Paper Citing NAMD - Abstract
Ruiz, Luis; Keten, Sinan
Multiscale Modeling of Elasticity and Fracture in Organic Nanotubes
JOURNAL OF ENGINEERING MECHANICS, 140:431-442, MAR 1 2014
Cyclic peptide nanotubes (CPNs) have unique chemical and mechanical features that squarely position them to tackle persistent challenges in sensor technologies, tissue scaffolds, templates for organic and hybrid electronics, and ultrasmall electromechanical systems. These self-assembled hierarchical nanostructures are highly organized at the nanoscale and feature exceptional thermodynamical stability arising from the collective action of secondary interactions, in particular intersubunit hydrogen-bond networks. Understanding the elasticity and fracture behavior of CPNs through a multiscale analysis is crucially important for developing science-based approaches for designing the molecular subunits and hierarchical assemblies of these materials. In pursuit of addressing this need, a methodology is proposed for linking atomistic simulation results into coarser descriptions of these self-assembling soft nanostructures. This approach involves estimation of the free-energy landscape of the system along the deformation reaction coordinate from atomistic simulation trajectories using nonequilibrium statistical thermodynamics formulations, which enables bridging scales through mapping to coarse-grain or continuum descriptions. In this study, a basic multiscale approach was demonstrated for investigating the mechanics of CPNs, mapping out the elastic range of intersubunit interactions along with the large deformation and fracture regimes. This work illustrates the potential of atomistically informed methods for predicting elastic as well as large deformation behavior of high-aspect-ratio self-assembling nanostructures.
