Fast Algorithm for Solving Electrostatic Potential of Macromolecules in Solvent
Date Issued
2008
Date
2008
Author(s)
Dong, Xian-Wen
Abstract
In this paper, we study the Poisson-Boltzmann equation (PBE) in three dimensions numerically for computing the electrostatic potential for molecules in solvent. There are three numerical difficulties:(i) discontinuity of the dielectric coefficients large contrast across the boundaries of the macromolecules and solvent, (ii) potential singularity arisen from point charges of the macromolecules, (iii) nonlinearities of the solvent response. We take the following steps to resolve these difficulties. For (i), we adopt the coupling interfaceethod, which can deal with elliptic interface problems with large jumps of elliptic coefficients across interfaces. For (ii), the point charge potential inree space is used to remove the singularity of the potential. For (iii), we implement the damped Newton''s method to achieve quadratic convergence.umerical investigation for convergence rate and computation solution are performed for test probe and for a hydrophobic protein (PDB ID:1crn) and a hydrophilic protein (PDB ID:1DNG). It is shown the method is second-order accurate even for both the electric potential and the electric field around the molecular boundary.
Subjects
Poisson-Boltzmann equation
electrostatic potential
coupling interface method
Multigrid method
Type
thesis
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