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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
first_indexed 2016-02-11T02:01:20Z
last_indexed 2019-06-05T10:04:22Z
id cronfa26113
recordtype SURis
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spelling 2019-05-30T14:33:16.8346180 v2 26113 2016-02-10 Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature 33985d0c2586398180c197dc170d7d19 0000-0002-1755-8807 Ankush Aggarwal Ankush Aggarwal true false 2016-02-10 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. Journal Article Physical Review E 93 1 2470-0045 2470-0053 28 1 2016 2016-01-28 10.1103/PhysRevE.93.012417 COLLEGE NANME COLLEGE CODE Swansea University 2019-05-30T14:33:16.8346180 2016-02-10T12:41:53.4740449 Faculty of Science and Engineering School of Engineering and Applied Sciences - Uncategorised Ankush Aggarwal 0000-0002-1755-8807 1 Eric R. May 2 Charles L. Brooks 3 William S. Klug 4
title Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
spellingShingle Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
Ankush Aggarwal
title_short Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
title_full Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
title_fullStr Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
title_full_unstemmed Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
title_sort Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature
author_id_str_mv 33985d0c2586398180c197dc170d7d19
author_id_fullname_str_mv 33985d0c2586398180c197dc170d7d19_***_Ankush Aggarwal
author Ankush Aggarwal
author2 Ankush Aggarwal
Eric R. May
Charles L. Brooks
William S. Klug
format Journal article
container_title Physical Review E
container_volume 93
container_issue 1
publishDate 2016
institution Swansea University
issn 2470-0045
2470-0053
doi_str_mv 10.1103/PhysRevE.93.012417
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Engineering and Applied Sciences - Uncategorised{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Engineering and Applied Sciences - Uncategorised
document_store_str 0
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description 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.
published_date 2016-01-28T15:21:42Z
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