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Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolec...

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Autores principales: Fenley, Andrew T., Muddana, Hari S., Gilson, Michael K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263534/
https://www.ncbi.nlm.nih.gov/pubmed/25503996
http://dx.doi.org/10.1371/journal.pone.0113119
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author Fenley, Andrew T.
Muddana, Hari S.
Gilson, Michael K.
author_facet Fenley, Andrew T.
Muddana, Hari S.
Gilson, Michael K.
author_sort Fenley, Andrew T.
collection PubMed
description Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.
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spelling pubmed-42635342014-12-19 Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules Fenley, Andrew T. Muddana, Hari S. Gilson, Michael K. PLoS One Research Article Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. Public Library of Science 2014-12-11 /pmc/articles/PMC4263534/ /pubmed/25503996 http://dx.doi.org/10.1371/journal.pone.0113119 Text en © 2014 Fenley et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Fenley, Andrew T.
Muddana, Hari S.
Gilson, Michael K.
Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title_full Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title_fullStr Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title_full_unstemmed Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title_short Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
title_sort calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263534/
https://www.ncbi.nlm.nih.gov/pubmed/25503996
http://dx.doi.org/10.1371/journal.pone.0113119
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