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Noah Benson

Graduated: November 1, 2010

Thesis/Dissertation Title:

Computational Methods for the Analysis of Molecular Dynamics Simulations

Proteins are macromolecules that are involved in virtually every biological process and structure. The three-dimensional structure of these molecules is extremely important as a window into how they work but is extremely difficult to predict, as direct observation of their motion and the folding pathway is possible only through very limited experimental techniques. Nonetheless, observing protein structure alone has proven insufficient for understanding how proteins fold or behave natively. Molecular dynamics (MD) is a computational technique by which protein dynamics can be examined at resolutions well beyond the capabilities of experiment. The decrease in cost of computer resources have lead biologists to turn to MD more frequently in recent years, yet MD simulations produce data in quantity and complexity well beyond the capabilities of conventional biological analysis techniques. We have curated a database of protein native-state and thermal unfolding simulations, which is the largest database of unfolding simulations to date. We examine this database using two existing and three novel analysis methods and demonstrate the utility of each for high throughput analysis. Finally, we demonstrate that these methods can be used to generate and support novel hypotheses concerning protein motion.

Last Known Position:

Postdoctoral Fellow, University of Pennslyvania


Valerie D. Daggett (Chair), James F. Brinkley III, Peter J. Myler, Walter L. Ruzzo (GSR)