Analysis of Velocity Autocorrelation Functions from Molecular Dynamics Simulations of a Small Peptide by the Generalized Langevin Equation with a Power-Law Kernel

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...

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Published inThe journal of physical chemistry. B Vol. 127; no. 50; pp. 10896 - 10902
Main Authors Abergel, Daniel, Polimeno, Antonino, Zerbetto, Mirco
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 21.12.2023
Subjects
B: Soft Matter, Fluid Interfaces, Colloids, Polymers, and Glassy Materials
Chemical Sciences
MD simulation
Zwanzig
memory
Fractional diffusion
Mori-Zwanzig
correlation functions
power law
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Summary: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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ISSN:1520-6106
1520-5207
1520-5207
DOI:10.1021/acs.jpcb.3c05645