Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules

doi:10.4208/cicp.2009.v6.p955

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	Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules
	Qin, Peihua 1,2; Xu, Zhenli 3; Cai, Wei 3; Jacobs, Donald 4
	2009-11-01
发表期刊	COMMUNICATIONS IN COMPUTATIONAL PHYSICS
ISSN	1815-2406
卷号	6 期号:5 页码:955-977
摘要	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.
关键词	Image charge methods distance-dependent dielectric permittivity hybrid implicit/explicit model reaction field Poisson-Boltzmann equation protein
DOI	10.4208/cicp.2009.v6.p955
语种	英语
资助项目	National Institutes of Health[1R01GM083600-02] ; Charlotte Research Institute through a Duke Postdoctoral Fellowship ; Department of Energy[DEFG0205ER25678]
WOS研究方向	Physics
WOS类目	Physics, Mathematical
WOS记录号	WOS:000269717500002
出版者	GLOBAL SCIENCE PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/7431
专题	中国科学院数学与系统科学研究院
通讯作者	Qin, Peihua
作者单位	1.Chinese Acad Sci, Inst Computat Math, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100190, Peoples R China 3.Univ N Carolina, Dept Math & Stat, Charlotte, NC 28223 USA 4.Univ N Carolina, Dept Phys & Opt Sci, Charlotte, NC 28223 USA
推荐引用方式 GB/T 7714	Qin, Peihua,Xu, Zhenli,Cai, Wei,et al. Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules[J]. COMMUNICATIONS IN COMPUTATIONAL PHYSICS,2009,6(5):955-977.
APA	Qin, Peihua,Xu, Zhenli,Cai, Wei,&Jacobs, Donald.(2009).Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules.COMMUNICATIONS IN COMPUTATIONAL PHYSICS,6(5),955-977.
MLA	Qin, Peihua,et al."Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules".COMMUNICATIONS IN COMPUTATIONAL PHYSICS 6.5(2009):955-977.