A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
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Publication:729546
DOI10.1016/J.JCP.2016.06.028zbMATH Open1351.78043OpenAlexW2469532421MaRDI QIDQ729546FDOQ729546
Authors: 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
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Biochemistry, molecular biology (92C40) Packaged methods for numerical algorithms (65Y15) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Electromagnetic theory (general) (78A25) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10)
Cites Work
- Automated solution of differential equations by the finite element method. The FEniCS book
- SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
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- The Mathematical Theory of Finite Element Methods
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- Continuum electrostatics for ionic solutions with non-uniform ionic sizes
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- A fast solver for a nonlocal dielectric continuum model
- A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
- Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
- A new numerical method for nonlocal electrostatics in biomolecular simulations
- Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
- Mean-field theory and computation of electrostatics with ionic concentration dependent dielectrics
- Poisson-Boltzmann equation boundary conditions for biological applications
Cited In (22)
- 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 fast solver for a nonlocal dielectric continuum model
- New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation
- A novel pseudospectral Fourier method for solving Poisson's equation for a solute in a non-uniform dielectric
- Efficient generation of membrane and solvent tetrahedral meshes for ion channel finite element calculation
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution
- A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- Energetic stable discretization for non-isothermal electrokinetics model
- A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule
- Nonlocal electrostatics in spherical geometries using eigenfunction expansions of boundary-integral operators
- Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
- Group preserving scheme and reproducing kernel method for the Poisson-Boltzmann equation for semiconductor devices
- AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
- A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
- Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
- Benchmarking electrostatic free energy of the nonlinear Poisson-Boltzmann model for the Kirkwood sphere
- A new numerical method for nonlocal electrostatics in biomolecular simulations
- Poisson-Fermi formulation of nonlocal electrostatics in electrolyte solutions
- An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations
- Study of local and nonlocal Poisson-Boltzmann equations for linear and nonlinear models with spherical symmetry
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