Thesis & Dissertation


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Thesis and Dissertation

The following Masters Thesis and Doctoral Dissertations were completed with assistance from the WFU DEAC Computational Cluster.


Ph.D Dissertations

    • Ph. D. Thesis by Nicholas Lepley, in partial fulfillment of the Wake Forest University requirements for the Doctor of Philosophy in Physics (December 2015) — “First Principles Investigations of Solid-Solid Interfaces in Lithium Battery Materials”.
    • Xu Xiao, “Orbital dependent functionals: An atom projector augmented wave method implementation”, PhD Physics (2011)
    • Ye Yuan, “Studies of the Electrostatic Properties of Peroxiredoxins”, PhD Physics (2009)
    • Jason Grigsby, “Analyzing and Improving Initial Data for Binary Black Holes”, PhD Physics (2009)
    • William Hirsch, “Quantum Effects of the Massles Spin One-Half Field in Static Spherically Symmetric Black Hole and Wormhole Spacetimes”, PhD Physics (2009)
    • William Hodge, “Constrained Variational Calculation of Second-Order Reduced Density Matrices for Hubbard Rings”, PhD Physics(2008)
    • Doug Bonessi, “Optical Forces and Torques: Theory and Experiment”, PhD Physics (2008)
    • Kevin Conley, “A Dirac All-Electron Basis and Spin-Orbit Coupled Projector Implementation of the Projector Augmented Wave Method for Atomic Systems”, PhD Physics (2008)
    • Matthew Rave, “Aspects of Berry’s Phase in Solid State Physics”, PhD Physics (2007)
    • Blythe Ashcraft, “Carbon-Hydrogen Stretching Vibrational Transitions:Experimental and Computational Studies”, PhD Chemistry (2007)
    • Ping Tang, “Computational Research on Lithium-Ion Battery Materials”, PhD Physics (2006)
    • Michael Budiman, “DNA specificity and biological impact of a platinum acridinylthiourea conjugate”, PhD Chemistry (2006)
    • Yonas Abraham, “Electronic states near surfaces — a) Analysis of calculation methods using semi-infinite boundary conditions; b) Sensitive detection using laser photoelectron spectroscopy”, PhD Physics (2004)
    • Guanghui Lei. Physics (1998-2004)
    • Andrew Graham, “Nucleation Rates for One-Dimensional Stochastic Systems with Asymmetric Quartic Potentials, Brownian Noise and Damping”, PhD Physics (1999)

Masters Thesis

    • Riana Freedman, MS Computer Science, “A Comparative Assessment of Methodologies for Solving Problems of Nonlinear Optimization in the Business Sector.”, 2017
    • Undergraduate honors thesis by Hannah Zhang, in partial fulfillment of the Wake Forest University requirements for graduation with Honors in Physics (May 2015) — “Computational Modeling of Li Diffusion Using Molecular Dynamics”
    • David Evanich, MS Physics “Aspects of Parametric Resonance in Chaotic Inflation”, 2006
    • Jason Fye, MS Computer Science, “Elucidation of Transcriptional Regulatory Relationships via Information Theoretic Clustering and Consensus Nucleotide Motif Extraction”, 2008
    • Richard T. Guy, MA Computer Science, “Machine Learning for Biostatistians: A Hypothesis Driven Approach”, 2010
    • Ryan Huff, MS Computer Science, “Active site profiling for identification of functional sites in protein sequences and stuctures”, 2005
    • M. Graham Lopez, MS Computer Science “A Computational Method to explore the time-evolution of protein cavities”, 2008
    • Amy Olex, MS Computer Science, “Development of novel microarray analysis tools and application to a dendritic cell maturation time course experiment”, 2007
    • Edward Pryor, MS Computer Science, “PASSS: Protein Active Site Structure Search”, 2006
    • Satria Sajuthi, MS Computer Science, “Refinement of Subnetwork Discovery Algorithm for Biological Networks”, 2010
    • Huan Tan, MS Computer Science, “Active Site Profile Scoring With Protein Features”, 2006
    • Yuhe Wang, MS Chemistry, “A COMPUTATIONAL STUDY OF KETO-ENOL EQUILIBRIA OF CATECHOL IN GAS A ND AQUEOUS SOLUTION PHASE”, 2009

First Year Rotation Graduate Students

    • Akash Das, Biochemistry, “Molecular dynamic simulation reveals deviation from the fully folded conformation around peroxidatic cysteine in the reduced structure of Tryparedoxin Peroxidase” (2004)
    • Michael Murray, Biochemistry, “Simulation of the Thermal Unfolding Pathway of Two Homologous Protease Inhibitors at Multiple Temperatures” (2005)