Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation

DOI10.2478/mlbmb-2013-0006zbMath1276.65063OpenAlexW2013220345MaRDI QIDQ2863928

Shan Zhao, Weihua Geng

Publication date: 5 December 2013

Published in: Computational and Mathematical Biophysics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.2478/mlbmb-2013-0006

zbMATH Keywords

operator splittingelectrostatic potentialnonlinear Poisson-Boltzmann equationsolvation free energymolecular surfacealternating direction implicit scheme

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Biophysics (92C05) Finite difference methods for boundary value problems involving PDEs (65N06) Computational methods for problems pertaining to biology (92-08)

Related Items

A new discontinuous Galerkin method for the nonlinear Poisson-Boltzmann equation ⋮ On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics ⋮ Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization ⋮ A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation ⋮ Galerkin-Chebyshev pseudo spectral method and a split step new approach for a class of two dimensional semi-linear parabolic equations of second order ⋮ A spatially second order alternating direction implicit (ADI) method for solving three dimensional parabolic interface problems ⋮ A matched Peaceman-Rachford ADI method for solving parabolic interface problems ⋮ A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation ⋮ A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states ⋮ Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes ⋮ A matched alternating direction implicit (ADI) method for solving the heat equation with interfaces

Uses Software

• APBS
• MIBPB
• TABI
• tabipb

Cites Work

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