• DOI:10.1137/120899078
• Corpus ID: 207066194

Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent

@article{Xie2013EfficientAF,
  title={Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent},
  author={Dexuan Xie and Yi Jiang and Leighton R. Scott},
  journal={SIAM J. Sci. Comput.},
  year={2013},
  volume={35}
}

• Dexuan Xie, Yi Jiang, L. R. Scott
• Published 3 December 2013
• Physics
• SIAM J. Sci. Comput.

The nonlocal dielectric approach can significantly enhance the classical Poisson dielectric model by including polarization correlations among water molecules. In this paper, a nonlocal dielectric model for protein in ionic solvent is proposed and analyzed, alongside a new efficient numerical algorithm and program package for solving the model. In particular, by using solution splitting and reformulation techniques, it is shown that the solution of the nonlocal dielectric model is unique, and can be found from solving two well-defined partial differential systems and one Poisson-like boundary value problem. Consequently, the singular and computational difficulties caused by Dirac delta distributions and convolution terms are overcome. Furthermore, a nonlocal linearized Poisson--Boltzmann equation with uniform ionic size effect is proposed and numerically tested on three protein molecules with up to 6062 atoms by using a fast finite element solver from the FEniCS project. A nonlocal point charge Born model...