Dissertation/Thesis Abstract

Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation
by Votapka, Lane William, Ph.D., University of California, San Diego, 2016, 280; 10062341
Abstract (Summary)

Computational tools provide the automation and power that enable detailed modeling and analysis of many biomolecular phenomena of interest. Open source programs and automated tools empower researchers and provide opportunities for improvement to existing software. In the past few years, I have developed several open-source scientific software packages for the purposes of automating difficult or menial tasks pertaining to computational biophysics. These software packages involve the analysis of molecular dynamics simulations, Brownian dynamics simulations, electrostatics, pocket volume measurement, solvent fragment mapping, binding site characterization, milestoning theory, and allosteric network communications. In addition to allowing my research group and me to approach biomedical challenges that would otherwise be intractable, I hope and intend that these tools will be useful to the computational and theoretical biophysics research community.

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Indexing (document details)
Advisor: Amaro, Rommie E.
Commitee: Amaro, Rommie E., Ghosh, Partho, McCammon, James A., Norman, Michael, Toor, Navtej, Weare, John
School: University of California, San Diego
Department: Chem w/Spec Computational Sci
School Location: United States -- California
Source: DAI-B 77/08(E), Dissertation Abstracts International
Source Type: DISSERTATION
Subjects: Chemistry, Bioinformatics, Biophysics
Keywords: Brownian dynamics, Computational biophysics, Milestoning, Molecular dynamics, Multiscale modeling, Scientific computing
Publication Number: 10062341
ISBN: 9781339577159
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