A Nonlocal size modified Poisson-Boltzmann Model and Its Finite Element Solver for Protein in Multi-Species Ionic Solution

TL;DR

This paper introduces a novel nonlocal size modified Poisson-Boltzmann model that accounts for ionic size effects and nonlocal dielectric correlations, solved with an efficient finite element method for complex protein and ionic solutions.

Contribution

The paper develops the first combined nonlocal size modified PB model and a finite element solver with a novel solution decomposition and robust iterative methods.

Findings

The solver demonstrates fast convergence and robustness.

Numerical experiments validate high performance and accuracy.

The package simplifies and accelerates protein simulation workflows.

Abstract

The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, have been developed to account for ionic size effects and nonlocal dielectric correlations, no existing PB variants simultaneously incorporate both, due to significant modeling and computational challenges. To address this gap, in this paper, a nonlocal size modified PB (NSMPB) model is introduced and solved using a finite element method for a protein with a three-dimensional molecular structure and an ionic solution containing multiple ion species. In particular, a novel solution decomposition is proposed to overcome the difficulties caused by the increased nonlinearity, nonlocality, and solution singularities of the model. It is then applied to the development of the NSMPB finite element solver, which includes an efficient modified Newton iterative method, an effective damping parameter selection strategy, and good selections of initial iterations. Moreover, the construction of the modified Newton iterative method is mathematically justified. Furthermore, an NSMPB finite element package is developed by integrating a mesh generation tool, a protein data bank file retrieval program, and the PDB2PQR package to simplify and accelerate its usage and application. Finally, numerical experiments are conducted on an ionic solution with four species, proteins with up to 11439 atoms, and irregular interface-fitted tetrahedral box meshes with up to 1188840 vertices. The numerical results confirm the fast convergence and strong robustness of the modified Newton iterative method, demonstrate the high performance of the package, and highlight the crucial roles played by the damping parameter and initial iteration selections in enhancing the method's convergence. The package will be a valuable tool in protein simulations.