Paper Citing NAMD - Abstract
Buehler, Markus J.
Computational Scale Linking in Biological Protein Materials
COMPUTATIONAL MODELING IN BIOMECHANICS, 491-531, 2010
The properties of biological materials have been the focal point of extensive studies over the past decades, leading to formation of a research field that connects biology, chemistry and materials science at multiple scales, here referred to as "materiomics." In this chapter we review atomistic based modeling approaches applied to study the scale-dependent mechanical behavior of biological protein materials, in particular focused on their elastic and fracture behavior. Specific examples are provided to illustrate the application of numerical methods that link atomistic scales to mesoscale material properties. We review the formulation of atomistic simulation methods and exemplify its application in several case studies focused on size effects of the fracture behavior of protein materials. These examples illustrate how atomistic scales of molecular structures can be linked to structural levels at length-scales of tens to hundreds of nanometers and micrometers. A study with a simple model of the nuclear lamin network provides a specific example for this coupling of scales, revealing how protein networks with structural defects respond to mechanical load and how the overall behavior relates to the chemical structure of the protein molecule and its hierarchical structural makeup.
