An implicit boundary integral method for computing electric potential of macromolecules in solvent
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level set methodelectrostaticsfast multipole methodPoisson-Boltzmann equationimplicit solvent modelimplicit boundary integral method
Biochemistry, molecular biology (92C40) Laplace operator, Helmholtz equation (reduced wave equation), Poisson equation (35J05) Electro- and magnetostatics (78A30) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Multipole methods applied to problems in optics and electromagnetic theory (78M16)
Abstract: A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit boundary integral formulation to derived a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separate the molecule and the solvent. The needed implicit surfaces is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.
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Cited in
(18)- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
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