Dynamics of polymer chain collapse into compact states

TL;DR

This study uses molecular dynamics simulations to investigate how polymer chains fold into compact cubic states, revealing how native-state organization influences folding success and pathways.

Contribution

It introduces a detailed simulation approach to analyze the effects of native-state packing and chain length on polymer folding mechanisms.

Findings

Native-state organization affects folding success

Contact maps reveal folding pathway details

Chain length influences folding dynamics

Abstract

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional interactions. Different native-state packing arrangements and chain lengths are explored; the organization of the native state is found to affect both the ability of the chain to fold successfully and the nature of the folding pathway as the system is gradually cooled. An order parameter based on contact counts is used to provide information about the folding process, with contacts additionally classified according to criteria such as core and surface sites or local and distant site pairs. Fully detailed contact maps and their evolution are also examined.