A SIMPLE AND EFFICIENT TECHNIQUE TO ACCELERATE THE COMPUTATION OF A NONLOCAL DIELECTRIC MODEL FOR ELECTROSTATICS OF BIOMOLECULE

作者：Li, Jiao; Ying, Jinyong^*

来源：Journal of Industrial and Management Optimization, 2020, 16(1): 357-369.

DOI：10.3934/jimo.2018155

• Nonlocal model
• implicit continuum model
• finite element method
• block iteration method
• biomolecular electrostatics

The nonlocal modified Poisson-Boltzmann equation (NMPBE) is one important variant of a commonly-used dielectric continuum model, Poisson-Boltzmann equation (PBE). In this paper, we use a nonlinear block relaxation method to develop a new nonlinear solver for the nonlinear equation of Phi and thus a new NMPBE solver, which is then programmed as a software package in C\C++, Fortran and Python for computing the electrostatics of a protein in a symmetric 1:1 ionic solvent. Numerical tests validate the new package and show that the new solver can improve the efficiency by at least 40% than the finite element NMPBE solver without compromising solution accuracy.

• 出版日期2020-1
• 单位中南大学; 长沙理工大学