Thesis (Ph.D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 113-118). Also available on the Internet.

Thesis (M.S.)--West Virginia University, 2006. / Title from document title page. Document formatted into pages; contains vii, 30 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 28-30).

Thesis (Ph.D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 113-118). Also available on the Internet.

Thesis -- Departmental honors in Computer Science. / Bibliography: ℓ. 73-74.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (p. 138-144).

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 218-233).

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, March 2001. / Includes bibliographical references. Also available on the Internet.

abstract: 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 ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase. / Dissertation/Thesis / Ph.D. Chemistry 2011

No description available.

Doctor of Philosophy / Department of Physics / Brett D. Esry / Strong-field ionization plays a central role in molecules interacting with an intense laser field since it is an essential step in high-order harmonic generation thus in attosecond pulse generation and serving as a probe for molecular dynamics through either the sensitivity of ionization to the internuclear separation or the laser-induced electron scattering. Strong-field molecular ionization has been studied both theoretically and experimentally, dominantly through the Born-Oppenheimer approximation and at equilibrium or small reaction distances. We have extended the theoretical studies of molecular ionization to a much broader extent. Specifically, due to the difficulty of treating ionization in Born-Oppenheimer representation especially for molecular dynamics involving strongly-correlated electron-nuclear motion, we have investigated an alternative time-independent--adiabatic hyperspherical--picture for a one-dimensional model of the hydrogen molecule. In the adiabatic hyperspherical representation, all the reaction channels--including ionization--for the hydrogen molecule have been identified in a single set of potential curves, showing the advantage of studying molecular dynamics involving multiple breakup channels coupled with each other. We have thus proposed a good candidate to study strongly-correlated molecular dynamics, such as autoionization and dissociative recombination. Moving to a time-dependent picture by numerically solving the time-dependent Schrödinger equation (TDSE), we have explored two extreme classes of strong-field ionization of hydrogen molecule ion: at large internuclear distances (R>30 a.u.) and for long-wavelength laser fields. Remarkably, we have found strong-field two-center effects in molecular ionization beyond the long-standing one-photon two-center interference as a manifestation of the double-slit interference. In particular, the total ionization probability at large internuclear distances shows strongly symmetry-dependent two-center dynamics in homonuclear diatomic molecules and two-center induced carrier-envelope phase effect in heteronuclear diatomic molecules. Such two-center effects are expected to generalize to other diatomic systems and could potentially be used to explain phenomena in multi-center strong-field physics. Moreover, we have theoretically confirmed, for the first time, the existence of low energy structure in molecular ionization in long-wavelength laser fields by solving the three-dimensional TDSE. Finally, we have performed a pump-probe study of the hydrogen molecular ion where a pump pulse first dissociates the molecule followed by a probe pulse which ionizes the dissociating wave packet, and surprisingly found a pronounced broad ionization peak at large R or large pump-probe delay (~150 fs). Numerically, we have developed and implemented new theoretical frameworks to more accurately and efficiently calculate quantum mechanical processes for small molecules--hydrogen molecule and its ion--which could readily be adapted to heavier diatomic systems.