Investigation on non-ergodicity of protein dynamics

TL;DR

This paper uses molecular dynamics simulations to investigate whether protein dynamics are non-ergodic, finding that apparent non-ergodicity results from incomplete convergence rather than true non-ergodic behavior.

Contribution

It challenges previous claims of non-ergodic protein dynamics by showing deviations are due to convergence issues, and discusses potential ergodicity breaking over larger timescales.

Findings

Deviations from ergodicity are due to incomplete convergence.

Simulations suggest proteins are ergodic over studied timescales.

Potential ergodic hypothesis breaking at larger time windows.

Abstract

The study of microscopic protein dynamics has historically presented significant challenges to researchers seeking to develop a comprehensive and detailed description of its diverse and intriguing features. Recent experimental and theoretical studies have proposed the hypothesis that protein dynamics may be non-ergodic. The implications of this finding are of paramount importance from both a practical and theoretical standpoint. In this study, we employ all-atom molecular dynamics simulations to examine these results over a time window spanning from picoseconds to nanoseconds. To this end, we utilize widely used statistical tools. Our findings challenge the conclusions of previous studies, which suggested that proteins exhibit non-ergodic dynamics. Instead, we demonstrate that deviations from ergodic behavior are due to incomplete convergence of the investigated quantities. Additionally, we discuss the implications of findings that suggest a potential breaking of the ergodic hypothesis over larger time windows, which were not directly investigated in this study.