New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics

DOI10.1016/j.jcp.2014.07.012zbMath1349.78077OpenAlexW2026757984MaRDI QIDQ349451

Dexuan Xie

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.2014.07.012

zbMATH Keywords

finite element methodPoisson-Boltzmann equationbiomolecular electrostaticsFEniCS projectvariational minimization

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) Electro- and magnetostatics (78A30)

Related Items (29)

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Uses Software

• TNPACK
• NAMD
• DOLFIN
• FEniCS
• F2PY
• APBS
• CHARMM
• GAMER
• PDB2PQR
• PBEQ-Solver
• DelPhi Web Server
• TABI
• tabipb

Cites Work

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• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A finite element method for interface problems in domains with smooth boundaries and interfaces
• Automated solution of differential equations by the finite element method. The FEniCS book
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• On the convergence of interior-reflective Newton methods for nonlinear minimization subject to bounds
• Regularity results for elliptic equations in Lipschitz domains
• Finite element methods and their convergence for elliptic and parabolic interface problems
• Accurate evaluation of electrostatics for macromolecules in solution
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
• A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces
• Minimization of Electrostatic Free Energy and the Poisson–Boltzmann Equation for Molecular Solvation with Implicit Solvent
• Line search algorithms with guaranteed sufficient decrease
• TNPACK—A truncated Newton minimization package for large-scale problems
• Remark on Algorithm 702—the updated truncated Newton minimization package
• Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications
• An Interior Trust Region Approach for Nonlinear Minimization Subject to Bounds
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• The Mathematical Theory of Finite Element Methods

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