A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
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binding free energydomain decompositionelectrostatic solvation free energyfinite difference methodfinite element methodPoisson-Boltzmann equation
Finite difference methods for boundary value problems involving PDEs (65N06) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Multigrid methods; domain decomposition for boundary value problems involving PDEs (65N55) Packaged methods for numerical algorithms (65Y15)
Abstract: The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an ionic solvent. In this paper, a new SMPBE hybrid solver is developed using a solution decomposition, the Schwartz's overlapped domain decomposition, finite element, and finite difference. It is then programmed as a software package in C, Fortran, and Python based on the state-of-the-art finite element library DOLFIN from the FEniCS project. This software package is well validated on a Born ball model with analytical solution and a dipole model with a known physical properties. Numerical results on six proteins with different net charges demonstrate its high performance. Finally, this new SMPBE hybrid solver is shown to be numerically stable and convergent in the calculation of electrostatic solvation free energy for 216 biomolecules and binding free energy for a DNA-drug complex.
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Cited in
(14)- On the analysis and application of an ion size-modified Poisson-Boltzmann equation
- An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
- A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation
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- A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule
- A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
- A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
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