molecular dynamics

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.