Thank you for your interest shown in my previously posted work.  Here's a post-print for an article of an extension to my previous work.  Extension in the sense that the MD simulation was performed on "larger" metallic nanowires (2.0 nm to 6.0 nm), and the behavior of gold (Au) nanowires were studied.  The mechanism behind strain-induced amorphization was explained and the phenomenon of multiple necking was observed, implying the presence of "localized" amorphization instead of a "globalized" one observed in shorter nanowires.

A special session on Multiscale Modeling and Simulation of the thirteenth Pacific Symposium on Biocomputing (PSB) will be held January 4-8, 2008, on the Big Island of Hawaii. Paper submissions are due on July 16, 2007. This special session is being co-organized by NIH National Center for Biomedical Computing (Simbios) and the NIH funded National Biomedical Computing Resource (NBCR). PSB brings together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology.

Dear Colleague,

We want to draw your attention to and encourage your participation in a special session on Multiscale Modeling and Simulation of the thirteenth Pacific Symposium on Biocomputing (PSB), to be held January 4-8, 2008, on the Big Island of Hawaii. PSB is an international, multidisciplinary conference with high impact on the theory and application of computational methods in problems of biological significance. 

This paper has been published in Journal of the Mechanics and Physics of Solids 56 (2008), pp. 1609-1623 (doi:10.1016/j.jmps.2007.07.013).

Abstract

An Australian Research Council funded PhD Scholarship is available in the Department of Civil Engineering at Monash University in Australia in the area of computational mechanics. The objective of this project is to develop a multi-scale bifurcation-based decohesion model within the framework of the Material Point Method (MPM), one of the meshfree methods, for simulating glass fragmentation under blast loading. The proposed multi-scale decohesion model will be calibrated by combining molecular dynamics and continuum mechanics approaches, and the simulation results will be verified by available experimental data.

I am trying to find out the theoretical adhesive strength limit of a few materials, or more precisely the ratio adhesive strength limit to elastic modulus. I think this is after all part of the Lennard-Jones constants potential - theoretical adhesive strength limit is simply the maximum of the curve.

Considering the MD (molecualr dynamics) simulation programs, they enable us to define the initial crack and then using different theories they propagate the crack. This process is actually a dynamic feature at least when the sample is going to fail. Here is the question that present in the most modellers assumptions, which will limit the simulation or maybe it is not possible to simulate the process with out these assumptions. One of them which I would like to know your ideas about is the linear velocity which come into conclusions before the simulations start. Actually is this linear velocity remains constant or increase with definite constant acceleration (rate) as crack propagates? I think the answer is No, so why we assume that this theory is accurate?

We report the direct molecular dynamics simulations for molecular ball bearings composed of fullerene molecules (C60 and C20) and multi-walled carbon nanotubes. The comparison of friction levels indicates that fullerene ball bearings have extremely low friction (with minimal frictional forces of  5.283×10-7 nN/atom and  6.768×10-7 nN/atom  for C60 and C20 bearings) and energy dissipation (lowest dissipation per cycle of  0.013 meV/atom  and  0.016 meV/atom  for C60 and C20 bearings). A single fullerene inside the ball bearings exhibits various motion statuses of mixed translation and rotation. The influences of the shaft's distortion on the long-ranged potential energy and normal force are discussed. The phonic dissipation mechanism leads to a non-monotonic function between the friction and the load rate for the molecular bearings.

I wanted to share some our work on the deformation behavior of metal nanowires that was recently published in Advanced Functional Materials. In this work, we considered the tensile deformation of three experimentally observed silver nanowire geometries, including five-fold twinned, pentagonal nanowires. The manuscript abstract and urls to videos of the tensile deformation of the three nanowire geometries are below. A copy of the manuscript is attached.

Abstract. This letter addresses the dependence of homogeneous dislocation nucleation on the crystallographic orientation of pure copper under uniaxial tension and compression.  Molecular dynamics simulation results with an embedded-atom method potential show that the stress required for homogeneous dislocation nucleation is highly dependent on the crystallographic orientation and the uniaxial loading conditions; certain orientations require a higher stress in compression (e.g., <110> and <111>) and other orientations require a higher stress in tension (<100>).  Furthermore, the resolved shear stress in the slip direction is unable to completely capture the dependence of homogeneous dislocation nucleation on crystal orientation and uniaxial loading conditions.

We show, through MD simulations, a new evolution pattern of the U-shaped dislocation in fcc Al that would enrich the FR mechanism. Direct atomistic investigation indicates that a U-shaped dislocation may behave in different manners when it emits the first dislocation loop by bowing out of an extended dislocation. One manner is that the glissile dislocation segment always bows in the original glide plane, as the conventional FR mechanism. Another is that non-coplanar composite dislocations appear owing to conservative motion of polar dislocation segments, and then bow out along each slip plane, creating a closed helical loop. The motion of these segments involves a cross-slip mechanism by which a dislocation with screw component moves from one slip plane into another. Ultimately, such non-coplanar evolution results in the formation of a FR source.

We know - or believe - protein function is determined by structure. Crystallographic and NMR studies can provide protein structures with atomic-level details at equilibrium. MD simulations can follow protein conformational changes in time with fs temporal resolution in the absence or presence of a bias mechanism, e.g., applied force, used to induce such changes.

Although it is more realistic to study the mechanical properties of nanostructures such as the carbon nanotubes (CNTs) at room temperature, atomistic simulations at finite temperature (such as molecular dynamics, MD) may cause the following problems: (1) Due to the limitation of the time scale achievable in MD (typically at the nanosecond scale), the loading rate in MD simulation at any finite temperature is not realistic. Very often, the loading rate used in MD simulations may well exceed 10m/s at 300K and thus many orders of magnitude higher than the real loading rate used in experiments. (2) A great advantage of simulation is to be able to turn on and turn off certain features and explore their effects, which is otherwise impossible in experiments. For example, the buckling behavior of CNTs is very sensitive to geometrical perturbations, which is prominent at room temperature and such perturbations causes severe uncertainties and makes it difficult to explore the intrinsic buckling behaviors. Therefore, by removing the temperature effect, we could better evaluate other key factors affecting the intrinsic buckling behavior, such as tube chirality, radius, and length, which could be otherwise covered by the thermal fluctuation effect. (3) Due to both time and length scale limitations, the MD simulations of large system are not yet possible, and thus the effective continuum models must be developed which need to be calibrated by atomistic simulations. At present, the temperature factor is still absent in most continuum models. Therefore, atomistic simulations at 0K or near 0K may provide a useful benchmark for the development of parallel continuum models, focusing on the most intrinsic and basic mechanical properties of nanostructures. Based on the above analysis, atomistic simulations at 0K by using the molecular mechanics (MM) method are still very useful, especially to us as mechanicians.

(originally written by Yuye Tang) A key procedure of the molecular-dynamics decorated finite element method (MDeFEM) is to determine the effective properties of components of a macromolecule. Here I illustrate how could one use the NMA computed from MD to estimate the elastic properties of loops in mechanosensitive channels, which is related with my research.