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Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

Fenley AT, Muddana HS, Gilson MK - PLoS ONE (2014)

Bottom Line: 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.The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms.Here, we review relevant theory and present illustrative applications.

View Article: PubMed Central - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America.

ABSTRACT
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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Related in: MedlinePlus

The delta in residue-averaged hydrostatic pressure between clusters 1 and 2 (solid, blue line) and the associated standard error of the mean (dashed, red line) for all 58 residues of BPTI.Residues with large (greater in magnitude than 500 bar) are labeled.
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pone-0113119-g002: The delta in residue-averaged hydrostatic pressure between clusters 1 and 2 (solid, blue line) and the associated standard error of the mean (dashed, red line) for all 58 residues of BPTI.Residues with large (greater in magnitude than 500 bar) are labeled.

Mentions: Estimates of the standard error of the mean (SEM) for the residue average stress values were computed using 'pymbar', a statistical software package capable of determining the statistical inefficiency within a time series of data [64]. We found the SEM values of cluster 1 to vary from 0.005 to 0.02 kbar, and those of cluster 2 to vary from 0.01 to 0.3 kbar. For a given residue, we combined the SEM values in quadrature when computing the differences in residue-averaged stresses. The combined SEM values associated with the delta between clusters ranged from 0.009 to 0.3 kbar. The delta in residue-averaged hydrostatic pressure between the two clusters per residue and the associated combined SEM values are shown in Fig. 2.


Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

Fenley AT, Muddana HS, Gilson MK - PLoS ONE (2014)

The delta in residue-averaged hydrostatic pressure between clusters 1 and 2 (solid, blue line) and the associated standard error of the mean (dashed, red line) for all 58 residues of BPTI.Residues with large (greater in magnitude than 500 bar) are labeled.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263534&req=5

pone-0113119-g002: The delta in residue-averaged hydrostatic pressure between clusters 1 and 2 (solid, blue line) and the associated standard error of the mean (dashed, red line) for all 58 residues of BPTI.Residues with large (greater in magnitude than 500 bar) are labeled.
Mentions: Estimates of the standard error of the mean (SEM) for the residue average stress values were computed using 'pymbar', a statistical software package capable of determining the statistical inefficiency within a time series of data [64]. We found the SEM values of cluster 1 to vary from 0.005 to 0.02 kbar, and those of cluster 2 to vary from 0.01 to 0.3 kbar. For a given residue, we combined the SEM values in quadrature when computing the differences in residue-averaged stresses. The combined SEM values associated with the delta between clusters ranged from 0.009 to 0.3 kbar. The delta in residue-averaged hydrostatic pressure between the two clusters per residue and the associated combined SEM values are shown in Fig. 2.

Bottom Line: 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.The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms.Here, we review relevant theory and present illustrative applications.

View Article: PubMed Central - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus