Relaxation folding and the principle of the minimum rate of energy dissipation for conformational motions in a viscous medium

Abstract

A numerical simulation of the folding of a model polymer chain of 50 units with valence bonds of a fixed length and fixed valence angle values has been performed using the strong friction approximation. The rate of energy dissipation in the system has been analyzed for conformational motions along a trajectory determined by the equations of mechanics and the trajectories characterized by random and variable deviations from the mechanical path. The validity of the principle of the minimum average rate of the energy dissipation for the conformational relaxation of a macromolecule in a viscous medium has been demonstrated. A profile of the relaxation energy funnel for the folding of a macromolecular chain has been constructed. Slow and rapid stages of folding could be distinguished in the energy funnel profile; the final state was separated from the nearest conformations of the folded chain by an energy gap.