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

  • 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


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)