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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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Stress decomposition of a wave pulse traveling left to right through graphene nanoribbons either in the armchair (top row of each pair) or zigzag (bottom row of each pair) configurations.
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pone-0113119-g005: Stress decomposition of a wave pulse traveling left to right through graphene nanoribbons either in the armchair (top row of each pair) or zigzag (bottom row of each pair) configurations.

Mentions: Next, we investigated wave propagation through graphene nanoribbons by applying a 23 km/s velocity pulse uniformly to an edge of the nanoribbon, where the carbons are either in the “zigzag” or “armchair” configuration [65]. This resulted in propagation of a sharply defined pressure wave along the nanoribbon, with a trailing pattern of excitations that are clearly visualized by the color-coded atomistic stresses, as illustrated for a series of time-points in Fig. 5. The main wave-front is slightly curved, suggesting a somewhat slower velocity at the edges of the ribbon. Interestingly, although the configuration of the ribbon (zigzag vs. armchair) does not greatly affect the shape and velocity of the total stress wavefront (Fig. 5, top row), decomposition of the stresses into bonded and nonbonded contributions showed striking differences and emergent patterns in some of the contributions (Fig. 5, lower 4 rows). In particular, the stresses resulting from the bond and angle terms show distinct patterns in the region of the nanoribbons behind the wavefront, including an “X” configuration of angle stresses in the armchair configuration, which is absent in the zigzag configuration. There are also clear distinctions between the two nanoribbon configurations in the bond and van der Waals stresses.


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 nanoribbons either in the armchair (top row of each pair) or zigzag (bottom row of each pair) configurations.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113119-g005: Stress decomposition of a wave pulse traveling left to right through graphene nanoribbons either in the armchair (top row of each pair) or zigzag (bottom row of each pair) configurations.
Mentions: Next, we investigated wave propagation through graphene nanoribbons by applying a 23 km/s velocity pulse uniformly to an edge of the nanoribbon, where the carbons are either in the “zigzag” or “armchair” configuration [65]. This resulted in propagation of a sharply defined pressure wave along the nanoribbon, with a trailing pattern of excitations that are clearly visualized by the color-coded atomistic stresses, as illustrated for a series of time-points in Fig. 5. The main wave-front is slightly curved, suggesting a somewhat slower velocity at the edges of the ribbon. Interestingly, although the configuration of the ribbon (zigzag vs. armchair) does not greatly affect the shape and velocity of the total stress wavefront (Fig. 5, top row), decomposition of the stresses into bonded and nonbonded contributions showed striking differences and emergent patterns in some of the contributions (Fig. 5, lower 4 rows). In particular, the stresses resulting from the bond and angle terms show distinct patterns in the region of the nanoribbons behind the wavefront, including an “X” configuration of angle stresses in the armchair configuration, which is absent in the zigzag configuration. There are also clear distinctions between the two nanoribbon configurations in the bond and van der Waals stresses.

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