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ASU Electronic Theses and Dissertations


This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.

In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.

Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.


This study aims to address the deficiencies of the Marcus model of electron transfer (ET) and then provide modifications to the model. A confirmation of the inverted energy gap law, which is the cleanest verification so far, is presented for donor-acceptor complexes. In addition to the macroscopic properties of the solvent, the physical properties of the solvent are incorporated in the model via the microscopic solvation model. For the molecules studied in this dissertation, the rate constant first increases with cooling, in contrast to the prediction of the Arrhenius law, and then decreases at lower temperatures. Additionally, the polarizability of …

Contributors
Waskasi, Morteza, Matyushov, Dmitry, Richert, Ranko, et al.
Created Date
2019

Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects …

Contributors
Spiriti, Justin Matthew, Van Der Vaart, Arjan, Chizmeshya, Andrew, et al.
Created Date
2011

Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the …

Contributors
Barr, Daniel, Van Der Vaart, Arjan, Matyushov, Dmitry, et al.
Created Date
2011