Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization

Sheik Ahmed Ullah and Shan Zhao

Applied Mathematics and Computation, 2020, vol. 380, issue C

Abstract: The Poisson Boltzmann equation (PBE) is a well-established implicit solvent continuum model for the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is still a challenge due to its exponential nonlinear term, strong singularity by the source terms, and distinct dielectric regions. In this paper, a new pseudo-transient approach is proposed, which combines an analytical treatment of singular charges in a two-component regularization, with an analytical integration of nonlinear term in pseudo-time solution. To ensure efficiency, both fully implicit alternating direction implicit (ADI) and unconditionally stable locally one-dimensional (LOD) methods have been constructed to decompose three-dimensional linear systems into one-dimensional (1D) ones in each pseudo-time step. Moreover, to accommodate the nonzero function and flux jumps across the dielectric interface, a modified ghost fluid method (GFM) has been introduced as a first order accurate sharp interface method in 1D style, which minimizes the information needed for the molecular surface. The 1D finite-difference matrix generated by the GFM is symmetric and diagonally dominant, so that the stability of ADI and LOD methods is boosted. The proposed pseudo-transient GFM schemes have been numerically validated by calculating solvation free energy, binding energy, and salt effect of various proteins. It has been found that with the augmentation of regularization and GFM interface treatment, the ADI method not only enhances the accuracy dramatically, but also improves the stability significantly. By using a large time increment, an efficient protein simulation can be realized in steady-state solutions. Therefore, the proposed GFM-ADI and GFM-LOD methods provide accurate, stable, and efficient tools for biomolecular simulations.

Keywords: Poisson-Boltzmann Equation; Regularization; Pseudo-transient continuation approach; Ghost Fluid Method; Alternating direction implicit (ADI) (search for similar items in EconPapers)
Date: 2020
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:apmaco:v:380:y:2020:i:c:s0096300320302368

DOI: 10.1016/j.amc.2020.125267

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