A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver

被引：3

作者：

Chen, Jiahui ^{[1
]}

Tausch, Johannes ^{[2
]}

Geng, Weihua ^{[2
]}

机构：

[1] Michigan State Univ, Dept Math, E Lansing, MI 48824 USA

[2] Southern Methodist Univ, Dept Math, Dallas, TX 75275 USA

来源：

JOURNAL OF COMPUTATIONAL PHYSICS | 2023年 / 478卷

关键词：

Fast multipole method; Electrostatic; Boundary integral; Poisson; -Boltzmann; Preconditioning; GMRES; FAST-MULTIPOLE-METHOD; MATCHED INTERFACE; ELEMENT SOLUTION; FINITE-ELEMENT; TREECODE; ELECTROSTATICS; EQUATION; VERSION; MACROMOLECULES; DECOMPOSITION;

D O I：

10.1016/j.jcp.2023.111981

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method for solving the linear Poisson-Boltzmann (PB) equation. The solver has combined advantages in accuracy, efficiency, and memory usage as it applies a well-posed boundary integral formulation to circumvent many numerical difficulties associated with the PB equation and uses an O(N) Cartesian Fast Multipole Method (FMM) to accelerate the GMRES iteration. In addition, special numerical treatments such as adaptive FMM order, block diagonal preconditioners, Galerkin discretization, and Duffy's transformation are combined to improve the performance of the solver, which is validated on benchmark Kirkwood's sphere and a series of testing proteins.

引用

页数：19

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