skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics

Abstract

The numerical solution of the Poisson Boltzmann (PB) equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Recently, we have described a boundary integral equation-based PB solver accelerated by a new version of the fast multipole method (FMM). The overall algorithm shows an order N complexity in both the computational cost and memory usage. Here, we present an updated version of the solver by using an adaptive FMM for accelerating the convolution type matrix-vector multiplications. The adaptive algorithm, when compared to our previous nonadaptive one, not only significantly improves the performance of the overall memory usage but also remarkably speeds the calculation because of an improved load balancing between the local- and far-field calculations. We have also implemented a node-patch discretization scheme that leads to a reduction of unknowns by a factor of 2 relative to the constant element method without sacrificing accuracy. As a result of these improvements, the new solver makes the PB calculation truly feasible for large-scale biomolecular systems such as a 30S ribosome molecule even on a typical 2008 desktop computer.

Authors:
 [1];  [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
981440
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Theory and Computation; Journal Volume: 5; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICAL METHODS AND COMPUTING; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ACCURACY; ALGORITHMS; BOUNDARY ELEMENT METHOD; ELECTROSTATICS; ELEMENTS; EQUATIONS; INTEGRALS; MOLECULES; MULTIPOLES; NUMERICAL SOLUTION; PERFORMANCE; REDUCTION; RIBOSOMES; SOLVATION; TOOLS

Citation Formats

Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. United States: N. p., 2009. Web. doi:10.1021/ct900083k.
Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, & McCammon, Jonathan. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. United States. doi:10.1021/ct900083k.
Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. Thu . "An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics". United States. doi:10.1021/ct900083k.
@article{osti_981440,
title = {An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics},
author = {Lu, Benzhuo and Cheng, Xiaolin and Huang, Jingfang and McCammon, Jonathan},
abstractNote = {The numerical solution of the Poisson Boltzmann (PB) equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Recently, we have described a boundary integral equation-based PB solver accelerated by a new version of the fast multipole method (FMM). The overall algorithm shows an order N complexity in both the computational cost and memory usage. Here, we present an updated version of the solver by using an adaptive FMM for accelerating the convolution type matrix-vector multiplications. The adaptive algorithm, when compared to our previous nonadaptive one, not only significantly improves the performance of the overall memory usage but also remarkably speeds the calculation because of an improved load balancing between the local- and far-field calculations. We have also implemented a node-patch discretization scheme that leads to a reduction of unknowns by a factor of 2 relative to the constant element method without sacrificing accuracy. As a result of these improvements, the new solver makes the PB calculation truly feasible for large-scale biomolecular systems such as a 30S ribosome molecule even on a typical 2008 desktop computer.},
doi = {10.1021/ct900083k},
journal = {Journal of Chemical Theory and Computation},
number = 6,
volume = 5,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}