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Article Dans Une Revue Journal of Physical Chemistry B Année : 2023

Analysis of velocity autocorrelation functions from molecular dynamics simulations of a small peptide by the generalized Langevin equation with a power-law kernel

Résumé

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 to 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 auto-correlation functions. Analytical expressions of the VACF 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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Dates et versions

hal-04334990 , version 1 (11-12-2023)

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Daniel Abergel, Antonino Polimeno, Mirco Zerbetto. Analysis of velocity autocorrelation functions from molecular dynamics simulations of a small peptide by the generalized Langevin equation with a power-law kernel. Journal of Physical Chemistry B, 2023, ⟨10.1021/acs.jpcb.3c05645⟩. ⟨hal-04334990⟩
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