2009/04/20 by Simone Marsili, Marsili, Simone, Piero Procacci +1
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #FOS: Physical sciences #Lipid Membrane Structure and Behavior #Protein Structure and Dynamics #Statistical Mechanics (cond-mat.stat-mech) #Supramolecular Self-Assembly in Materials #cond-mat.stat-mech
paper · pdf · doi:10.48550/arxiv.0904.3005
arxiv created 2009/04/20 · openalex publication_date 2009/04/20 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.