Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.

ABSTRACT: Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared

SUBMITTER: Singharoy A 

PROVIDER: S-EPMC3361912 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature