An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson-Boltzmann-Based Molecular Electrostatics

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson–Boltzmann equation. Our approach combines several important features, including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. Key words. Poisson–Boltzmann equation, boundary element method, fast multipole method AMS subject classifications. 92C40, 65N38 DOI. 10.1137/090764645

• Type: Journal
• Year: 2011
• Where: SIAMSC
• Authors: Chandrajit L. Bajaj, Shun-Chuan Albert Chen, Alexander Rand
• Keywords: Boundary Element, Poisson–Boltzmann Equation, Polarization Energy, SIAMSC 2011, Software Engineering