Literature DB >> 21929140

Diffusion in periodic potentials with path integral hyperdynamics.

T Ikonen1, M D Khandkar, L Y Chen, S C Ying, T Ala-Nissila.   

Abstract

We consider the diffusion of brownian particles in one-dimensional periodic potentials as a test bench for the recently proposed stochastic path integral hyperdynamics (PIHD) scheme [Chen and Horing, J. Chem. Phys. 126, 224103 (2007)]. First, we consider the case where PIHD is used to enhance the transition rate of activated rare events. To this end, we study the diffusion of a single brownian particle moving in a spatially periodic potential in the high-friction limit at low temperature. We demonstrate that the boost factor as compared to straight molecular dynamics (MD) has nontrivial behavior as a function of the bias force. Instead of growing monotonically with the bias, the boost attains an optimal maximum value due to increased error in the finite path sampling induced by the bias. We also observe that the PIHD method can be sensitive to the choice of numerical integration algorithm. As the second case, we consider parallel resampling of multiple bias force values in the case of a brownian particle in a periodic potential subject to an external ac driving force. We confirm that there is no stochastic resonance in this system. However, while the PIHD method allows one to obtain data for multiple values of the ac bias, the boost with respect to MD remains modest due to the simplicity of the equation of motion in this case.

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Year:  2011        PMID: 21929140      PMCID: PMC3177431          DOI: 10.1103/PhysRevE.84.026703

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  7 in total

1.  Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

Authors:  Donald Hamelberg; John Mongan; J Andrew McCammon
Journal:  J Chem Phys       Date:  2004-06-22       Impact factor: 3.488

2.  Path integral approach to Brownian motion driven with an ac force.

Authors:  L Y Chen; P L Nash
Journal:  J Chem Phys       Date:  2004-09-01       Impact factor: 3.488

3.  Polymer escape from a metastable Kramers potential: path integral hyperdynamics study.

Authors:  Jaeoh Shin; Timo Ikonen; Mahendra D Khandkar; Tapio Ala-Nissila; Wokyung Sung
Journal:  J Chem Phys       Date:  2010-11-14       Impact factor: 3.488

4.  A targeted reweighting method for accelerating the exploration of high-dimensional configuration space.

Authors:  R I Cukier; M Morillo
Journal:  J Chem Phys       Date:  2005-12-15       Impact factor: 3.488

5.  An exact formulation of hyperdynamics simulations.

Authors:  L Y Chen; N J M Horing
Journal:  J Chem Phys       Date:  2007-06-14       Impact factor: 3.488

6.  Exact low-force kinetics from high-force single-molecule unfolding events.

Authors:  Jeremiah Nummela; Ioan Andricioaei
Journal:  Biophys J       Date:  2007-08-17       Impact factor: 4.033

7.  Kramers problem in periodic potentials: Jump rate and jump lengths.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1993-10
  7 in total

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