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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

Stress decomposition of a wave pulse traveling left to right through graphene nanotubes either in the armchair (upper) or zigzag (lower) configurations.Data are shown for the 450 fs time-point.
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pone-0113119-g006: Stress decomposition of a wave pulse traveling left to right through graphene nanotubes either in the armchair (upper) or zigzag (lower) configurations.Data are shown for the 450 fs time-point.

Mentions: In order to determine which of the patterns observed in the nanoribbons (Fig. 5) resulted from edge effects, we performed the same analysis on graphene nanotubes, where edge effects are absent. Fig. 6 shows that, while the leading wavefront from the initial pulse is no longer slowed down by the edges, there are now far more uniform trailing stress waves of opposite sign and in different locations depending on the carbon configurations. The bond stresses are the primary origin of these bands, and the differences in the angle stresses between the two carbon configurations are less striking in the nanotubes than the nanoribbons. Therefore, edge effects seem to play a major role in the propagation and dispersion of stress waves in graphene sheets.


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

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

Stress decomposition of a wave pulse traveling left to right through graphene nanotubes either in the armchair (upper) or zigzag (lower) configurations.Data are shown for the 450 fs time-point.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113119-g006: Stress decomposition of a wave pulse traveling left to right through graphene nanotubes either in the armchair (upper) or zigzag (lower) configurations.Data are shown for the 450 fs time-point.
Mentions: In order to determine which of the patterns observed in the nanoribbons (Fig. 5) resulted from edge effects, we performed the same analysis on graphene nanotubes, where edge effects are absent. Fig. 6 shows that, while the leading wavefront from the initial pulse is no longer slowed down by the edges, there are now far more uniform trailing stress waves of opposite sign and in different locations depending on the carbon configurations. The bond stresses are the primary origin of these bands, and the differences in the angle stresses between the two carbon configurations are less striking in the nanotubes than the nanoribbons. Therefore, edge effects seem to play a major role in the propagation and dispersion of stress waves in graphene sheets.

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