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A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

Weihua Geng — 2015

Molecular Based Mathematical Biology

Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both...

Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation

Weihua GengShan Zhao — 2013

Molecular Based Mathematical Biology

The Poisson-Boltzmann (PB) model is an effective approach for the electrostatics analysis of solvated biomolecules. The nonlinearity associated with the PB equation is critical when the underlying electrostatic potential is strong, but is extremely difficult to solve numerically. In this paper, we construct two operator splitting alternating direction implicit (ADI) schemes to efficiently and stably solve the nonlinear PB equation in a pseudo-transient continuation approach. The operator splitting...

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