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

DOI10.1016/J.AMC.2020.125267MaRDI QIDQ2180707zbMATH OpenOpenAlexFDO

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

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)

Recommendations

• Adaptive pseudo-time methods for the Poisson-Boltzmann equation with Eulerian solvent excluded surface
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• 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
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation

Cites work

• scientific article; zbMATH DE number 1522321 (Why is no real title available?)
• scientific article; zbMATH DE number 2152342 (Why is no real title available?)
• A boundary condition capturing method for Poisson's equation on irregular domains
• A coupling interface method for elliptic interface problems
• A matched Peaceman-Rachford ADI method for solving parabolic interface problems
• A matched alternating direction implicit (ADI) method for solving the heat equation with interfaces
• A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
• A regularized Newton-like method for nonlinear PDE
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• Alternating direction ghost-fluid methods for solving the heat equation with interfaces
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• Convergence Analysis of Pseudo-Transient Continuation
• Differential geometry based solvation model II: Lagrangian formulation
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
• High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces
• IIM-based ADI finite difference scheme for nonlinear convection-diffusion equations with interfaces
• Imposing mixed Dirichlet-Neumann-Robin boundary conditions in a level-set framework
• Multiscale molecular dynamics using the matched interface and boundary method
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
• Parameter Selection for Newton-Like Methods Applicable to Nonlinear Partial Differential Equations
• Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
• Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
• 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
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• The immersed finite volume element methods for the elliptic interface problems
• Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules

Cited in

(10)

• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• Ghost-Fluid-Based Sharp Interface Methods for Multi-Material Dynamics: A Review
• 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

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• MIBPB

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