An implicit Euler finite‐volume scheme for a degenerate cross‐diffusion system describing the ion transport through biological membranes is proposed. The strongly coupled equations for the ion concentrations include drift terms involving the electric potential, which is coupled to the concentrations through the Poisson equation. The cross‐diffusion system possesses a formal gradient‐flow structure revealing nonstandard degeneracies, which lead to considerable mathematical difficulties. The finite‐volume scheme is based on two‐point flux approximations with “double” upwind mobilities. The existence of solutions to the fully discrete scheme is proved. When the particles are not distinguishable and the dynamics is driven by cross diffusion only, it is shown that the scheme preserves the structure of the equations like nonnegativity, upper bounds, and entropy dissipation. The degeneracy is overcome by proving a new discrete Aubin–Lions lemma of “degenerate” type. Numerical simulations of a calcium‐selective ion channel in two space dimensions show that the scheme is efficient even in the general case of ion transport.

A cross-diffusion system describing ion transport through biological membranes or nanopores in a bounded domain with mixed Dirichlet-Neumann boundary conditions is analyzed. The ion concentrations solve strongly coupled diffusion equations with a drift term involving the electric potential which is coupled to the concentrations through a Poisson equation. The global-in-time existence of bounded weak solutions and the uniqueness of weak solutions under moderate regularity assumptions are shown. The main difficulties of the analysis are the cross-diffusion terms and the degeneracy of the diffusion matrix, preventing the use of standard tools. The proofs are based on the boundedness-by-entropy method, extended to nonhomogeneous boundary conditions, and the uniqueness technique of Gajewski. A finite-volume discretization in one space dimension illustrates the large-time behavior of the numerical solutions and shows that the equilibration rates may be very small.

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A structure-preserving implicit Euler finite-element scheme for a degenerate cross-diffusion system for ion transport is analyzed. The scheme preserves the nonnegativity and upper bounds of the ion concentrations, the total relative mass, and it dissipates the entropy (or free energy). The existence of discrete solutions to the scheme and their convergence towards a solution to the continuous system is proved. Numerical simulations of two-dimensional ion channels using the finite-element scheme with linear elements and an alternative finite-volume scheme are presented. The advantages and drawbacks of both schemes are discussed in detail.