Assessing the mechanical behavior of proteins and metal nanowires using long timescale atomistic simulations

Abstract

Classical molecular dynamics (MD) simulations have been widely used to study the physical properties of nanomaterials. However, MD suffers from the well-known drawback where it cannot, in the absence of special high-performance computing environments, simulate processes that take longer than microseconds. Nevertheless, many important processes in various fields of science and engineering take place on time scales that cannot be reached by MD. For example, while MD simulations have been used extensively to study the plasticity of nanostructures such as proteins and nanowires, their time scale limitations have prevented the study of the deformation mechanisms at experimentally-relevant forces, time scales and strain rates. In this thesis, a generic history-penalized self-learning metabasin escape (SLME) algorithm, which efficiently explores the potential energy surface, is utilized to overcome this issue by studying three canonical problems of interest: the unfolding of biological proteins under experimentally-relevant mechanical forces; the strain-rate-dependent plastic deformation mechanisms of bicrystalline FCC metal nanowires, and finally the constant stress (creep-induced) plastic deformation of single crystalline metallic nanowires at experimental time scales. The SLME method is first utilized to study the force-induced unfolding of biological proteins. The long time scale simulations not only provide atomistic details of time-dependent structural evolution under experimentally-relevant forces, but also show novel intermediate states that cannot be observed in MD simulations, which sheds new insight into the understanding of protein unfolding dynamics. This method is then utilized to investigate the strain rate effect on the plastic mechanisms of bicrystalline metal nanowires. A strain-rate-dependent incipient plasticity and yielding transition for bicrystalline metal nanowires at experimentally-relevant strain rates is observed. This transition leads to a ductile-to-brittle transition in failure mode, which is driven by differences in dislocation activity and grain boundary mobility at low strain rate as compared to the high strain rate case. Finally, the SLME method is also utilized to study the creep behavior of single crystalline metal nanowires at experimental time scales. Both copper and silver nanowires show significantly increased ductility and superplasticity under experimentally-relevant creep stresses, where the superplasticity is driven by a thermally-activated transition in defect nucleation from twinning to trailing partial dislocations at the micro or millisecond timescale