Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization

DOI10.1016/J.AMC.2020.125267zbMATH Open1460.92087OpenAlexW3000905040MaRDI QIDQ2180707FDOQ2180707

Authors: Sheik Ahmed Ullah, Shan Zhao 

Publication date: 14 May 2020

Published in: Applied Mathematics and Computation (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.amc.2020.125267

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zbMATH Keywords

regularizationpseudo-transient continuation approachghost fluid methodPoisson-Boltzmann equationalternating direction implicit (ADI)

Mathematics Subject Classification ID

PDEs in connection with biology, chemistry and other natural sciences (35Q92) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Numerical methods for partial differential equations, boundary value problems (65N99)

Cites Work

• Title not available (Why is that?)
• A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
• A boundary condition capturing method for Poisson's equation on irregular domains
• High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• Differential geometry based solvation model II: Lagrangian formulation
• The immersed finite volume element methods for the elliptic interface problems
• Multiscale molecular dynamics using the matched interface and boundary method
• A coupling interface method for elliptic interface problems
• Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
• IIM-based ADI finite difference scheme for nonlinear convection-diffusion equations with interfaces
• Convergence Analysis of Pseudo-Transient Continuation
• A regularized Newton-like method for nonlinear PDE
• Parameter Selection for Newton-Like Methods Applicable to Nonlinear Partial Differential Equations
• Second order finite-difference ghost-point multigrid methods for elliptic problems with discontinuous coefficients on an arbitrary interface
• Solving Poisson-type equations with Robin boundary conditions on piecewise smooth interfaces
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
• Imposing mixed Dirichlet-Neumann-Robin boundary conditions in a level-set framework
• Title not available (Why is that?)
• A matched alternating direction implicit (ADI) method for solving the heat equation with interfaces
• Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• A matched Peaceman-Rachford ADI method for solving parabolic interface problems
• Alternating direction ghost-fluid methods for solving the heat equation with interfaces

Cited In (10)

• Ghost-Fluid-Based Sharp Interface Methods for Multi-Material Dynamics: A Review
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• Adaptive pseudo-time methods for the Poisson-Boltzmann equation with Eulerian solvent excluded surface
• Alternating direction ghost-fluid methods for solving the heat equation with interfaces
• A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
• Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules

Uses Software

• MIBPB

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