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An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics. (English) Zbl 1227.92005

Summary: In order to compute the 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 a 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.

MSC:

92C05 Biophysics
92C40 Biochemistry, molecular biology
65N38 Boundary element methods for boundary value problems involving PDEs
35Q92 PDEs in connection with biology, chemistry and other natural sciences
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