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 583 for “"molecular dynamics simulations"”.
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GPU-Optimized Molecular Dynamics Simulations
Protein and RNA biomolecular folding and assembly problems have important applications because misfolding events are associated with diseases like Alzheimer's and Parkinson's. However, simulating biologically relevant sized biomolecules on timescales that correspond to biological functions is an …
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Molecular dynamics simulations of polyelectrolyte brushes
… charged polyelectrolyte brushes. Extensive molecular dynamics simulations are performed on different polyelectrolyte brush systems using local compute servers and massively parallel supercomputers. The full Coulomb interaction of charged monomers, counterions, and salt ions is treated …
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Performance Engineering of Reactive Molecular Dynamics Simulations
Reactive molecular dynamics is the best-performing option for simulating chemical systems on the order of thousands of atoms, but its high computational cost often limits the temporal scale of simulation. In order to observe scientific phenomena of interest, we need implementations of interatomic …
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Study of Nanowires Using Molecular Dynamics Simulations
… nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by observing grain sizes over time for temperatures from …
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Molecular-dynamics simulations of polymers in a solvent
Molecular-dynamics simulations were carried out for linear, flexible polymers in a solvent environment. Both static and dynamic properties were calculated for polymer chains of 8, 16, 24, 32, and 40 monomers in length. The effects of solvent density on the diffusion coefficient, the average radius …
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CNT-reinforced polymer nanocomposite by molecular dynamics simulations
… interactions in the interfacial region and local molecular changes in polymer due to the vicinity of the CNTs. Strong adhesive interactions between the matrix and CNT leads to good compatibility preventing the aggregation of the reinforcements and results in optimal mechanical response. Even …
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Coarse-Grained Molecular Dynamics Simulations of Macromolecular Complexes
"Molecular dynamics simulations provide critical insights into molecular mechanisms underlying cellular processes. Most such processes, however, remain out of reach, due to large system sizes and long time scales involved. This thesis describes molecular dynamics simulations of large macromolecular …
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Analysis of Molecular Dynamics Simulations of Protein Folding
Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over …
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Molecular dynamics simulations of calamitic and discotic liquid crystals
… liquid crystal phases using the Monte Carlo and molecular dynamics simulation techniques. We describe the technique of molecular dynamics in the microcanonical ensemble that we have used in simulations of liquid crystal systems. A review and discussion of some of the important simulations that …
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Scale-bridging molecular dynamics simulations of plasma-surface interactions
… the material. In this dissertation, atomic scale simulations coupled with micromechanics models are used to study the patterning of graphene and the ablation of thermal protection systems resulting from controlled and erosive plasma-surface interactions, respectively. Scalable and precise …
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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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A study of Asphalt Aging Behavior Using Molecular Dynamics Simulations
… change due to the difficulties of studying the molecular structures and their dynamic behavior in asphalt. Therefore, Molecular Dynamics (MD) simulation method is used in this study to understand how the chemical composition and property changes of asphalt after oxidative aging affect the …
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Interactions of Proteins with Membranes: Insights from Molecular Dynamics Simulations
… processes, including signal transduction, molecular transport, and cell recognition. Due to their involve- ment in fundamental physiological functions and their relevance as pharmacological targets, understanding their structure and dynamics is of paramount importance. However, experimental …
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Molecular Dynamics Simulations Provide Insight into Stability of Hyperthermophilic Endoglucanases
… utilize in the hydrolytic process. In this study molecular dynamics simulations were performed on structurally similar endoglucanases with varying levels of thermostability to gain insight on what factors contribute to thermostability in endoglucanases. RMSD, RMSF, PCA, hydrogen bonding and salt …
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Molecular dynamics simulations of pressure shocks in liquid phase nitromethane
… have been investigated by nonequilibrium molecular dynamics methods using a previously developed, fully flexible NM force field (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. J. Phys. Chem. B 2000, 104, 8406). Generally good qualitative agreement with the corresponding experimental values …
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Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations
<p>Molecular dynamics (MD) simulation has been widely used in understanding the physical basis of the structure and function of biological macromolecules. However, its application in pharmaceutical research is still at an early stage. This dissertation attempts to establish the use of MD simulation …
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Molecular Dynamics Simulations In The Study Of Biological Lipid Membranes
Molecular dynamics simulations solve Newton’s equations of motion for a system of interactingatoms using the energy gradient calculated from a potential function which describes the system of atoms. Subsequently, the trajectories generated from the classical mechanical calculations are used to gain …
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