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Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature

Ankush Aggarwal Orcid Logo, Eric R. May, Charles L. Brooks, William S. Klug

Physical Review E, Volume: 93, Issue: 1

Swansea University Author: Ankush Aggarwal Orcid Logo

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DOI (Published version): 10.1103/PhysRevE.93.012417

Abstract

Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the n...

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Published in: Physical Review E
ISSN: 2470-0045 2470-0053
Published: 2016
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URI: https://cronfa.swan.ac.uk/Record/cronfa26113
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Abstract: Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.
College: Faculty of Science and Engineering
Issue: 1

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