Literature DB >> 19466854

Faster strain fluctuation methods through partial volume updates.

Sander Pronk1, Phillip L Geissler.   

Abstract

Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of homogeneous deformations, whose magnitudes can be severely restricted by its stiffest parts. Here we present a Monte Carlo algorithm designed to circumvent this difficulty, which can be prohibitive in many systems of modern interest. By deforming randomly selected subvolumes alone, it naturally distributes the amplitude of spontaneous elastic fluctuations according to intrinsic heterogeneity. We describe in detail implementations of such "slice moves" that are consistent with detailed balance. Their practical application is illustrated for crystals of two-dimensional hard disks and random networks of cross-linked polymers.

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Year:  2009        PMID: 19466854      PMCID: PMC2832050          DOI: 10.1063/1.3122383

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

1.  Influence of vacancies on the melting transition of hard disks in two dimensions

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-05

2.  Elastic moduli, dislocation core energy, and melting of hard disks in two dimensions

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-06

3.  Elasticity of stiff polymer networks.

Authors:  Jan Wilhelm; Erwin Frey
Journal:  Phys Rev Lett       Date:  2003-09-05       Impact factor: 9.161

4.  Nonuniversality of elastic exponents in random bond-bending networks.

Authors:  D A Head; F C MacKintosh; A J Levine
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-08-12

5.  Atomistic simulations incorporating nonlinear elasticity: Slow-stress relaxation and symmetry breaking.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1994-05-01

6.  Elastic behavior of cross-linked and bundled actin networks.

Authors:  M L Gardel; J H Shin; F C MacKintosh; L Mahadevan; P Matsudaira; D A Weitz
Journal:  Science       Date:  2004-05-28       Impact factor: 47.728

7.  Nonuniversal critical dynamics in Monte Carlo simulations.

Authors: 
Journal:  Phys Rev Lett       Date:  1987-01-12       Impact factor: 9.161

8.  Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles.

Authors:  Stephen Whitelam; Phillip L Geissler
Journal:  J Chem Phys       Date:  2007-10-21       Impact factor: 3.488

  8 in total

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