A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

Weihua Geng

Molecular Based Mathematical Biology (2015)

  • Volume: 3, Issue: 1
  • ISSN: 2299-3266

Abstract

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Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both efficiency and accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solvers in pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features and functions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitatively report the solvation free energy computation of these boundary integral PB solvers benchmarked with Matched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite difference Poisson-Boltzmann solver.

How to cite

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Weihua Geng. "A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations." Molecular Based Mathematical Biology 3.1 (2015): null. <http://eudml.org/doc/270875>.

@article{WeihuaGeng2015,
abstract = {Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both efficiency and accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solvers in pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features and functions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitatively report the solvation free energy computation of these boundary integral PB solvers benchmarked with Matched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite difference Poisson-Boltzmann solver.},
author = {Weihua Geng},
journal = {Molecular Based Mathematical Biology},
keywords = {Electrostatics; Solvated biomolecule; Poisson-Boltzmann equation; Boundary integral equation; Treecode},
language = {eng},
number = {1},
pages = {null},
title = {A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations},
url = {http://eudml.org/doc/270875},
volume = {3},
year = {2015},
}

TY - JOUR
AU - Weihua Geng
TI - A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
JO - Molecular Based Mathematical Biology
PY - 2015
VL - 3
IS - 1
SP - null
AB - Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both efficiency and accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solvers in pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features and functions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitatively report the solvation free energy computation of these boundary integral PB solvers benchmarked with Matched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite difference Poisson-Boltzmann solver.
LA - eng
KW - Electrostatics; Solvated biomolecule; Poisson-Boltzmann equation; Boundary integral equation; Treecode
UR - http://eudml.org/doc/270875
ER -

References

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