Paper Citing NAMD - Abstract
Buehler, M. J.
Hierarchical nanomechanics of collagen fibrils: Atomistic and molecular modeling
Collagen: Structure and Mechanics, 175-247, 2008
This chapter describes hierarchical multi-scale modeling of collagenous tissues, with a particular focus on the mechanical properties. Studies focus on elastic behavior, plastic behavior and fracture. Starting at the atomistic scale, we review development and application of a hierarchical multi-scale model that is capable of describing the dynamical behavior of a large number of tropocollagen molecules, reaching length scales of several micrometers and time scales of tens of microseconds. Particular emphasis is on elucidating the deformation mechanisms that operate at various scales, the scale-dependent properties, the effect of specific hierarchical features and length scales (cross-link densities, intermolecular adhesion, etc.) as well as on the effect of addition of mineral platelets during formation of nascent bone. This chapter contains a review of numerical techniques associated with modeling of chemically complex and hierarchical biological tissue, including first principles-based reactive force fields, empirical force fields, large-scale parallelization and visualization methods. A set of scaling relationships are summarized that enable one to predict deformation mechanisms and properties based on atomistic, molecular and other hierarchical features. The results are presented in deformation maps that summarize deformation modes, strength, dissipative properties and elastic behavior for various conditions, providing structure-property relationships for collagenous tissue. This chapter is concluded with a discussion of how insight of nanomechanical behavior at the smallest scales relates with the physiological role of collagen. The significance of universal structural patterns such as the staggered collagen fibril architecture versus specific structures in different collagen tissues is reviewed in light of the question of universality versus diversity of structural components.
