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Geometry entrapment in Walk-on-Subdomains

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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)

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.

Suggested Citation

  • Hamlin Preston & Thrasher W. John & Keyrouz Walid & Mascagni Michael, 2019. "Geometry entrapment in Walk-on-Subdomains," Monte Carlo Methods and Applications, De Gruyter, vol. 25(4), pages 329-340, December.
    • Handle: RePEc:bpj:mcmeap:v:25:y:2019:i:4:p:329-340:n:5
    DOI: 10.1515/mcma-2019-2052
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