Paper Citing NAMD - Abstract
Buehler, Markus J.
Large-scale hierarchical molecular modeling of nanostructured biological materials
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:603-623, OCT 2006
The atomistic and molecular mechanisms that occur during mechanical deformation of natural and biological materials remain largely unknown. In recent years, development of new quantitative experimental, analytical, and computational methods have led to advances in understanding of some details of these deformation mechanisms. Particular progress has been made in how to relate the molecular-scale chemistry to mesoscopic and macroscopic material properties. Here we review large-scale atomistic and molecular modeling methods to investigate the mechanical properties of natural and biological materials with nanostructured hierarchical designs. We discuss basic concepts of hierarchical multi-scale modeling capable of providing a bottom-up description of chemically complex materials. We compare the deformation mechanisms of biological materials with crystalline materials such as metals or ceramics. We emphasize on the importance of entropic contributions to elasticity, and the interplay of chemical bonding of different strengths, at different length- and time scales. We exemplify some of the techniques in studies of the mechanics of polypeptides, tropocollagen molecules, and collagen fibrils.
