User:James Fitzgerald

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I am an undergraduate majoring in physics and mathematics. I work on computational and theoretical aspects of protein folding with Professors Sosnick and Freed.

My primary research interest has been the dynamics of proteins. My first project was to investigate the fundamental local motions of proteins. Through numerous simulations we find a fundamental anticorrelation between the motions of the phi torsion angle of the ith residue and the psi angle of the (i-1)st residue. This motion is accomplished through the rocking of the rigid peptide group. This motion is independent of solvent model, force field, and is seen both in the presence and absence of long range interactions. This fundamental local motion is robust enough to describe both equilibrium fluctuations and basin transitions. No longer range correlations are necessary in either type of motion to conserve the global structure of the peptide.

More recently I have been studying the fundamental motions of proteins by investigating topological constraints in protein folding. Using a mixture of classical differential geometry, knot theory, and computer simulations I am attempting to delineate the conditions under which certain conformational transitions of proteins are probable (or even possible). This is a work in progress, but interesting progress and been made and further results will follow when available.