Kramers Theory for Conformational Transitions of Macromolecules

TL;DR

This paper applies Kramers theory to calculate conformational transition rates in macromolecules, introducing a method to identify transition states without predefined reaction coordinates, validated through molecular dynamics simulations.

Contribution

It presents a novel approach to locate transition states along the most probable pathway, enabling microscopic rate calculations without prior reaction coordinate assumptions.

Findings

Successfully identifies transition states in complex configuration spaces.

Accurately computes activation energies and rate constants.

Validated results against molecular dynamics simulations.

Abstract

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.