Time- and ensemble-average statistical mechanics of the Gaussian network model

DOI10.1088/1751-8121/AC16E4MaRDI QIDQ5877433zbMATH OpenOpenAlexFDO

Authors Alessio Lapolla, Maximilian Vossel, Aljaž Godec

Publication date 13 February 2023

Published in Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/2102.11847

zbMATH Keywords

covariance matrixoccupation timeFokker-Planck equationconformation dynamicselastic networknetwork models of macromoleculesprojected physical observables

Mathematics Subject Classification ID

Classical equilibrium statistical mechanics (general) (82B05)

Abstract: We present analytical results (up to a numerical diagonalization of a real symmetric matrix) for a set of time- and ensemble-average physical observables in the non-Hookean Gaussian Network Model (GNM) - a generalization of the Rouse model to elastic networks with links with a certain degree of extensional and rotational stiffness. We focus on a set of coarse-grained observables that may be of interest in the analysis of GNM in the context of internal motions in proteins and mechanical frames in contact with a heat bath. A C++ computer code is made available that implements all analytical results.

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Cited in

(2)

• Efficient perturbation analysis of elastic network models -- application to acetylcholinesterase of T. Californica
• Fast Non-mean-field Networks: Uniform in Time Averaging

Describes a project that uses

Uses Software

• ProDy
• Arb
• Armadillo
• Mathematica

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