Volume 6, Issue 5
Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules

Peihua Qin, Zhenli Xu, Wei Cai & Donald Jacobs

DOI:

Commun. Comput. Phys., 6 (2009), pp. 955-977.

Published online: 2009-06

Preview Full PDF 202 1156
Export citation
  • Abstract

This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the Poisson-Boltzmann equation. In this model, an interior spherical cavity will contain the solute and some explicit solvent molecules, and an intermediate buffer layer and an exterior layer contain the bulk solvent. A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer. The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion. Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions. Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects. In particular, the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent. Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.

  • Keywords

  • AMS Subject Headings

  • Copyright

COPYRIGHT: © Global Science Press

  • Email address
  • BibTex
  • RIS
  • TXT
@Article{CiCP-6-955, author = {}, title = {Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules}, journal = {Communications in Computational Physics}, year = {2009}, volume = {6}, number = {5}, pages = {955--977}, abstract = {

This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the Poisson-Boltzmann equation. In this model, an interior spherical cavity will contain the solute and some explicit solvent molecules, and an intermediate buffer layer and an exterior layer contain the bulk solvent. A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer. The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion. Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions. Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects. In particular, the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent. Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.

}, issn = {1991-7120}, doi = {https://doi.org/}, url = {http://global-sci.org/intro/article_detail/cicp/7713.html} }
TY - JOUR T1 - Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules JO - Communications in Computational Physics VL - 5 SP - 955 EP - 977 PY - 2009 DA - 2009/06 SN - 6 DO - http://doi.org/ UR - https://global-sci.org/intro/article_detail/cicp/7713.html KW - AB -

This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the Poisson-Boltzmann equation. In this model, an interior spherical cavity will contain the solute and some explicit solvent molecules, and an intermediate buffer layer and an exterior layer contain the bulk solvent. A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer. The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion. Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions. Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects. In particular, the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent. Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.

Peihua Qin, Zhenli Xu, Wei Cai & Donald Jacobs. (2020). Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules. Communications in Computational Physics. 6 (5). 955-977. doi:
Copy to clipboard
The citation has been copied to your clipboard