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A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

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成果类型:
期刊论文
作者:
Li, J.;Ying, J.*
通讯作者:
Ying, J.
作者机构:
School of Mathematics and Statistics, Changsha University of Science and Technology, Changsha, Hunan, 410114, China
School of Mathematics and Statistics, Central South University, Changsha, Hunan, 410083, China
通讯机构:
School of Mathematics and Statistics, Central South University, Changsha, Hunan, China
语种:
英文
关键词:
Biomolecular electrostatics;Block iteration method;Finite element method;Implicit continuum model;Nonlocal model
期刊:
JOURNAL OF INDUSTRIAL AND MANAGEMENT OPTIMIZATION
ISSN:
1547-5816
年:
2020
卷:
16
期:
1
页码:
325-356
机构署名:
本校为第一机构
院系归属:
数学与统计学院
摘要:
The nonlocal mofied Poisson-Boltzmann equation (NMPBE) is one important variant of a commonly-used dielectric continuum model, Poisson-Boltzmann equation (PBE). In this paper, we use a nonlinear block relaxation method to develop a new nonlinear solver for the nonlinear equation of Φ and thus a new NMPBE solver, which is then programmed as a software package in C\C++, Fortran and Python for computing the electrostatics of a protein in a symmetric 1:1 ionic solvent. Numerical tests validate the new package and show that the new solver can impro...

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