Dynamically induced conformation depending on excited normal modes of fast oscillation

TL;DR

This paper investigates how fast oscillations in a bead-spring model influence molecular conformation, revealing that excited normal modes dynamically induce specific conformations through an effective potential.

Contribution

The authors develop a multiple-scale analysis method to derive an effective potential that accounts for fast spring oscillations affecting conformation.

Findings

Effective potential depends on excited normal modes.

Numerical verification confirms the theory.

Dynamically induced conformations emerge from fast oscillations.

Abstract

We present dynamical effects on conformation in a simple bead-spring model consisting of three beads connected by two stiff springs. The conformation defined by the bending angle between the two springs is determined not only by a given potential energy function depending on the bending angle, but also fast motion of the springs which constructs the effective potential. A conformation corresponding with a local minimum of the effective potential is hence called the dynamically induced conformation. We develop a theory to derive the effective potential by using multiple-scale analysis and the averaging method. A remarkable consequence is that the effective potential depends on the excited normal modes of the springs and amount of the spring energy. Efficiency of the obtained effective potential is numerically verified.