Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format

The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong singularities and nonlinearity caused by the singular source...

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Bibliographic Details
Published inarXiv.org
Main Authors Kweyu, Cleophas, Khoromskaia, Venera, Khoromskij, Boris, Stein, Matthias, Benner, Peter
Format Paper
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 10.06.2023
Subjects
Biomolecules
Boltzmann transport equation
Boundary conditions
Continuum modeling
Decomposition
Discretization
Mathematical analysis
Nonlinearity
Regularization
Regularization methods
Singularities
Solvents
Tensors
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Summary:The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong singularities and nonlinearity caused by the singular source terms and the exponential nonlinear terms, respectively. An efficient method for the treatment of singularities in the linear PBE was introduced in \cite{BeKKKS:18}, that is based on the RS tensor decomposition for both electrostatic potential and the discretized Dirac delta distribution. In this paper, we extend this regularization method to the nonlinear PBE. We apply the PBE only to the regular part of the solution corresponding to the modified right-hand side via extraction of the long-range part in the discretized Dirac delta distribution. The total electrostatic potential is obtained by adding the long-range solution to the directly precomputed short-range potential. The main computational benefit of the approach is the automatic maintaining of the continuity in the Cauchy data on the solute-solvent interface. The boundary conditions are also obtained from the long-range component of the precomputed canonical tensor representation of the Newton kernel. In the numerical experiments, we illustrate the accuracy of the nonlinear regularized PBE (NRPBE) over the classical variant.
ISSN:2331-8422