Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide

We present non equilibrium molecular dynamics experiments of the unfolding and refolding of a single molecule alanine decapeptide in vacuo subject to a Nosé 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. Feng, G. Crooks, Phys. Rev. Lett. 101, 090602 (2008)]. Results on the alanine decapeptide are found similar to recent experimental data on m-RNA molecule in solution, 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 reproduces with surprising accuracy the observed non Markovian work distributions.