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Numerical Integration Techniques for Curved-Element Discretizations of Molecule–Solvent Interfaces

机译:分子-溶剂界面的弯曲元素离散化的数值积分技术

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摘要

Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, we have developed methods to model several important surface formulations using exact surface discretizations. Following and refining Zauhar’s work (J. Comp.-Aid. Mol. Des. 9:149-159, 1995), we define two classes of curved elements that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. We then present numerical integration techniques that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, we present a set of calculations that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planartriangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute–solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved approximations with increasing discretization and associated increases in computational resources. The results clearly demonstrate that our methods for approximate integration on an exact geometry are far more accurate than exact integration on an approximate geometry. A MATLAB implementation of the presented integration methods and sample data files containing curved-element discretizations of several small molecules are available online at .
机译:生物物理建模问题的表面配方提供了有吸引力的理论和计算特性。基于这些公式的数值模拟通常始于考虑中的表面的离散化。通常,表面是弯曲的,具有复杂的结构和可能的奇异之处。数值模拟通常基于这些表面的近似而不是精确的离散化。为了评估模拟精度对表面表示保真度的依赖性,我们开发了使用精确的表面离散化对几种重要的表面配方进行建模的方法。跟随并完善Zauhar的工作(J. Comp.-Aid。Mol。Des。9:149-159,1995年),我们定义了两类弯曲元素,它们可以精确地区分范德华,溶剂可及和溶剂除外。 (分子)表面。然后,我们提出了可以精确评估这些曲面上的非奇异和奇异积分的数值积分技术。在验证了表面离散化的准确性并证明了所提出的积分方法的正确性之后,我们提出了一组计算方法,用于比较近似的,基于平面三角形的离散化方法和基于精确的,基于弯曲元素的表面广义模拟的精度。 -出生(sGB),表面连续范德华(scvdW)和边界元法(BEM)静电问题。结果表明,对于具有可比较大小的基础集,使用弯曲元素,分段常数基函数和质心搭配的BEM连续统静电计算比平面三角形BEM精确近十倍。即使对于可获得的最粗糙的离散曲面,sGB和scvdW计算也能提供出色的精度。额外的准确性归因于溶质-溶剂界面的精确表示。相反,通常使用的平面三角形离散化只能随着离散化的增加和计算资源的相关增加而提供更好的近似值。结果清楚地表明,我们在精确几何图形上进行近似积分的方法比在近似几何图形上进行精确积分的方法要精确得多。可通过以下网址在线获取所提出的积分方法和包含几个小分子的弯曲元素离散化的示例数据文件的MATLAB实现。

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