A new numerical method for nonlocal electrostatics in biomolecular simulations

The electrostatic behavior of biomolecules solved in water can be described by an elliptic system of partial differential equations for the potential. In previous studies, this system has been solved by the Boundary Element Method (BEM). In this paper, we apply the Explicit Jump Immersed Interface Method (EJIIM) as an alternative method to the BEM. Such a finite difference approach allows for a completely automatized software for analyzing biomolecules in their natural surrounding. The new method shows excellent agreement with the BEM results and has good convergence properties and runtimes. In addition, in contrast to the BEM, where the fundamental solutions of operators are necessary, the EJIIM approach can be easily extended to more complex, especially nonlinear models. (C) 2010 Elsevier Inc. All rights reserved.