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Geometry Entrapment in Walk-on-Subdomains

Published

Author(s)

Walid Keyrouz, Preston Hamlin, W. J. Thrasher, Michael V. Mascagni

Abstract

One method of computing the electrostatic energy of a biomolecule in a solution combines the Walk-On-Spheres and Walk-On-Subdomains Monte Carlo algorithms. In the course of examining an implementation of this method, a performance issue was discovered in the Walk-On-Subdomains portion of the algorithm. The problem occurs when a walker repeatedly oscillates between two subdomains and is trapped eventually in a small area, which causes a large increase in runtime. This issue is described in detail and a potential solution is examined.
Citation
Monte Carlo Methods and Applications
Volume
25
Issue
4

Keywords

Monte Carlo, Walk on Subdomains, Brownian Motion, Poisson-Boltzmann, Walk Entrapment

Citation

Keyrouz, W. , Hamlin, P. , Thrasher, W. and Mascagni, M. (2019), Geometry Entrapment in Walk-on-Subdomains, Monte Carlo Methods and Applications, [online], https://doi.org/10.1515/mcma-2019-2052, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=928248 (Accessed April 22, 2024)
Created November 18, 2019, Updated October 12, 2021