A macroscopic model to describe the dynamics of ion transport in ion channels is the Poisson-Nernst-Planck(PNP) equations. In this paper, we develop a finite-difference method for solving PNP equations, which is second-order accurate in both space and time. We use the physical parameters specifically suited toward the modelling of ion channels. We present a simple iterative scheme to solve the system of nonlinear equations resulting from discretizing the equations implicitly in time, which is demonstrated to converge in a few iterations. We place emphasis on ensuring numerical methods to have the same physical properties that the PNP equations themselves also possess, namely conservation of total ions and correct rates of energy dissipation. We describe in detail an approach to derive a finite-difference method that preserves the total concentration of ions exactly in time. Further, we illustrate that, using realistic values of the physical parameters, the conservation property is critical in obtaining correct numerical solutions over long time scales.

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Reaction-diffusion-advection equations provide precise interpretations for many important phenomena in complex interactions between natural and artificial systems. This paper studies second-order semi-discretizations for the numerical solution of reaction-diffusion-advection equations modeling quenching types of singularities occurring in numerous applications. Our investigations particularly focus at cases where nonuniform spatial grids are utilized. Detailed derivations and analysis are accomplished. Easy-to-use and highly effective second-order schemes are acquired. Computational experiments are presented to illustrate our results as well as to demonstrate the viability and capability of the new methods for solving singular quenching problems on arbitrary grid platforms.