Literature DB >> 17949126

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

Stephen Whitelam1, Phillip L Geissler.   

Abstract

We introduce a "virtual-move" Monte Carlo algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an important realization being self-assembling particles endowed with strong, short-ranged, and angularly specific ("patchy") attractions. Standard Monte Carlo techniques employ sequential updates of particles and can suffer from low acceptance rates when attractions are strong. In this event, collective motion can be strongly suppressed. Our algorithm avoids this problem by proposing simultaneous moves of collections (clusters) of particles according to gradients of interaction energies. One particle first executes a "virtual" trial move. We determine which of its neighbors move in a similar fashion by calculating individual bond energies before and after the proposed move. We iterate this procedure and update simultaneously the positions of all affected particles. Particles move according to an approximation of realistic dynamics without requiring the explicit computation of forces and without the step size restrictions required when integrating equations of motion. We employ a size- and shape-dependent damping of cluster movements, motivated by collective hydrodynamic effects neglected in simple implementations of Brownian dynamics. We discuss the virtual-move algorithm in the context of other Monte Carlo cluster-move schemes and demonstrate its utility by applying it to a model of biological self-assembly.

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Year:  2007        PMID: 17949126     DOI: 10.1063/1.2790421

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


  31 in total

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4.  Mechanisms of kinetic trapping in self-assembly and phase transformation.

Authors:  Michael F Hagan; Oren M Elrad; Robert L Jack
Journal:  J Chem Phys       Date:  2011-09-14       Impact factor: 3.488

5.  Monte Carlo simulation of kinetically slowed down phase separation.

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6.  Rational design of self-assembly pathways for complex multicomponent structures.

Authors:  William M Jacobs; Aleks Reinhardt; Daan Frenkel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-04       Impact factor: 11.205

7.  The role of multivalency in the association kinetics of patchy particle complexes.

Authors:  Arthur C Newton; Jan Groenewold; Willem K Kegel; Peter G Bolhuis
Journal:  J Chem Phys       Date:  2017-06-21       Impact factor: 3.488

8.  How to simulate patchy particles.

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Journal:  Eur Phys J E Soft Matter       Date:  2018-05-14       Impact factor: 1.890

9.  The role of collective motion in examples of coarsening and self-assembly.

Authors:  Stephen Whitelam; Edward H Feng; Michael F Hagan; Phillip L Geissler
Journal:  Soft Matter       Date:  2008-11-07       Impact factor: 3.679

10.  Localisation of DivIVA by targeting to negatively curved membranes.

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Journal:  EMBO J       Date:  2009-05-28       Impact factor: 11.598

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