Physical Sciences and Mathematics Commons^™

Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal

All Dissertations

Molecular dynamics (MD) simulations were carried out for aqueous dipeptides, water over self-assembled monolayer (SAM) surfaces, and the nicotinic acetylcholine receptor (nAChR) ion channel. The main goal is to use advanced methods to increase the accuracy of molecular dynamics simulations while seeking solutions to problems relevant to chemistry, biophysics and materials science. In addition, activation energies of several cyclodimerization reactions were studied quantum mechanically. The simulations of the aqueous dipeptides and SAM surfaces involve modeling and detailed analysis of interfacial water, which is of interest to a range of fields from biology to materials science. For example, water has a …

Hybrid Lattice Boltzmann - Molecular Dynamics Simulations With Both Simple And Complex Fluids, Frances E. Mackay

Electronic Thesis and Dissertation Repository

The behaviour and properties of colloidal suspensions strongly depend on the interactions arising between the immersed colloidal particles and the solvent. However, modelling such interactions is not at all straightforward; the larger time and length scales experienced by the colloidal particles compared to the solvent molecules makes all-atom molecular dynamics (MD) simulations of such systems completely impractical. Therefore a coarse-grained representation of the fluid is required, along with a method to couple this fluid to the colloidal particles.

In the first part of this thesis, we propose a new method for coupling both point and composite MD particles to an …

Advanced Optimization Techniques For Monte Carlo Simulation On Graphics Processing Units, Eyad Hailat

Wayne State University Dissertations

The objective of this work is to design and implement a self-adaptive parallel GPU optimized Monte Carlo algorithm for the simulation of adsorption in porous materials. We focus on Nvidia's GPUs and CUDA's Fermi architecture specifically. The resulting package supports the different ensemble methods for the Monte Carlo simulation, which will allow for the simulation of multi-component adsorption in porous solids. Such an algorithm will have broad applications to the development of novel porous materials for the sequestration of CO2 and the filtration of toxic industrial chemicals.

The primary objective of this work is the release of a massively parallel …

Computational Approaches To Anti-Toxin Therapies And Biomarker Identification, Rebecca Jane Swett

Wayne State University Dissertations

This work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data.

Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and …

Non-Equilibrium Melting And Sublimation Of Graphene Simulated With Two Interatomic Potentials, Brad Steele

USF Tampa Graduate Theses and Dissertations

The mechanisms of the sublimation of graphene at zero pressure and the condensation of carbon vapor is investigated by molecular dynamics (MD) simulations. The interatomic interactions are described by the Reactive Empirical Bond Order potential (REBO). It is found that graphene sublimates at a temperature of 5,200 K. At the onset of sublimation, defects that contain several pentagons and heptagons are formed, that are shown to evolve from double vacancies and stone wales defects. These defects consisting of pentagons and heptagons act as nucleation sites for the gaseous phase. The influence of the interatomic interactions on the sublimation process are …