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隐式溶剂模型中电荷奇点的处理。

Treatment of charge singularities in implicit solvent models.

作者信息

Geng Weihua, Yu Sining, Wei Guowei

机构信息

Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, USA.

出版信息

J Chem Phys. 2007 Sep 21;127(11):114106. doi: 10.1063/1.2768064.

Abstract

This paper presents a novel method for solving the Poisson-Boltzmann (PB) equation based on a rigorous treatment of geometric singularities of the dielectric interface and a Green's function formulation of charge singularities. Geometric singularities, such as cusps and self-intersecting surfaces, in the dielectric interfaces are bottleneck in developing highly accurate PB solvers. Based on an advanced mathematical technique, the matched interface and boundary (MIB) method, we have recently developed a PB solver by rigorously enforcing the flux continuity conditions at the solvent-molecule interface where geometric singularities may occur. The resulting PB solver, denoted as MIBPB-II, is able to deliver second order accuracy for the molecular surfaces of proteins. However, when the mesh size approaches half of the van der Waals radius, the MIBPB-II cannot maintain its accuracy because the grid points that carry the interface information overlap with those that carry distributed singular charges. In the present Green's function formalism, the charge singularities are transformed into interface flux jump conditions, which are treated on an equal footing as the geometric singularities in our MIB framework. The resulting method, denoted as MIBPB-III, is able to provide highly accurate electrostatic potentials at a mesh as coarse as 1.2 A for proteins. Consequently, at a given level of accuracy, the MIBPB-III is about three times faster than the APBS, a recent multigrid PB solver. The MIBPB-III has been extensively validated by using analytically solvable problems, molecular surfaces of polyatomic systems, and 24 proteins. It provides reliable benchmark numerical solutions for the PB equation.

摘要

本文提出了一种求解泊松-玻尔兹曼(PB)方程的新方法,该方法基于对电介质界面几何奇点的严格处理以及电荷奇点的格林函数公式。电介质界面中的几何奇点,如尖点和自相交表面,是开发高精度PB求解器的瓶颈。基于一种先进的数学技术——匹配界面和边界(MIB)方法,我们最近通过在可能出现几何奇点的溶剂-分子界面严格执行通量连续性条件,开发了一种PB求解器。由此产生的PB求解器,记为MIBPB-II,能够为蛋白质分子表面提供二阶精度。然而,当网格尺寸接近范德华半径的一半时,MIBPB-II无法保持其精度,因为携带界面信息的网格点与携带分布奇异电荷的网格点重叠。在当前的格林函数形式中,电荷奇点被转化为界面通量跳跃条件,在我们的MIB框架中,这些条件与几何奇点同等对待。由此产生的方法,记为MIBPB-III,能够在低至1.2埃的粗网格上为蛋白质提供高精度的静电势。因此,在给定精度水平下,MIBPB-III比最近的一种多重网格PB求解器APBS快约三倍。MIBPB-III已通过使用可解析求解的问题、多原子系统的分子表面和24种蛋白质进行了广泛验证。它为PB方程提供了可靠的基准数值解。

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