Efficient calculation of fully resolved electrostatics around large biomolecules

We present a simple framework for calculating the electric potential by solving the nonlinear Poisson-Boltzmann equation and the free solvation energies of large biomolecules. To achieve this we build upon the work of Bochkov and Gibou [9] to develop a novel solver capable of solving nonlinear elliptic equations, where the diffusion coefficient, the source term, the solution and its flux are discontinuous across the interface. The interface is represented by the zero-level set of a signed distance function, empowering a natural and systematic approach to generate adaptive Cartesian grids, which drastically reduce the computational cost by focusing resources to regions near the surface of the molecules. The solver is implemented on a forest of Octree grids in parallel to enable fast computations over large molecules. Published by Elsevier Inc.

Automated summary

The study introduces a simple framework for calculating the electric potential by solving the nonlinear Poisson-Boltzmann equation and the free solvation energies of large biomolecules. By developing a novel solver capable of solving nonlinear elliptic equations and generating adaptive Cartesian grids, the computational cost is significantly reduced. The solver is implemented on a forest of Octree grids in parallel to enable fast computations over large molecules.