A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid

DOI10.1016/J.JCP.2011.02.010zbMath1369.76033OpenAlexW1986577020MaRDI QIDQ544559

Frédéric Gibou, Ásdís Helgadóttir

Publication date: 15 June 2011

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2011.02.010

zbMATH Keywords

finite difference methodNeumann boundary conditionlevel setRobin boundary conditionirregular domainadaptive gridoctreePoisson-Boltzmann solver

Mathematics Subject Classification ID

Finite difference methods applied to problems in fluid mechanics (76M20) Rarefied gas flows, Boltzmann equation in fluid mechanics (76P05) Mesh generation, refinement, and adaptive methods for boundary value problems involving PDEs (65N50) Finite difference methods for boundary value problems involving PDEs (65N06)

Related Items (13)

Efficient calculation of fully resolved electrostatics around large biomolecules ⋮ Adaptive finite difference methods for nonlinear elliptic and parabolic partial differential equations with free boundaries ⋮ The island dynamics model on parallel quadtree grids ⋮ Imposing mixed Dirichlet-Neumann-Robin boundary conditions in a level-set framework ⋮ A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation ⋮ Geometric discretization of the multidimensional Dirac delta distribution -- application to the Poisson equation with singular source terms ⋮ A review of level-set methods and some recent applications ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ PDE-Based Multidimensional Extrapolation of Scalar Fields over Interfaces with Kinks and High Curvatures ⋮ A cell-centred finite volume method for the Poisson problem on non-graded quadtrees with second order accurate gradients ⋮ Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules ⋮ 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

• APBS
• UHBD
• SG

Cites Work

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