Skip to content

A Simple "Boxed Molecular Kinetics" Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation

Research output: Contribution to journalArticle

Original languageEnglish
Pages (from-to)1531-1541
Number of pages11
JournalJournal of Physical Chemistry A
Volume122
Issue number6
Early online date12 Jan 2018
DOIs
DateAccepted/In press - 20 Dec 2017
DateE-pub ahead of print - 12 Jan 2018
DatePublished (current) - 15 Feb 2018

Abstract

The chemical master equation is a powerful theoretical tool for analyzing the kinetics of complex multiwell potential energy surfaces in a wide range of different domains of chemical kinetics spanning combustion, atmospheric chemistry, gas-surface chemistry, solution phase chemistry, and biochemistry. There are two well-established methodologies for solving the chemical master equation: a stochastic "kinetic Monte Carlo" approach and a matrix-based approach. In principle, the results yielded by both approaches are identical; the decision of which approach is better suited to a particular study depends on the details of the specific system under investigation. In this Article, we present a rigorous method for accelerating stochastic approaches by several orders of magnitude, along with a method for unbiasing the accelerated results to recover the "true" value. The approach we take in this paper is inspired by the so-called "boxed molecular dynamics" (BXD) method, which has previously only been applied to accelerate rare events in molecular dynamics simulations. Here we extend BXD to design a simple algorithmic strategy for accelerating rare events in stochastic kinetic simulations. Tests on a number of systems show that the results obtained using the BXD rare event strategy are in good agreement with unbiased results. To carry out these tests, we have implemented a kinetic Monte Carlo approach in MESMER, which is a cross-platform, open-source, and freely available master equation solver.

    Research areas

  • Journal Article

Download statistics

No data available

Documents

Documents

  • Full-text PDF (accepted author manuscript)

    Rights statement: This is the accepted author manuscript (AAM). The final published version (version of record) is available online via ACS Publications at https://doi.org/10.1021/acs.jpca.7b12521 . Please refer to any applicable terms of use of the publisher.

    Accepted author manuscript, 1 MB, PDF document

DOI

View research connections

Related faculties, schools or groups