A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation

Abstract

This work proposes a boundary integral formulation based Cartesian grid method for the nonlinear Poisson-Boltzmann (PB) interface problem in biophysics. The method (a) does not have the limitation associated with the standard finite difference method for complex interfaces, (b) avoids the generation of any unstructured volume or surface grids needed by the finite element method, and (c) solves the nonlinear and variable coefficient PDE in the framework of boundary integral equations. The method solves the nonlinear PB equation with the Newton iterative method. It first reformulates the linearized PB equation in each Newton iteration as a Fredholm system of two boundary integral (BI) equations of the second kind, which is well-conditioned, and then solves the BI system with a Krylov subspace method. The evaluation of boundary and volume integrals involved in the solution of the BI system is done with a kernel-free method, which does not need to know Green's function associated with the variable coefficient PB equation. The kernel-free method evaluates volume and boundary integrals by solving equivalent simple interface problems on Cartesian grids with either a fast Fourier transform based Poisson solver or a geometric multigrid preconditioned conjugate gradient solver, either of which involves computational work essentially linearly proportional to the number of nodes on the Cartesian grid. Numerical examples in both two and three space dimensions are presented to demonstrate the efficiency and accuracy of the proposed numerical method.