A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

Yi Jiang; Jinyong Ying; Dexuan Xie

Molecular Based Mathematical Biology (2014)

  • Volume: 2, Issue: 1
  • ISSN: 2299-3266

Abstract

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The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.

How to cite

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Yi Jiang, Jinyong Ying, and Dexuan Xie. "A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications." Molecular Based Mathematical Biology 2.1 (2014): null. <http://eudml.org/doc/267053>.

@article{YiJiang2014,
abstract = {The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.},
author = {Yi Jiang, Jinyong Ying, Dexuan Xie},
journal = {Molecular Based Mathematical Biology},
keywords = {Poisson-Boltzmann equation; continuum electrostatics; finite element method; finite difference method; electrostatic potential},
language = {eng},
number = {1},
pages = {null},
title = {A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications},
url = {http://eudml.org/doc/267053},
volume = {2},
year = {2014},
}

TY - JOUR
AU - Yi Jiang
AU - Jinyong Ying
AU - Dexuan Xie
TI - A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications
JO - Molecular Based Mathematical Biology
PY - 2014
VL - 2
IS - 1
SP - null
AB - The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.
LA - eng
KW - Poisson-Boltzmann equation; continuum electrostatics; finite element method; finite difference method; electrostatic potential
UR - http://eudml.org/doc/267053
ER -

References

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