Arrow of time and non-Markovianity in the non equilibrium folding/unfolding of alanine decapeptide in vacuo

TL;DR

This study uses non-equilibrium molecular dynamics to analyze the folding and unfolding of alanine decapeptide, verifying Crooks theorem and exploring non-Markovian effects with a bimodal distribution model, revealing universal and patent features.

Contribution

It introduces a bimodal distribution model to describe non-Markovian work distributions in peptide folding, validated by molecular dynamics simulations and Crooks theorem.

Findings

Crooks theorem is verified across all regimes.

Work distributions are well described by a bimodal model.

Results suggest universal behavior similar to RNA molecules.

Abstract

We present non equilibrium molecular dynamics experiments of the unfolding and refolding of an alanine decapeptide in vacuo subject to a Nose-Hoover thermostat. Forward (unfolding) and reverse (refolding) work distribution are numerically calculated for various duration times of the non equilibrium experiments. Crooks theorem is accurately verified for all non equilibrium regimes and the time asymmetry of the process is measured using the recently proposed Jensen-Shannon divergence [E.H. Fend, G. Crooks, Phys. Rev. Lett, 101, 090602] . Results on the alanine decapeptide are found similar to recent experimental data on m-RNA molecule, thus evidencing the universal character of the Jensen-Shannon divergence. The patent non-Markovianity of the process is rationalized by assuming that the observed forward and reverse distributions can be each described by a combination of two normal distributions satisfying the Crooks theorem, representative of two mutually exclusive linear events. Such bimodal approach reproduce with surprising accuracy the observed non Markovian work distributions.