On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics

DOI10.1016/j.cam.2017.09.004zbMath1383.78036OpenAlexW2756016894MaRDI QIDQ1675978

Weishan Deng, Jin Xu, Shan Zhao

Publication date: 3 November 2017

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

Full work available at URL: https://doi.org/10.1016/j.cam.2017.09.004

zbMATH Keywords

finite element methodPoisson-Boltzmann equationelectrostatic free energymolecular surfacepseudo-time approachregularized Poisson-Boltzmann equation

Mathematics Subject Classification ID

Smoothness and regularity of solutions to PDEs (35B65) PDEs in connection with optics and electromagnetic theory (35Q60) Biological applications of optics and electromagnetic theory (78A70) Biochemistry, molecular biology (92C40) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Stability and convergence of numerical methods for initial value and initial-boundary value problems involving PDEs (65M12) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Mesh generation, refinement, and adaptive methods for boundary value problems involving PDEs (65N50) Electro- and magnetostatics (78A30) Boltzmann equations (35Q20)

Related Items (7)

Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization ⋮ 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 ⋮ Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential ⋮ On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary ⋮ A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• TetGen
• MIBPB
• TMSmesh
• SDPBS
• TABI
• tabipb

Cites Work

• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Geometric and potential driving formation and evolution of biomolecular surfaces
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Spectral methods on triangles and other domains
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• Accurate evaluation of electrostatics for macromolecules in solution
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
• Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
• High-Order Methods for Incompressible Fluid Flow
• Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation
• TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• An Iterative Discontinuous Galerkin Method for Solving the Nonlinear Poisson Boltzmann Equation
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
• tabipb
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