Energy-Conserving Numerical Scheme for the Poisson-Nerst-Plank Equations

Preliminary report.The Poisson-Nernst-Planck equations are a system of nonlinear partial differential equations that describe flow of charged particles in solution. In particular, we are interested in the transport of ions in the biological membrane proteins (ion channels). This work is about the design of numerical schemes that preserve exactly (up to roundoff error) a discretized form of the energy dynamics of the system. We will present a scheme that achieves the goal of preserving the energy dissipation law and some preliminary numerical results

A Conservative Finite Difference Scheme for Poisson-Nernst-Planck Equations

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

Second-Order Semi-Discretized Schemes for Solving Stochastic Quenching Models on Arbitrary Spatial Grids

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

Energy-Conserving Numerical Scheme for the Poisson-Nerst-Plank Equations

The Poisson-Nernst-Planck equations are a system of nonlinear partial differential equations that describe flow of charged particles in solution. In particular, we are interested in the transport of ions in the biological membrane proteins (ion channels). This work is about the design of numerical schemes that preserve exactly (up to round off error) a discretized form of the energy dynamics of the system. We will present a scheme that achieves the conservation of energy law, and the numerical results

An energy-preserving scheme for the Poisson -Nernst-Planck equations

Transport of ionic particles is ubiquitous in all biology. The Poisson-Nernst- Planck (PNP) equations have recently been used to describe the dynamics of ion transport through biological ion channels (besides being widely employed in semiconductor industry). This dissertation is about the design of a numerical scheme to solve the PNP equations that preserves exactly (up to roundoff error) a discretized form of the energy dynamics of the system. The proposed finite difference scheme is of second-order accurate in both space and time. Comparisons are made between this energy dynamics preserving scheme and a standard finite difference scheme, showing a difference in satisfying the energy law. Numerical results are presented for validating the orders of convergence in both time and space of the new scheme for the PNP system. The energy preserving scheme presented here is one dimensional in space. A highlight of an extension to the multi-dimensional case is shown.Ph.D. in Applied Mathematics, July 201