The "White Rat" of Numerical Reprodicibility

Name:    Prof. Michael Mascagni                 
Address: Department of Computer Science and
         Department of Mathematics and
	 Department of Scientific Computing and
         Graduate Program in Molecular Biophysics	
         Florida State University
         Tallahassee, FL  32306-4530  USA
         AND
         Information Technology Laboratory
         Applied and Computational Mathematics Division
         100 Bureau Drive M/S 8910
         National Institute of Standards and Technology (NIST)
         Gaithersburg, MD  20899-8910  USA

Offices: 498 Dirac Science Library/207A Love Building (FSU) Building 225/Room B154 (NIST)
Phone:   +1.850.644.3290 (FSU) +1.301.975.2051 (NIST)
FAX:     +1.850.644.0058
e-mail:  mascagni@fsu.edu (FSU) mascagni@nist.gov (NIST)

Title: Geometry Entrapment in Walk-on-Subdomains Monte Carlo

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. Our solutions uses the relatively new concept of first-passage under restart to propose a solution.

This is joint work with John Thrasher, who is currently my graduate student.