A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

作者：Ying Jinyong; Xie Dexuan^*

来源：Journal of Computational Physics, 2015, 298: 636-651.

DOI：10.1016/j.jcp.2015.06.016

• Poisson-Boltzmann equation
• Finite element method
• Finite difference method
• Biomolecular electrostatics
• Domain decomposition
• Multigrid preconditioning
• Solvation free energy

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1: 1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.

• 出版日期2015-10-1