Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

Details Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

1997-11-22

arxiv.org/abs/cond-mat/9711230v1

Physics

Condensed Matter

Statistical Mechanics

9 pages RevTeX, 3 eps-figures included, submitted to PRL

Scientific paper

10.1103/PhysRevLett.80.5015

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.

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