Geometry entrapment in Walk-on-Subdomains

Hamlin Preston (), Thrasher W. John (), Keyrouz Walid () and Mascagni Michael ()
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Hamlin Preston: Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530; and National Institute of Standards & Technology, ITL, Gaithersburg, MD 20899-8970, USA
Thrasher W. John: Department of Computer Science, Florida State University, Tallahassee, FL 32306-453, USA
Keyrouz Walid: National Institute of Standards & Technology, ITL, Gaithersburg, MD 20899-8970, USA
Mascagni Michael: Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530; and National Institute of Standards & Technology, ITL, Gaithersburg, MD 20899-8910, USA

Monte Carlo Methods and Applications, 2019, vol. 25, issue 4, 329-340

Abstract: One method of computing the electrostatic energy of a biomolecule in a solution uses a continuum representation of the solution via the Poisson–Boltzmann equation. This can be solved in many ways, and we consider a Monte Carlo method of our design that combines the Walk-on-Spheres and Walk-on-Subdomains algorithms. In the course of examining the Monte Carlo implementation of this method, an issue was discovered in the Walk-on-Subdomains portion of the algorithm which caused the algorithm to sometimes take an abnormally long time to complete. As the problem occurs when a walker repeatedly oscillates between two subdomains, it is something that could cause a large increase in runtime for any method that used a similar algorithm. This issue is described in detail and a potential solution is examined.

Keywords: Monte Carlo; walk on subdomains; Brownian motion; Poisson–Boltzmann; walk entrapment (search for similar items in EconPapers)
Date: 2019
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DOI: 10.1515/mcma-2019-2052

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