Key points are not available for this paper at this time.
This article is the first of two articles on the adaptive multilevel finite element treatment of the nonlinear Poisson–Boltzmann equation (PBE), a nonlinear eliptic equation arising in biomolecular modeling. Fast and accurate numerical solution of the PBE is usually difficult to accomplish, due to the presence of discontinuous coefficients, delta functions, three spatial dimensions, unbounded domain, and rapid (exponential) nonlinearity. In this first article, we explain how adaptive multilevel finite element methods can be used to obtain extremely accurate solutions to the PBE with very modest computational resources, and we present some illustrative examples using two well-known test problems. The PBE is first discretized with piece-wise linear finite elements over a very coarse simplex triangulation of the domain. The resulting nonlinear algebraic equations are solved with global inexact Newton methods, which we have described in an article appearing previously in this journal. A posteriori error estimates are then computed from this discrete solution, which then drives a simplex subdivision algorithm for performing adaptive mesh refinement. The discretize–solve–estimate–refine procedure is then repeated, until a nearly uniform solution quality is obtained. The sequence of unstructured meshes is used to apply multilevel methods in conjunction with global inexact Newton methods, so that the cost of solving the nonlinear algebraic equations at each step approaches optimal O(N) linear complexity. All of the numerical procedures are implemented in MANIFOLD CODE (MC), a computer program designed and built by the first author over several years at Caltech and UC San Diego. MC is designed to solve a very general class of nonlinear elliptic equations on complicated domains in two and three dimensions. We describe some of the key features of MC, and give a detailed analysis of its performance for two model PBE problems, with comparisons to the alternative methods. It is shown that the best available uniform mesh-based finite difference or box-method algorithms, including multilevel methods, require substantially more time to reach a target PBE solution accuracy than the adaptive multilevel methods in MC. In the second article, we develop an error estimator based on geometric solvent accessibility, and present a series of detailed numerical experiments for several complex biomolecules. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1319–1342, 2000
Holst et al. (Sat,) studied this question.