Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2109.14073

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

Cleophas Kweyu·Venera Khoromskaia·Boris Khoromskij·Matthias Stein·Peter Benner
View original source ↗Read source document ↗Export metadata ↓

Abstract

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.

Explore related subjects

math.NAcs.NA

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Cleophas Kweyu, Venera Khoromskaia, Boris Khoromskij, Matthias Stein, Peter Benner. 2023-06-10. Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format. https://arxiv.org/abs/2109.14073

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Fully spectral scheme for the linear BGK equation on the whole space

In this article, we design a fully spectral method in both space and velocity for a linear inhomogeneous kinetic equation with mass, momentum and energy conservation. We focus on the linear BGK equation with a confinement potential $Φ$, even if the method could be applied to different collision operators. It is based upon the projection on Hermite polynomials in velocity and orthonormal polynomials with respect to the weight $e^{-$Φ$}$ in space. The potential $Φ$ is assumed to be a polynomial. It is, to the author's knowledge, the first scheme which preserves hypocoercive behavior in addition to the conservation laws. These different properties are illustrated numerically on both quadratic and double well potential.

math.NA↗
arXiv2026

Inverse inequalities for kernel-based approximation on bounded domains and Riemannian manifolds

This paper establishes inverse inequalities for kernel-based approximation spaces defined on bounded Lipschitz domains in $\mathbb{R}^d$ and compact Riemannian manifolds. While inverse inequalities are well-studied for polynomial spaces, their extension to kernel-based trial spaces poses significant challenges. For bounded Lipschitz domains, we extend prior Bernstein inequalities, which only apply to a limited range of Sobolev orders, to the full range of lower and upper orders, and derive Nikolskii inequalities that bound $L_\infty$ norms by $L_2$ norms. For compact Riemannian manifolds, we focus on restricted kernels, which are defined as the restriction of positive definite kernels from the ambient Euclidean space to the manifold, and prove their counterparts.

math.NA↗
arXiv2026

Error Estimates for Hyperbolic Scaling Limits of Linear Kinetic Models on Networks

This paper studies linear discrete kinetic models on networks and their asymptotic behavior in the small Knudsen number limit. For coupling conditions at an n-edge junction under a symmetric formulation, we introduce a change of variables that reformulates the system into n independent initial-boundary value problems. The asymptotic expansions are then constructed and rigorously justified by deriving an error estimate based on the energy method.

math.NA↗