Electrical double layer defines the reaction environment by influencing transport of CO2, local pH, electrical field strength and solvent polarization.

Abstract. We derive a numerical method for Darcy flow, hence also for Poisson's equation in first order form, based on discrete exterior calculus (DEC). Exterior calculus is a generalization of vector calculus to smooth manifolds and DEC is its discretization on simplicial complexes such as triangle and tetrahedral meshes. We start by rewriting the governing equations of Darcy flow using the language of exterior calculus. This yields a formulation in terms of flux differential form and pressure. The numerical method is then derived by using the framework provided by DEC for discretizing differential forms and operators that act on forms. We also develop a discretization for spatially dependent Hodge star that varies with the permeability of the medium. This also allows us to address discontinuous permeability. The matrix representation for our discrete non-homogeneous Hodge star is diagonal, with positive diagonal entries. The resulting linear system of equations for flux and pressure are saddle type, with a diagonal matrix as the top left block. Our method requires the use of meshes in which each simplex contains its circumcenter. The performance of the proposed numerical method is illustrated on many standard test problems. These include patch tests in two and three dimensions, comparison with analytically known solution in two dimensions, layered medium with alternating permeability values, and a test with a change in permeability along the flow direction. A short introduction to the relevant parts of smooth and discrete exterior calculus is included in this paper. We also include a discussion of the boundary condition in terms of exterior calculus.

The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and results in solutions with finite ion concentrations. Here, we evaluate numerical methods for solving the modified Poisson-Nernst-Planck equations by modeling electric field-driven transport of ions through a nanopore. We describe a novel, robust finite element solver that combines the applications of the Newton's method to the nonlinear Galerkin form of the equations, augmented with stabilization terms to appropriately handle the drift-diffusion processes. To make direct comparison with particle-based simulations possible, our method is specifically designed to produce solutions under periodic boundary conditions and to conserve the number of ions in the solution domain. We test our finite element solver on a set of challenging numerical experiments that include calculations of the ion distribution in a volume confined between two charged plates, calculations of the ionic current though a nanopore subject to an external electric field, and modeling the effect of a DNA molecule on the ion concentration and nanopore current.

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. The least-squares finite element approximation naturally provides an a posteriori error estimator and we present numerical evidence in support of the method. The computational results highlight optimality in the case of adaptive mesh refinement for a variety of molecular configurations. In particular, we show promising performance for the Born ion, Fasciculin 1, methanol, and a dipole, which highlights robustness of our approach.

Implicit-Explicit (IMEX) schemes are an important and widely used class of time integration methods for both parabolic and hyperbolic partial differential equations. We develop accurate a posteriori error estimates for a user-defined quantity of interest for two classes of multi-step IMEX schemes for advection-diffusion-reaction problems. The analysis proceeds by recasting the IMEX schemes into a variational form suitable for a posteriori error analysis employing adjoint problems and computable residuals. The a posteriori estimates quantify distinct contributions from various aspects of the spatial and temporal discretizations, and can be used to evaluate discretization choices. Numerical results are presented that demonstrate the accuracy of the estimates for a representative set of problems. Published by Elsevier B.V.