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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Bibliographic Details
Published inPloS one Vol. 9; no. 12; p. e113119
Main Authors Fenley, Andrew T, Muddana, Hari S, Gilson, Michael K
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 11.12.2014
Public Library of Science (PLoS)
Subjects
Analysis
Animals
Aprotinin - chemistry
Biochemistry
Biology and Life Sciences
Biomolecules
Cams
Cattle
Computer programs
Computer simulation
Graphite - chemistry
Licensure
Mathematical analysis
Mechanical properties
Molecular dynamics
Molecular Dynamics Simulation
Nanomaterials
Nanotechnology
Nanotubes, Carbon - chemistry
Open source software
Pharmaceutical sciences
Pharmacy
Physical Sciences
Protein Conformation
Proteins
Simulation
Software - legislation & jurisprudence
Software packages
Source code
Stress
Stress analysis
Stress, Mechanical
Stresses
Theory
Topology
La Jolla California
United States > US
California
Online AccessGet full text

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Summary: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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Conceived and designed the experiments: ATF HSM MKG. Performed the experiments: ATF HSM. Analyzed the data: ATF HSM MKG. Contributed reagents/materials/analysis tools: ATF HSM. Wrote the paper: ATF HSM MKG.
Competing Interests: MKG has an equity interest in, and is a cofounder and scientific advisor of VeraChem LLC. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0113119