Kramers Theory for Conformational Transitions of Macromolecules

Details Kramers Theory for Conformational Transitions of Macromolecules Kramers Theory for Conformational Transitions of Macromolecules

2008-08-29

arxiv.org/abs/0809.0027v1

Biology

Quantitative Biology

Biomolecules

4 pages, 3 figures

Scientific paper

We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space. We present a method which identifies the transition state along the most probable reaction pathway. It is then possible to microscopically compute the activation energy, the damping coefficient, the eigenfrequencies at the transition state and obtain the rate, without any a-priori choice of a reaction coordinate. Our theoretical results are tested against the results of Molecular Dynamics simulations for transitions in a 2-dimensional double well and for the cis-trans isomerization of a linear molecule.

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