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

J. Chem. Phys. 127, 154101 (2007); doi:10.1063/1.2790421

Published 15 October 2007 | See: Erratum

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Stephen Whitelam and Phillip L. Geissler
Department of Chemistry, University of California at Berkeley, California 94720, USA, Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA, and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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. ©2007 American Institute of Physics
History: Received 26 March 2007; accepted 5 September 2007; published 15 October 2007
Permalink: http://link.aip.org/link/?JCPSA6/127/154101/1
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ERRATUM

  1. Erratum: “Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles” [J. Chem. Phys. 127, 154101 (2007)]
    Stephen Whitelam et al.
    J. Chem. Phys. 128, 219901 (2008)

KEYWORDS and PACS

Keywords
PACS
  • 05.40.Jc
    Brownian motion
  • 87.16.Ac
    Theory and modeling of subcellular structure and processes; computer simulation
  • 87.15.-v
    Biomolecules: structure and physical properties
  • 05.10.Ln
    Monte Carlo methods (statistical physics/nonlinear dynamics)
  • 45.50.Tn
    Collisions (particle dynamics/kinematics)
  • YEAR: 2007

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (37)
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