A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

DOI10.1016/j.jcp.2015.06.016zbMath1349.78103OpenAlexW794320856MaRDI QIDQ2374668

Dexuan Xie, Jinyong Ying

Publication date: 5 December 2016

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2015.06.016

zbMATH Keywords

finite element methodfinite difference methoddomain decompositionPoisson-Boltzmann equationsolvation free energybiomolecular electrostaticsmultigrid preconditioning

Mathematics Subject Classification ID

Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Finite difference methods applied to problems in optics and electromagnetic theory (78M20) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Composite media; random media in optics and electromagnetic theory (78A48) Finite difference methods for boundary value problems involving PDEs (65N06)

Related Items

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery ⋮ A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation ⋮ SDPBS web server for calculation of electrostatics of ionic solvated biomolecules ⋮ An a posteriori-driven adaptive mixed high-order method with application to electrostatics ⋮ Improved enrichments and numerical integrations in SGFEM for interface problems ⋮ Immersed virtual element methods for electromagnetic interface problems in three dimensions ⋮ Unnamed Item ⋮ A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver ⋮ Multi-scale fusion network: a new deep learning structure for elliptic interface problems ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule ⋮ On the analysis and application of an ion size-modified Poisson-Boltzmann equation ⋮ A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models ⋮ A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference ⋮ On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• PETSc
• TetGen
• DOLFIN
• SWIG
• F2PY
• APBS
• Delphi
• UHBD
• MIBPB
• GAMER
• PDB2PQR
• PBEQ-Solver

Cites Work

• Unnamed Item
• Unnamed Item
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• Iterative Methods by Space Decomposition and Subspace Correction
• Some Nonoverlapping Domain Decomposition Methods
• TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications