Ph.D Dissertations

• 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)
• Blythe Ashcraft, "Carbon-Hydrogen Stretching Vibrational Transitions:Experimental and Computational Studies", PhD Chemistry (2007)
• Michael Budiman, "DNA specificity and biological impact of a platinum acridinylthiourea conjugate", PhD Chemistry (2006)
• 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)
• Andrew Graham, "Nucleation Rates for One-Dimensional Stochastic Systems with Asymmetric Quartic Potentials, Brownian Noise and Damping", PhD Physics (1999)
• 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)
• Guanghui Lei. Physics (1998-2004)
• Matthew Rave, "Aspects of Berry's Phase in Solid State Physics", PhD Physics (2007)
• Ping Tang, "Computational Research on Lithium-Ion Battery Materials", PhD Physics (2006)
• Ye Yuan, "Studies of the Electrostatic Properties of Peroxiredoxins", PhD Physics (2009)

Masters Thesis

• 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 AND 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)