Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent

DOI10.1137/120899078zbMath1287.35092OpenAlexW2035385790MaRDI QIDQ5404628

L. Ridgway Scott, Dexuan Xie, Yi Jiang

Publication date: 28 March 2014

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Full work available at URL: https://semanticscholar.org/paper/f6aef3b22da0c2b3ded845a686c497932af25abd

zbMATH Keywords

protein simulationPoisson-Boltzmann equationelectrostatic potentialprogram libraryfinite element solversnonlocal dielectric continuum modelFeniCS project

Mathematics Subject Classification ID

PDEs in connection with biology, chemistry and other natural sciences (35Q92) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08) Boltzmann equations (35Q20) Electrochemistry (78A57)

Related Items (10)

Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation ⋮ A computational model of protein induced membrane morphology with geodesic curvature driven protein-membrane interface ⋮ SDPBS web server for calculation of electrostatics of ionic solvated biomolecules ⋮ Nonlocal electrostatics in spherical geometries using eigenfunction expansions of boundary-integral operators ⋮ A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels ⋮ Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms ⋮ Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules ⋮ Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules ⋮ A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• PETSc
• DOLFIN
• FEniCS
• F2PY

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