Computer simulations allow researchers to study the dynamics and interactions of biological molecules in ways that cannot be currently achieved in experiments. In this work, I have used computer simulations to study the following systems: (1) carbohydrate-carbohydrate and carbohydrate-amino acid interactions using all-atom molecular dynamics simulations, and (2) protein-protein interactions using coarse-grained implicit solvent models. My first studies involved simulating carbohydrate and amino acid systems using atomistic force fields. During my initial simulations, I observed that carbohydrates were interacting too favorably leading them to aggregate in conditions under which they experimentally remain soluble. To alleviate this issue, I surgically modified the carbohydrate-carbohydrate interaction parameters in order to match osmotic pressure data from experiment. This approach was successful while preserving many of the correct features of the original force field. Next, I observed similar issues in carbohydrate-amino acid simulations and used the same methodology to correct carbohydrate-amino acid parameters. I showed that the modified parameters also worked well in simulations of much larger systems, allowing realistic simulations to be performed on polymeric sugars such as dextran and the peptidoglycan layer of the cell wall. In a more recent and separate study, I have attempted to parameterize very coarse-grained models of proteins (for eventual use in cellular scale simulations) using experimental osmotic second virial coefficients. I found that a 10 residue-per-bead model including electrostatic interactions could approximately match most of the second virial coefficient data obtained from experiment. In contrast, a more simplified, spherical model of proteins could not adequately reproduce experiment. Although more work will be required to establish a better quantitative agreement with experiment, my results indicate that even very coarse models of proteins can produce reasonably accurate simulations of protein-protein interactions.

Typescript (Photocopy) Bibliography: leaves vii-xiv. (second sequence)

Thesis (Ph. D.)--University of Nevada, Reno, 2005. / "December 2005." Includes bibliographical references. Online version available on the World Wide Web.

In this study, the molecular dynamics simulation method was used to investigate the mechanical properties of non-crystalline PEEK mixed with SiO2 nanoparticle. It is found the SiO2/PEEK nano-composite has higher mechanical properties in comparison with pure PEEK composite. Therefore, we wish to obtain the reason. The radial distribution function was used to explain the conformation of the change of microstructure and mechanical properties. The parametric study of different SiO2 particle size was discussed, such on the effects on the structure of PEEK and the strength of the structure.

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Abstract This study is to examine the phenomena caused by rolling action of a nano-particle against the work surface. The analysis was done by the molecular dynamics method. The distributed computing scheme was adopted in these simulations to increase the computing efficiency. The study includes the interfacial force between the nano-particle, the work and the roughness of the work surface, and the damage layer thickness of the work surface. It is done by first identifying the main factors, and then to understand how the phenomena is affected by these factors. Finally, the results of these simulations were discussed. The results show that the interactive force most comes from the breaking process between the work surface and the nano-particle. When the nano-particle¡¦s rolling speed is increased, the interactive force is enhanced. But if the speed has reached a high value, the interactive force will be saturated. The interactive force is not significantly affected by temperature. When the adhesive strength between the nano-particle and the work is higher, the interactive force is higher. The roughness of the work surface is affected by the rolling speed of the nano-particle, the temperature, and the adhesive strength between the nano-particle and the work. If the temperature or the interactive force is higher, the roughness of the work surface is higher. If the rolling speed is higher, the roughness of the work surface will increase. But if the rolling speed has reached a high value, the roughness of the work surface will not increase. The damage layer thickness of the work surface is little affected by the rolling speed of the nano-particle or temperature or the adhesive strength between the nano-particle and the work surface.

Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 94-99). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of Texas at Austin, 2003. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 118-126).

Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Ludovice, Pete; Committee Member: Chen, Rachel; Committee Member: Harvey, Steve; Committee Member: Sambanis, Athanassios; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.