%0 DATA
%A Abhishek, Singharoy
%A Yuriy, Sereda
%A Peter J., Ortoleva
%D 2012
%T Hierarchical Order Parameters
for Macromolecular Assembly
Simulations. 1. Construction and Dynamical Properties of Order Parameters
%U https://acs.figshare.com/articles/Hierarchical_Order_Parameters_for_Macromolecular_Assembly_Simulations_1_Construction_and_Dynamical_Properties_of_Order_Parameters/2532343
%R 10.1021/ct200574x.s002
%2 https://acs.figshare.com/ndownloader/files/4175344
%K Langevin equations
%K Dynamical properties
%K Macromolecular Assembly Simulations
%K system organization
%K nonhierarchical ones
%K 1. Construction
%K OP dynamics
%K atom solvated
%K Order ParametersMacromolecular assemblies
%K multiscale analysis
%K Hierarchical Order Parameters
%K Dynamical Properties
%K transition pathways
%K 100 ns
%X Macromolecular assemblies often display a hierarchical
organization
of macromolecules or their subassemblies. 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 to those of our previous nonhierarchical
ones, and implied conceptual and computational advantages are discussed
for a 100 ns, 2 million atom solvated human Papillomavirus-like particle
simulation. In the second article, the hierarchical OPs are shown
to enable a multiscale analysis that starts with the *N*-atom Liouville equation and yields rigorous Langevin equations of
stochastic OP dynamics. The latter is demonstrated via a force-field-based
simulation algorithm that probes key structural transition pathways,
simultaneously accounting for all-atom details and overall structure.