Related papers: Efficient mesh refinement for the Poisson-Boltzman…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
A widely used electrostatics model in the biomolecular modeling community, the nonlinear Poisson-Boltzmann equation, along with its finite element approximation, are analyzed in this paper. A regularized Poisson-Boltzmann equation is…
In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
The Poisson-Boltzmann equation (PBE) models the electrostatic interactions of charged bodies such as molecules and proteins in an electrolyte solvent. The PBE is a challenging equation to solve numerically due to the presence of…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
In the discretization of differential problems on complex geometrical domains, discretization methods based on polygonal and polyhedral elements are powerful tools. Adaptive mesh refinement for such kind of problems is very useful as well…
We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a…
Mesh adaptivity is a useful tool for efficient solution to partial differential equations in very complex geometries. In the present paper we discuss the use of polygonal mesh refinement in order to tackle two common issues: first,…
Removing geometrical details from a complex domain is a classical operation in computer aided design. This procedure simplifies the meshing process, and it enables faster simulations with less memory requirements. However, depending on the…
This work delves into solving the two dimensional Poisson problem through the Finite Element Method which is relevant in various physical scenarios including heat conduction, electrostatics, gravity potential, and fluid dynamics. However,…
Consider the Poisson equation with the Dirichlet boundary condition on a three-dimensional polyhedral domain. For singular solutions from the non-smoothness of the domain boundary, we propose new anisotropic tetrahedral mesh refinement…
The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we…
In this article we study adaptive finite element methods (AFEM) with inexact solvers for a class of semilinear elliptic interface problems. We are particularly interested in nonlinear problems with discontinuous diffusion coefficients, such…
We analyze a new framework for expressing finite element methods on arbitrarily many intersecting meshes: multimesh finite element methods. The multimesh finite element method, first presented in [40], enables the use of separate meshes to…
This paper is concerned with approximations and related discretization error estimates for the normal derivatives of solutions of linear elliptic partial differential equations. In order to illustrate the ideas, we consider the Poisson…
We consider a class of nonlinear elliptic problems associated with models in biophysics, which are described by the Poisson-Boltzmann equation (PBE). We prove mathematical correctness of the problem, study a suitable class of…
Stochastic models of chemical systems are often analysed by solving the corresponding Fokker-Planck equation which is a drift-diffusion partial differential equation for the probability distribution function. Efficient numerical solution of…