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Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation.
Journal of Computational Physics ( IF 4.1 ) Pub Date : 2020-07-23 , DOI: 10.1016/j.jcp.2020.109725
George Borleske 1 , Y C Zhou 1
Affiliation  

Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is proposed to calculate these quantities on the dielectric interface from the numerical solutions of the Poisson-Boltzmann equation. Our method reconstructs a potential field locally in the least square sense on the polynomial basis enriched with Green's functions, the latter characterize the Coulomb potential induced by charges near the position of reconstruction. This enrichment resembles the decomposition of electrostatic potential into singular Coulomb component and the regular reaction field in the Generalized Born methods. Numerical experiments demonstrate that the enrichment recovery produces drastically more accurate and stable potential gradients on molecular surfaces compared to classical recovery techniques.



中文翻译:

Poisson-Boltzmann 方程界面解的增强梯度恢复。

精确计算分子表面上的静电势和梯度对于溶剂中生物分子大规模变形的连续和混合建模是非常需要的。在本文中,提出了一种新的数值方法,用于根据 Poisson-Boltzmann 方程的数值解计算介电界面上的这些量。我们的方法在富含格林函数的多项式基础上以最小二乘意义局部重建势场,后者表征由重建位置附近的电荷引起的库仑势。这种富集类似于将静电势分解为奇异的库仑分量和广义玻恩方法中的规则反应场。

更新日期:2020-08-03
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