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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

Time series of wave propagation through a monolayer of graphene after the impact of a hypervelocity fullerene.The passage of time is measured relative to the point of impact. After the initial collision, longitudinal stress waves (purple tensile band) propagate radially outward at a greater velocity than the transverse deformation wave. Within 165 fs since the moment of impact, regions of the longitudinal wavefront reflected (orange compressive regions) at the boundaries and headed towards the wavefront of the transverse deformation wave. Nonuniform interaction between the two waves has distorted the spherical transverse deformation wave.
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pone-0113119-g004: Time series of wave propagation through a monolayer of graphene after the impact of a hypervelocity fullerene.The passage of time is measured relative to the point of impact. After the initial collision, longitudinal stress waves (purple tensile band) propagate radially outward at a greater velocity than the transverse deformation wave. Within 165 fs since the moment of impact, regions of the longitudinal wavefront reflected (orange compressive regions) at the boundaries and headed towards the wavefront of the transverse deformation wave. Nonuniform interaction between the two waves has distorted the spherical transverse deformation wave.

Mentions: First, we investigated stress waves in a monolayer of graphene initiated by the impact of a hypervelocity C60 fullerene (∼20.5 km/s; 1.8 keV) [66], [71]. Fig. 4 shows the time-evolution of the waves from the moment of impact. Initially, radially symmetric longitudinal tensile waves (colored purple in Fig. 4) rapidly spread out from the point of impact, moving at ∼12 km/s, which is just over half the experimental speed of sound in graphene (21 km/s) [72], [73]. A transverse wave, traveling at ∼7 km/s, lags the longitudinal waves as the collision visibly deforms the graphene sheet out of its plane. The reflection of the longitudinal wave from the edge of the sheet results in compression (orange in Fig. 4) at the edges of the graphene monolayer and interacts with the leading edge of the transverse wave. The collision of the two wavefronts impedes regions of the transverse wave and thus alters the shape of the transverse wavefront. Visualization of the resulting tensile and compressive stresses as the waves propagate throughout the material clearly highlights the shapes and interaction regions of the waves. These reported pressures, shown in Fig. 4, are within the tolerance of the material, as graphene has been measured to have an intrinsic (ultimate tensile) strength of 1.3 Mbar [74].


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

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

Time series of wave propagation through a monolayer of graphene after the impact of a hypervelocity fullerene.The passage of time is measured relative to the point of impact. After the initial collision, longitudinal stress waves (purple tensile band) propagate radially outward at a greater velocity than the transverse deformation wave. Within 165 fs since the moment of impact, regions of the longitudinal wavefront reflected (orange compressive regions) at the boundaries and headed towards the wavefront of the transverse deformation wave. Nonuniform interaction between the two waves has distorted the spherical transverse deformation wave.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113119-g004: Time series of wave propagation through a monolayer of graphene after the impact of a hypervelocity fullerene.The passage of time is measured relative to the point of impact. After the initial collision, longitudinal stress waves (purple tensile band) propagate radially outward at a greater velocity than the transverse deformation wave. Within 165 fs since the moment of impact, regions of the longitudinal wavefront reflected (orange compressive regions) at the boundaries and headed towards the wavefront of the transverse deformation wave. Nonuniform interaction between the two waves has distorted the spherical transverse deformation wave.
Mentions: First, we investigated stress waves in a monolayer of graphene initiated by the impact of a hypervelocity C60 fullerene (∼20.5 km/s; 1.8 keV) [66], [71]. Fig. 4 shows the time-evolution of the waves from the moment of impact. Initially, radially symmetric longitudinal tensile waves (colored purple in Fig. 4) rapidly spread out from the point of impact, moving at ∼12 km/s, which is just over half the experimental speed of sound in graphene (21 km/s) [72], [73]. A transverse wave, traveling at ∼7 km/s, lags the longitudinal waves as the collision visibly deforms the graphene sheet out of its plane. The reflection of the longitudinal wave from the edge of the sheet results in compression (orange in Fig. 4) at the edges of the graphene monolayer and interacts with the leading edge of the transverse wave. The collision of the two wavefronts impedes regions of the transverse wave and thus alters the shape of the transverse wavefront. Visualization of the resulting tensile and compressive stresses as the waves propagate throughout the material clearly highlights the shapes and interaction regions of the waves. These reported pressures, shown in Fig. 4, are within the tolerance of the material, as graphene has been measured to have an intrinsic (ultimate tensile) strength of 1.3 Mbar [74].

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