A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules

DOI10.1016/j.jcp.2016.06.028zbMath1351.78043OpenAlexW2469532421MaRDI QIDQ729546

Dexuan Xie, Yi Jiang

Publication date: 20 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.2016.06.028

zbMATH Keywords

finite element methodNewton methodelectrostaticsPoisson-Boltzmann equationnonlocal dielectric model

Mathematics Subject Classification ID

Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Biochemistry, molecular biology (92C40) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Electromagnetic theory (general) (78A25) Packaged methods for numerical algorithms (65Y15)

Related Items (7)

Energetic stable discretization for non-isothermal electrokinetics model ⋮ 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 ⋮ Unnamed Item ⋮ Group preserving scheme and reproducing kernel method for the Poisson-Boltzmann equation for semiconductor devices ⋮ Study of local and nonlocal Poisson-Boltzmann equations for linear and nonlinear models with spherical symmetry ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• DOLFIN
• PDB2PQR
• AQUASOL
• SDPBS

Cites Work

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• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• 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
• Automated solution of differential equations by the finite element method. The FEniCS book
• Poisson-Boltzmann equation boundary conditions for biological applications
• Mean-field theory and computation of electrostatics with ionic concentration dependent dielectrics
• A new numerical method for nonlocal electrostatics in biomolecular simulations
• A Fast Solver for a Nonlocal Dielectric Continuum Model
• Continuum electrostatics for ionic solutions with non-uniform ionic sizes
• Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
• The Mathematical Theory of Finite Element Methods
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules

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