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A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

Oliver, R, Read, DJ, Harlen, OG and Harris, SA A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules. Journal of Computational Physics. ISSN 0021-9991 (Submitted)

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Abstract

We describe a novel coarse grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a viscoelastic continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations.

Item Type: Article
Institution: The University of Leeds
Academic Units: The University of Leeds > Faculty of Maths and Physical Sciences (Leeds) > School of Mathematics (Leeds) > Applied Mathematics (Leeds)
Depositing User: Symplectic Publications
Date Deposited: 22 Oct 2012 10:15
Last Modified: 10 Jun 2014 18:48
Status: Submitted
Publisher: Elsevier
URI: http://eprints.whiterose.ac.uk/id/eprint/43552

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