@Article{CiCP-13-150,
author = {Mohammad Mirzadeh, Maxime Theillard, Asdís Helgadóttir, David Boy and Frédéric Gibou},
title = {An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations},
journal = {Communications in Computational Physics},
year = {2013},
volume = {13},
number = {1},
pages = {150--173},
abstract = {<p style="text-align: justify;">We present a solver for the Poisson-Boltzmann equation and demonstrate
its applicability for biomolecular electrostatics computation. The solver uses a level
set framework to represent sharp, complex interfaces in a simple and robust manner.
It also uses non-graded, adaptive octree grids which, in comparison to uniform grids,
drastically decrease memory usage and runtime without sacrificing accuracy. The basic solver was introduced in earlier works [16, 27], and here is extended to address
biomolecular systems. First, a novel approach of calculating the solvent excluded and
the solvent accessible surfaces is explained; this allows to accurately represent the location of the molecule&#39;s surface. Next, a hybrid finite difference/finite volume approach
is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing
the jump boundary conditions at the interface. Since the interface is implicitly represented by a level set function, imposing the jump boundary conditions is straightforward and efficient.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.290711.181011s},
url = {http://global-sci.org/intro/article_detail/cicp/7216.html}
}