论文标题

带有欧拉溶剂的Poisson-Boltzmann方程的自适应伪时间方法排除了表面

Adaptive pseudo-time methods for the Poisson-Boltzmann equation with Eulerian solvent excluded surface

论文作者

Jones, Benjamin, Ullah, Sheik Ahmed, Wang, Siwen, Zhao, Shan

论文摘要

这项工作进一步改善了溶剂分析静电分析中泊松玻尔兹曼方程(PBE)的伪透射方法。已知非线性PBE的数值解决方案涉及许多困难,例如指数非线性项,源术语的强奇异性以及复杂的介电界面。最近,[S. Ahmed Ullah和S. Zhao,《应用数学与计算》,380,125267,(2020)],通过分析处理非线性和奇异来源。 GFM界面处理不仅捕获了正则电势的不连续性及其在分子表面的通量,而且还可以保证时间整合的稳定性和效率。但是,已知基于MSMS封装的分子表面定义在某些情况下会诱导不稳定,而对于GFM有限的差异离散化,非平凡的Lagrangian to-Eulerian转换是必不可少的。在本文中,实现了欧拉溶剂排除的表面(ESE),以替换定义介电界面的MSMS。静电分析表明,ESES自由能比MSMS更准确,而没有不稳定性问题。此外,这项工作在PBE文献中首次探讨了伪频率模拟的自适应时间集成技术。一个主要发现是,随着时间的增加,时间增加$ΔT$应该变得较小,以保持时间准确性。这与稳态收敛的共同实践相反,并且据信是由于PBE非线性及其时间分裂处理。已经构建了有效的自适应方案,以使伪时间GFM方法比常数$ΔT$更有效。

This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties, such as exponential nonlinear term, strong singularity by the source terms, and complex dielectric interface. Recently, a pseudo-time ghost-fluid method (GFM) has been developed in [S. Ahmed Ullah and S. Zhao, Applied Mathematics and Computation, 380, 125267, (2020)], by analytically handling both nonlinearity and singular sources. The GFM interface treatment not only captures the discontinuity in the regularized potential and its flux across the molecular surface, but also guarantees the stability and efficiency of the time integration. However, the molecular surface definition based on the MSMS package is known to induce instability in some cases, and a nontrivial Lagrangian-to-Eulerian conversion is indispensable for the GFM finite difference discretization. In this paper, an Eulerian Solvent Excluded Surface (ESES) is implemented to replace the MSMS for defining the dielectric interface. The electrostatic analysis shows that the ESES free energy is more accurate than that of the MSMS, while being free of instability issues. Moreover, this work explores, for the first time in the PBE literature, adaptive time integration techniques for the pseudo-transient simulations. A major finding is that the time increment $Δt$ should become smaller as the time increases, in order to maintain the temporal accuracy. This is opposite to the common practice for the steady state convergence, and is believed to be due to the PBE nonlinearity and its time splitting treatment. Effective adaptive schemes have been constructed so that the pseudo-time GFM methods become more efficient than the constant $Δt$ ones.

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