A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
From MaRDI portal
Publication:630460
DOI10.1016/J.JCP.2010.12.008zbMath1390.82056OpenAlexW2022860012MaRDI QIDQ630460
Frédéric Gibou, Mohammad Mirzadeh, Maxime Theillard
Publication date: 17 March 2011
Published in: Journal of Computational Physics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jcp.2010.12.008
nonlinear Poisson-Boltzmann equationsupercapacitorssecond-order discretizationarbitrary geometriesnon-graded adaptive gridoctree data structure
Related Items (20)
Solving elliptic interface problems with jump conditions on Cartesian grids ⋮ Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery ⋮ A volume-preserving reference map method for the level set representation ⋮ Computational modeling of protein conformational changes -- application to the opening SARS-CoV-2 spike ⋮ Efficient calculation of fully resolved electrostatics around large biomolecules ⋮ Adaptive finite difference methods for nonlinear elliptic and parabolic partial differential equations with free boundaries ⋮ A level-set multigrid technique for nonlinear diffusion in the numerical simulation of marble degradation under chemical pollutants ⋮ A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation ⋮ JAX-DIPS: neural bootstrapping of finite discretization methods and application to elliptic problems with discontinuities ⋮ A review of level-set methods and some recent applications ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ Computational mean-field modeling of confined active fluids ⋮ Adaptive mesh refinement in the fast lane ⋮ A Voronoi interface approach to cell aggregate electropermeabilization ⋮ A cell-centred finite volume method for the Poisson problem on non-graded quadtrees with second order accurate gradients ⋮ A conservative discretization of the Poisson-Nernst-Planck equations on adaptive Cartesian grids ⋮ Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules ⋮ A high-order embedded domain method combining a predictor-corrector-Fourier-continuation-Gram method with an integral Fourier pseudospectral collocation method for solving linear partial differential equations in complex domains ⋮ A sharp numerical method for the simulation of Stefan problems with convective effects ⋮ A sharp computational method for the simulation of the solidification of binary alloys
Uses Software
Cites Work
- A supra-convergent finite difference scheme for the variable coefficient Poisson equation on non-graded grids
- A second order accurate level set method on non-graded adaptive Cartesian grids
- The electric potential of a macromolecule in a solvent: A fundamental approach
- Tree methods for moving interfaces
- A partial differential equation approach to multidimensional extrapolation.
- Geometric integration over irregular domains with application to level-set methods
- A supra-convergent finite difference scheme for the Poisson and heat equations on irregular domains and non-graded adaptive Cartesian grids
This page was built for publication: A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids