Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

• Published in: Journal of computational chemistry 2003-02, Vol.24 (3), p.353-367
• Main Authors: Bordner, A. J., Huber, G. A.
• Format: Article
• Language: English
• Subjects: Actins - chemistry; Algorithms; boundary element method; Brownian dynamics; cell multipole method; Chemistry, Physical - methods; Computer Simulation; Macromolecular Substances; Models, Molecular; molecular dynamics; Poisson-Boltzmann equation; Solutions; Static Electricity; Water - chemistry
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.10195

The Poisson–Boltzmann equation is widely used to describe the electrostatic potential of molecules in an ionic solution that is treated as a continuous dielectric medium. The linearized form of this equation, applicable to many biologic macromolecules, may be solved using the boundary element method. A single‐layer formulation of the boundary element method, which yields simpler integral equations than the direct formulations previously discussed in the literature, is given. It is shown that the electrostatic force and torque on a molecule may be calculated using its boundary element representation and also the polarization charge for two rigid molecules may be rapidly calculated using a noniterative scheme. An algorithm based on a fast adaptive multipole method is introduced to further increase the speed of the calculation. This method is particularly suited for Brownian dynamics or molecular dynamics simulations of large molecules, in which the electrostatic forces must be calculated for many different relative positions and orientations of the molecules. It has been implemented as a set of programs in C++, which are used to study the accuracy and speed of this method for two actin monomers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 353–367, 2003