in Polyimine/MCM-41 Hybrid System: Modeling and Simulation Approach
… including First Principles Calculations and Molecular Dynamics (MD) simulations, to understand molecular behaviors in the CO2 capture processes. This involves the development of new force field parameters to accurately describe interactions between CO2, water, amine groups, and silica …
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Investigation of the interaction of water with the calcite {1014} surface using ab-initio simulation
… state 1.77eV higher in energy was found. Molecular dynamics (MD) simulations of low water coverage reveal fluctuations in the H-O water bond when the H atom is directed towards a surface CO3 ion. Desorption of an H2O molecule was observed in simulations above 900K. Water was found to be …
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Theoretical and computational modeling of peptide-lipid bilayer interaction studied by dynamic force spectroscopy
… lipid and polar E. Coli membranes. Furthermore, molecular dynamics (MD) simulations are used to explored the conformational dynamics of SecA2-11 during its interaction with both POPC and anionic POPG lipid bilayers. (3) Finally, MD simulations are used to explore the conformational dynamics and …
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Design, Fabrication, and Characterization of Metals Reinforced with Two-Dimensional (2D) Materials
… is studied using experimental techniques and molecular dynamics (MD) simulations.
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