Folding Kinetics of a Polymer

TL;DR

This study investigates the folding kinetics of a flexible homopolymer, revealing differences between effective and thermodynamic transition temperatures, and proposes a new way to quantify kinetic hindering using spectral analysis of the dynamical matrix.

Contribution

It introduces a novel approach to analyze polymer folding by comparing simulation methods and utilizing spectral properties as reaction coordinates.

Findings

Effective and thermodynamic transition temperatures differ.

Spectral analysis provides insights into folding and unfolding trajectories.

Proposes a new reaction coordinate based on the top eigenvalue.

Abstract

By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are different and we propose a way of quantifying the kinetic hindering. We then also observe that the top eigenvalue in the spectrum of the dynamical (contact or adjacency) matrix provides insight into the ensembles of folding and unfolding trajectories, and may be a suitable additional reaction coordinate for the folding transition of chain molecules.