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Full-Text Articles in Physics

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega May 2013

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose ...


Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier Apr 2013

Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier

Bioelectrics Publications

Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that ...


Thermophysical Properties Study Of Graphene, Jingchao Zhang Jan 2013

Thermophysical Properties Study Of Graphene, Jingchao Zhang

Graduate Theses and Dissertations

Graphene is a two-dimensional (2D) material that exhibits exceptional electric and optical properties. The high electron mobility and thermal conductivity of graphene are of great interest for interconnects, electronic devices and radio frequency devices. In spite of the extensive experimental and theoretical studies on single layer graphene (SLG), its thermal properties have not yet been fully addressed and vast work need to be done to reveal the phonon transport mechanism within this micro/nanoscale material.

A transient molecular dynamics technique is developed to characterize the thermophysical properties of two-dimensional graphene nanoribbons (GNRs). By directly tracking the thermal relaxation history of ...


Organic Photovoltaics: A Charge Transfer Perspective In The Study Of Donor-Acceptor Systems, Marco Olguin Jan 2013

Organic Photovoltaics: A Charge Transfer Perspective In The Study Of Donor-Acceptor Systems, Marco Olguin

Open Access Theses & Dissertations

The present research involves the study of donor-acceptor (D/A) dyad complexes from a charge transfer energy perspective. The aim is to provide insight and predictive understanding into the charge transfer processes of the molecular-level components in donor-acceptor based organic solar cells using computational methods to describe photochemical processes at the quantum mechanical level within the Density Functional Theory (DFT) approximation. Predictive understanding is anchored in reproducing experimental results, wherein the present work a perturbative excited-state DFT method is described in detail and shown to give Charge Transfer (CT) energies in excellent agreement with benchmark experimental data. With an accurate ...