About: TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid
Creator	Barsegov, Valeri Kononova, Olga Maksudov, Farkhad Marx, Kenneth
source	PMC
abstract	A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and [Formula: see text] -based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.
has issue date	2018-01-31(xsd:dateTime)
bibo:doi	10.1088/1361-648x/aaa0f6
bibo:pmid	29231176
has license	no-cc
sha1sum (hex)	fe7a2c245a84ec67c283cc9f95d7f739e99c8e6b
schema:url	https://doi.org/10.1088/1361-648x/aaa0f6
resource representing a document's title	TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid
has PubMed Central identifier	PMC7104887
has PubMed identifier	29231176
schema:publication	J Phys Condens Matter
resource representing a document's body	covid:fe7a2c245a84ec67c283cc9f95d7f739e99c8e6b#body_text
is schema:about of	named entity 'defects' named entity 'capsid' named entity 'numerical' named entity 'mechanical stress' named entity 'virus' named entity 'principal stress' named entity 'mechanical stress' named entity 'LARGE' named entity 'VIRAL' named entity 'PRINCIPAL' named entity 'STRUCTURAL' named entity 'CAPSID' named entity 'MECHANICAL FAILURE' named entity 'CALCULATION' named entity 'FINITE ELEMENT ANALYSIS' named entity 'TOTAL' named entity 'PROTEIN ' named entity 'PACKAGE' named entity 'EXAMPLE' named entity 'COMPUTATIONAL' named entity 'PERMITS' named entity 'based' named entity 'virus structure' named entity 'simulations' named entity 'methodology' named entity 'total' named entity 'explore' named entity 'predict' named entity 'tensors' named entity 'analysis' named entity 'viral capsid' named entity 'calculation' named entity 'stress' named entity 'computational methodology' named entity 'continuum mechanics' named entity 'elastic deformation' named entity 'viral capsid' named entity 'CCMV' named entity 'evolution' named entity 'CCMV' named entity 'stress measures' named entity 'outer surface' named entity '5.0' named entity 'polymers' named entity 'mechanical stress' named entity 'potential energy' named entity 'capsid' named entity 'Brownian' named entity 'CCMV' named entity 'coarse-grained' named entity 'mechanical stress' named entity 'CCMV' named entity 'orders of magnitude' named entity 'kcal' named entity 'molecular chain' named entity 'atom' named entity 'CCMV' named entity 'free energy' named entity 'prefactor' named entity 'capsid' named entity 'yield strength' named entity 'kcal' named entity 'CCMV' named entity 'spectra' named entity 'nanomechanics' named entity 'stress tensor' named entity 'thermal fluctuations' named entity 'CCMV' named entity 'protein assemblies' named entity 'protein' named entity 'materials science' named entity 'evolution' named entity 'cantilever' named entity 'cellular organelles' named entity 'stress tensor' named entity 'stress tensor' named entity 'structure defects' named entity 'amino acid residues'

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