Paper Citing NAMD - Abstract
Ruiz, Luis; Keten, Sinan
ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES
INTERNATIONAL JOURNAL OF APPLIED MECHANICS, 3:667-684, DEC 2011
Organic building blocks inspired by biological systems are promising for fabricating nanostructured materials for a broad range of applications such as antimicrobials, biosensors, electronics, and biomaterials. Self-assembling cyclic peptide organic nanotubes have shown great promise for these applications due to their precise structural features, diverse chemical functionalization capabilities and exceptional stability arising from arrangement of hydrogen bonds into cooperative clusters. Mechanical behavior of organic nanotubes is important for various possible applications ranging from subnanoporous selective membranes to molecular templates for electronics. However, large-scale deformation mechanisms of organic nanotubes have not been studied thus far. Here we investigate the mechanisms involved in the large deformation and failure of self-assembled organic nanotubes, focusing on geometry effects characteristic of protein nanostructures. We carry out molecular dynamics simulations to assess the role of hydrogen bonds as weak interactions in the context of deformation and failure processes involving bending and shear loads. Mechanisms of failure are found to depend on the cross-sectional geometry and the deformation rate, where a transition to localized shear failure is observed at high-strain rates. Our results provide important physical insight into the mechanics of organic nanotubes central to emerging applications of self-assembling peptides in biomedicine and biotechnology.
