Communications in Information and Systems

Volume 21 (2021)

Number 1

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

Pages: 85 – 123

DOI: https://dx.doi.org/10.4310/CIS.2021.v21.n1.a5

Authors

Benjamin Jones (Department of Mathematics, University of Alabama, Tuscaloosa, Al., U.S.A.)

Sheik Ahmed Ullah (Department of Mathematics, Stillman College, Tuscaloosa, Al., U.S.A.)

Siwen Wang (Department of Mathematics, University of Alabama, Tuscaloosa, Al., U.S.A.)

Shan Zhao (Department of Mathematics, University of Alabama, Tuscaloosa, Al., U.S.A.)

Abstract

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 $\Delta t$ 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 $\Delta t$ ones.

Keywords

Poisson–Boltzmann equation, pseudo-transient continuation, molecular surface, adaptive time integration, alternating direction implicit (ADI), ghost fluid method

This research is partially supported by the National Science Foundation (NSF) of USA under grant DMS-1812930.

Received 23 September 2020