Convergent finite element discretizations of the Navier-Stokes-Nernst-Planck-Poisson system (original) (raw)

The finite element approximation of the nonlinear Poisson-Boltzmann equation

2007

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 introduced as an auxiliary problem, making it possible to study the original nonlinear equation with delta distribution sources. A priori error estimates for the finite element approximation are obtained for the regularized Poisson-Boltzmann equation based on certain quasi-uniform grids in two and three dimensions. Adaptive finite element approximation through local refinement driven by an a posteriori error estimate is shown to converge. The Poisson-Boltzmann equation does not appear to have been previously studied in detail theoretically, and it is hoped that this paper will help provide molecular modelers with a better foundation for their analytical and computational work with the Poisson-Boltzmann equation. Note that this article apparently gives the first rigorous convergence result for a numerical discretization technique for the nonlinear Poisson-Boltzmann equation with delta distribution sources, and it also introduces the first provably convergent adaptive method for the equation. This last result is currently one of only a handful of existing convergence results of this type for nonlinear problems. References 21

Modeling electrochemical systems with weakly imposed Dirichlet boundary conditions

ArXiv, 2020

Finite element modeling of charged species transport has enabled analysis, design and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Plank equations coupled with the Navier-Stokes equation, with a key quantity of interest being the current at the system boundaries. Accurately computing the current flux is challenging due to the small critical dimension of the boundary layers (small Debye layer) that require fine mesh resolution at the boundaries. We resolve this challenge by using the Dirichlet-to-Neumann transformation to weakly impose the Dirichlet conditions for the Poisson-Nernst-Plank equations. The results obtained with weakly imposed Dirichlet boundary conditions showed excellent agreement with those obtained when conventional boundary conditions with highly resolved mesh were employed. Furthermore, the calculated current flux showed faster mesh convergence using weakly imposed conditions comp...

Asymptotic analysis of the Poisson–Boltzmann equation describing electrokinetics in porous media

Nonlinearity, 2013

We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of N chemical species diluted in a liquid at rest, occupying the pore space with charged solid boundaries. We study the asymptotic behavior of its solution depending on a parameter β which is the square of the ratio between a characteristic pore length and the Debye length. For small β we identify the limit problem which is still a nonlinear Poisson equation involving only one species with maximal valence, opposite to the average of the given surface charge density. This result justifies the Donnan effect, observing that the ions for which the charge is the one of the solid phase are expelled from the pores. For large β we prove that the solution behaves like a boundary layer near the pore walls and is constant far away in the bulk. Our analysis is valid for Neumann boundary conditions (namely for imposed surface charge densities) and establishes rigorously that solid interfaces are uncoupled from the bulk fluid, so that the simplified additive theories, such as the one of the popular Derjaguin, Landau, Verwey and Overbeek (DLVO) approach, can be used. We show that the asymptotic behavior is completely different in the case of Dirichlet boundary conditions (namely for imposed surface potential).

Computer simulations of electrodiffusion problems based on Nernst–Planck and Poisson equations

Computational Materials Science, 2012

A numerical procedure based on the method of lines for time-dependent electrodiffusion transport has been developed. Two types of boundary conditions (Neumann and Dirichlet) are considered. Finite difference space discretization with suitably selected weights based on a non-uniform grid is applied. Consistency of this method and the method put forward by Brumleve and Buck are analysed and compared. The resulting stiff system of ordinary differential equations is effectively solved using the RADAU5, RODAS and SEULEX integrators. The applications to selected electrochemical systems: liquid junction, bi-ionic case, ion selective electrodes and electrochemical impedance spectroscopy have been demonstrated. In the paper we promote the use of the full form of the Nernst-Planck and Poisson (NPP) equations, that is including explicitly the electric field as an unknown variable with no simplifications like electroneutrality or constant field assumptions. An effective method of the numerical solution of the NPP problem for arbitrary number of ionic species and valence numbers either for a steady state or a transient state is shown. The presented formulae-numerical solutions to the NPP problem-are ready to be implemented by anyone. Moreover, we make the resulting software freely available to anybody interested in using it.

A first‐order system least‐squares finite element method for the Poisson‐Boltzmann equation

2010

Abstract The Poisson-Boltzmann equation is an important tool in modeling solvent in biomolecular systems. In this article, we focus on numerical approximations to the electrostatic potential expressed in the regularized linear Poisson-Boltzmann equation. We expose the flux directly through a first-order system form of the equation. Using this formulation, we propose a system that yields a tractable least-squares finite element formulation and establish theory to support this approach.

Entropy method for generalized Poisson–Nernst–Planck equations

Analysis and Mathematical Physics

A proper mathematical model given by nonlinear Poisson-Nernst-Planck (PNP) equations which describe electrokinetics of charged species is considered. The model is generalized with entropy variables associating the pressure and quasi-Fermi electrochemical potentials in order to adhere to the law of conservation of mass. Based on a variational principle for suitable free energy, the generalized PNP system is endowed with the structure of a gradient flow. The well-posedness theorems for the mixed formulation (using the entropy variables) of the gradient-flow problem are provided within the Gibbs simplex and supported by a-priori estimates of the solution.

Diffusion approach to the linear Poisson–Boltzmann equation

1998

. The linear Poisson-Boltzmann equation LPBE is mapped onto a transient diffusion problem in which the charge density becomes an initial distribution, the dielectric permittivity plays the role of either a diffusion coefficient or a potential of interaction and screening becomes a sink term. This analogy can be useful in two ways. From the analytical point of view, solutions of the LPBE with seemingly different functional forms are unified as Laplace transforms of the fundamental Gaussian solution for diffusion. From the numerical point of view, a first off-grid algorithm for solving the LPBE is constructed by running Brownian trajectories in the presence of scavenging. q 1998 Elsevier Science B.V.