UC San Diego

Incorporation of van der Waals interactions enables the continuum model of electrodiffusion in biomolecular system to avoid the artifacts of introducing a molecular surface and the painful task of the surface mesh generation. Calculation examples show that the electrostatics, diffusion-reaction kinetics, and molecular surface defined as an isosurface of a certain density distribution can be extracted from the solution of the Poisson-Nernst-Planck equations using this model. The molecular surface-free model enables a wider usage of some modern numerical methodologies such as finite element methods for biomolecular modeling, and sheds light on a new paradigm of continuum modeling for biomolecular systems. (C) 2007 Elsevier B.V. All rights reserved.