Computational techniques at the organic− inorganic interface in biomineralization

JH Harding, DM Duffy, ML Sushko, PM Rodger… - Chemical …, 2008 - ACS Publications
Just over ninety years ago, the first edition of D'Arcy Thompson's book On Growth and Form
appeared. 1 Much of it is long out of date, but D'Arcy Thompson makes a point of …

Multiscale simulation of microbe structure and dynamics

H Joshi, A Singharoy, YV Sereda… - Progress in biophysics …, 2011 - Elsevier
A multiscale mathematical and computational approach is developed that captures the
hierarchical organization of a microbe. It is found that a natural perspective for …

All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling

Y Miao, JE Johnson, PJ Ortoleva - The Journal of Physical …, 2010 - ACS Publications
An all-atom multiscale computational modeling approach, molecular dynamics/order
parameter extrapolation (MD/OPX), has recently been developed for simulating large …

Order parameters for macromolecules: Application to multiscale simulation

A Singharoy, S Cheluvaraja, P Ortoleva - The Journal of Chemical …, 2011 - pubs.aip.org
Order parameters (OPs) characterizing the nanoscale features of macromolecules are
presented. They are generated in a general fashion so that they do not need to be …

Determining optimal coarse‐grained representation for biomolecules using internal cluster validation indexes

Z Wu, Y Zhang, JZ Zhang, K Xia… - Journal of Computational …, 2020 - Wiley Online Library
The development of ultracoarse‐grained models for large biomolecules needs to derive the
optimal number of coarse‐grained (CG) sites to represent the targets. In this work, we …

Thermal nanostructure: An order parameter multiscale ensemble approach

S Cheluvaraja, P Ortoleva - The Journal of chemical physics, 2010 - pubs.aip.org
Deductive all-atom multiscale techniques imply that many nanosystems can be understood
in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium …

Self-assembly of nanocomponents into composite structures: Derivation and simulation of Langevin equations

S Pankavich, Z Shreif, Y Miao… - The Journal of chemical …, 2009 - pubs.aip.org
The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other
composite structure is analyzed via a multiscale approach. The objective is to achieve …

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation

Y Miao, PJ Ortoleva - Biopolymers: Original Research on …, 2010 - Wiley Online Library
On the basis of an all‐atom multiscale analysis theory of nanosystem dynamics, a multiscale
molecular dynamics/order parameter extrapolation (MD/OPX) approach has recently been …

Space warping order parameters and symmetry: Application to multiscale simulation of macromolecular assemblies

A Singharoy, H Joshi, Y Miao… - The Journal of Physical …, 2012 - ACS Publications
Coarse-grained features of macromolecular assemblies are understood via a set of order
parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be …

Liquid-crystal transitions: A first-principles multiscale approach

Z Shreif, S Pankavich, P Ortoleva - … Review E—Statistical, Nonlinear, and Soft …, 2009 - APS
A rigorous theory of liquid-crystal transitions is developed starting from the Liouville
equation. The starting point is an all-atom description and a set of order-parameter field …