Faculty Advisor

Stroe, Izabela RC

Abstract

Protein misfolding results in a wide range of highly debilitating and increasingly prevalent diseases. Despite success in atomic protein folding simulations, timescales for results are long and hinder research into the stochastic folding process. Performing Langevin dynamics simulations with NAMD on amino acids shows that atoms within the amide and carboxyl groups remain rigid enough to suggest motion of the amino acid can be characterized by these two groups. Ramachandran plots verify this when compared to those from experimental literature for glycine. Early results suggest that it is possible to reduce the number of computational elements in protein folding simulation by rescaling the physical analysis to the atom groups.

Publisher

Worcester Polytechnic Institute

Date Accepted

April 2013

Major

Physics

Project Type

Major Qualifying Project

Accessibility

Unrestricted

Advisor Department

Physics

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