Thesis (Ph. D.)--University of Pennsylvania, 1930.

In this thesis, we focus on theoretical investigations on metal interfaces where many heterogeneous chemical reactions take place. Surface-enhanced Raman scattering (SERS) spectroscopy and the modern electrochemical methods are important in-situ techniques that have been widely employed for a variety of applications. Theoretical simulations have become an indispensable tool to infer the molecular details of interfacial structures that are not directly accessible from experimental measurements. In this context, we have proposed several new theoretical models for both SERS and interfacial electrochemistry, which allow us to provide molecular-level understanding of the interfacial structures under the realistic experimental conditions.   The first part of the thesis has addressed the basic theory of SERS that offers the vibrational structure of the interfacial molecules. It is well known that the huge enhancement of Raman intensity in this technique can be attributed to two independent factors, namely the physical and chemical enhancements. The former is resulted from the enhanced electromagnetic field induced by the plasmonic excitations, while the latter comes from the changing of interaction between the molecule and the surface. The interplay between these two enhancement factors, which has long been an issue of debate, is revealed in this thesis. They are coupled through molecular polarizability. A practical computational approach is proposed and used to demonstrate the importance of the coupling on different molecular systems. It is found that for certain systems the coupling factor can be as large as 106. This finding is of great importance towards a comprehensive understanding of the SERS mechanisms and a quantitative prediction of the enhancement factor.   The other part of the thesis is devoted to the theory of interfacial electrochemistry, in particular the effects of water solution. A novel protocol that combines classical molecular dynamics (MD) and the first principles density functional theory (DFT) calculations is proposed to address the statistical behavior of interfacial properties. Special attention has been paid to the work function of Pt(111) surface and CO adsorption energy on Pt(111) surface in aqueous solution. It has been found that in this case the work function of Pt surface illustrates a surprisingly broad distribution under the room temperature, sheds new light on the understanding of reaction activity of the surface. The proposed protocol is able to provide results in very good agreement with experiments and should be applied routinely in future studies. / <p>QC 20120515</p>

Molecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively dry state for the DNA molecule. Simulations were performed at two different temperatures, 300 K and 450 K. The B-form DNA structure was shown to be stable at both temperatures. The analysis of hydrogen bonds between trehalose/water and DNA revealed that trehalose and backbone DNA formed the largest number of hydrogen bonds and thus constituted the major effect of structural protection for DNA. The number of hydrogen bonds formed by each OH group of trehalose with the backbone DNA was compared. Different types of trehalose-DNA interactions were analyzed, with no prevalent pattern recognized. Diffusion constants for trehalose and water were also calculated, suggesting a glassy/viscose state of the simulation system. It is believed that trehalose protects DNA in the dry state through the network of hydrogen bonds built by the sugars, which reduces the structural fluctuations of DNA and prevents its denaturation.

Thesis--Catholic University of America. / Bibliography: p. 81-85.

Thesis (Ph. D.)--University of Pennsylvania, 1943. / Bibliography: p. 195-197.

Thesis--Catholic University of America. / Includes bibliographical references (p. 61-65).

There are twenty standard amino acids that are the structural units of biomolecules and biomaterials such as proteins and peptide amphiphiles (PAs). The focus of this study was to develop accurate transferable coarse-grained (CG) models of those amino acids. In CG models, several atoms are represented together as a single pseudo-atom or "bead," which can allow the modeling of processes like self-assembly of biomolecules and biomaterials through reduction of degrees of freedom and corresponding increased computational speed. A 2:1 to 4:1 mapping scheme, in which a CG bead is comprised of two to four heavy atoms, respectively, and associated hydrogens, has been employed to represent functional groups in the amino acids. The amino acid backbone atoms are modeled as two beads while the side chains are modeled with one to three beads, and each terminus is modeled as one bead. The bonded parameters for the CG models were obtained from bond, angle, and dihedral distributions from all-atom molecular dynamics (MD) simulations of dipeptides. Non-bonded parameters were optimized using the particle swarm optimization (PSO) method to reproduce experimental properties (heat of vaporization, surface tension, and density) of analogues of the side chains, termini, and backbone groups of the amino acids. These CG models were used to study the self-assembly pathways and mechanisms of the PA c16-AHL3K3-CO2H in the presence of explicit CG water. / Master of Science / In this study, models of the amino acids were developed for computer simulations. In these models, the amino acids are represented as a collection of two or more “beads” bonded together rather than as a collection of atoms bonded together. The beads were created in such a way that their characteristics reflect those of the molecules and atom groups that they represent. This was accomplished in part by selecting parameters for each bead that approximately reproduce experimental properties (density, heat of vaporization, and surface tension) and structures (bonds and angles) of the molecules and atom groups of which they are representative. Amino acids can link together to form short segments, known as peptides, or longer chains that form proteins. The bead models that were developed in this study can be linked together in the same way. They can also be linked with other beads that represent other atom groups—carbon groups of a carbon chain, for example. Certain types of molecules known as peptide amphiphiles (PAs) are often composed of amino acids and a carbon chain. The amino acid bead models were created especially to study these molecules, so once the models were developed, they were used in computer simulations to represent PAs. Many types of PAs can automatically assemble into structures that resemble fibers, and it is this behavior in particular that was studied. By using these models in computer simulations, we are able to see things that cannot be seen in a lab with a microscope or other lab tools. This may help with future efforts to study and design molecules such as PAs which show promise for medical applications like drug delivery.

Thesis (M.A.)--Ohio University, June, 2006. / Title from PDF t.p. Includes bibliographical references (p. 85-96)

Thesis (M.A.)--George Mason University, 2008. / Vita: p. 163. Submitted in partial fulfillment of the requirements for the degree of Master of Arts in Anthropology. Title from PDF t.p. (viewed July 18, 2008). Thesis director: Rebecca Bryant. Includes bibliographical references (p. 157-162). Also issued in print.

Thesis (M.A.)--Ohio University, June, 2004. / Includes bibliographical references (p. 97-100).