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

DOI10.1016/J.JCP.2011.02.010MaRDI QIDQ544559zbMATH OpenOpenAlexFDO

Authors Ásdís Helgadóttir, Frédéric Gibou

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

adaptive gridfinite difference methodirregular domainlevel setNeumann boundary conditionoctreePoisson-Boltzmann solverRobin boundary condition

Mathematics Subject Classification ID

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

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Cites work

• A finite difference method and analysis for 2D nonlinear Poisson-Boltzmann equations
• A fourth order accurate discretization for the Laplace and heat equations on arbitrary domains, with applications to the Stefan problem
• A Jump Condition Capturing Finite Difference Scheme for Elliptic Interface Problems
• A level set approach for the numerical simulation of dendritic growth
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• A second order accurate level set method on non-graded adaptive Cartesian grids
• A second order accurate projection method for the incompressible Navier-Stokes equations on non-graded adaptive grids
• A second-order-accurate symmetric discretization of the Poisson equation on irregular domains
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• A supra-convergent finite difference scheme for the variable coefficient Poisson equation on non-graded grids
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• Adaptive mesh enrichment for the Poisson-Boltzmann equation
• Adaptive numerical method for Poisson-Boltzmann equation and its application
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• An efficient fluid-solid coupling algorithm for single-phase flows
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• Geometric integration over irregular domains with application to level-set methods
• scientific article; zbMATH DE number 5669486 (Why is no real title available?)
• scientific article; zbMATH DE number 5038548 (Why is no real title available?)
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• Numerical analysis of blood flow in the heart
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Cited in

(18)

• The island dynamics model on parallel quadtree grids
• Imposing mixed Dirichlet-Neumann-Robin boundary conditions in a level-set framework
• 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
• A sharp numerical method for the simulation of Stefan problems with convective effects
• Efficient calculation of fully resolved electrostatics around large biomolecules
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• A sharp computational method for the simulation of the solidification of binary alloys
• Lattice evolution solution for the nonlinear Poisson-Boltzmann equation in confined domains
• Adaptive finite difference methods for nonlinear elliptic and parabolic partial differential equations with free boundaries
• PDE-based multidimensional extrapolation of scalar fields over interfaces with kinks and high curvatures
• Adaptive mesh enrichment for the Poisson-Boltzmann equation
• A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation
• A super-convergence analysis of the Poisson solver with octree grids and irregular domains
• A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
• A non-parametric gradient-based shape optimization approach for solving inverse problems in directed self-assembly of block copolymers
• A cell-centred finite volume method for the Poisson problem on non-graded quadtrees with second order accurate gradients

Describes a project that uses

Uses Software

• UHBD
• APBS
• SG

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