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Published on: December 4, 2017
Analysis of Velocity Autocorrelation Functions from Molecular Dynamics Simulations of a Small Peptide by the
Daniel Abergel1, Antonino Polimeno2, Mirco Zerbetto2
1Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris 75005, France.
Abstract:
Internal motions play an essential role in the biological functions of proteins and have been the subject of numerous theoretical and spectroscopic studies. Such complex environments are associated with anomalous diffusion where, in contrast to the classical Brownian motion, the relevant correlation functions have power law decays with time. In this work, we investigate the presence of long memory stochastic processes through the analysis of atomic velocity autocorrelation functions. Analytical expressions of the velocity autocorrelation function spectrum obtained through a Mori-Zwanzig projection approach were shown to be compatible with molecular dynamics simulations of a small helical peptide (8-polyalanine).
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