An implicit boundary integral method for computing electric potential of macromolecules in solvent
An implicit boundary integral method for computing electric potential of macromolecules in solvent
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DOI：
10.1016/j.jcp.2018.01.021
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发表时间：
2017-09
期刊：
影响因子：
--
通讯作者：
Yimin Zhong;Kui Ren;R. Tsai
中科院分区：
文献类型：
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作者：
Yimin Zhong;Kui Ren;R. Tsai
提出了一种使用隐式表面表示的数值方法来求解线性化的Poisson-Boltzmann方程，该方程出现在溶剂中分子静电的数学模型中。所提出的方法使用隐式边界积分公式来推导出定义在围绕分离分子和溶剂的封闭表面的窄带中的笛卡尔节点上的线性系统。所需的隐式表面构造从给定的分子的原子描述，通过一系列的标准水平集算法。采用快速多极子方法加速线性方程组的求解。一些数值研究涉及一些标准的测试用例，并与其他现有的结果进行比较。
A numerical method using implicit surface representations is proposed to solve the linearized Poisson–Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.