New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
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Publication:349451
DOI10.1016/J.JCP.2014.07.012zbMATH Open1349.78077OpenAlexW2026757984MaRDI QIDQ349451FDOQ349451
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
finite element methodPoisson-Boltzmann equationbiomolecular electrostaticsFEniCS projectvariational minimization
Biochemistry, molecular biology (92C40) Electro- and magnetostatics (78A30) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10)
Cites Work
- Title not available (Why is that?)
- Title not available (Why is that?)
- Title not available (Why is that?)
- Title not available (Why is that?)
- Title not available (Why is that?)
- Automated solution of differential equations by the finite element method. The FEniCS book
- Line search algorithms with guaranteed sufficient decrease
- The Mathematical Theory of Finite Element Methods
- Finite element methods and their convergence for elliptic and parabolic interface problems
- An Interior Trust Region Approach for Nonlinear Minimization Subject to Bounds
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- A finite element method for interface problems in domains with smooth boundaries and interfaces
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- Regularity results for elliptic equations in Lipschitz domains
- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
- Accurate evaluation of electrostatics for macromolecules in solution
- ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
- 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
- On the convergence of interior-reflective Newton methods for nonlinear minimization subject to bounds
- 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
Cited In (34)
- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- Title not available (Why is that?)
- 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
- On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
- A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation
- A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- An Effective Finite Element Iterative Solver for a Poisson--Nernst--Planck Ion Channel Model with Periodic Boundary Conditions
- 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
- SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
- An efficient finite element solver for a nonuniform size-modified Poisson-Nernst-Planck ion channel model
- An a posteriori-driven adaptive mixed high-order method with application to electrostatics
- On the analysis and application of an ion size-modified Poisson-Boltzmann equation
- A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
- Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation
- A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
- On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
- A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
- A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
- Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format
- A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
- Title not available (Why is that?)
- Fast solution of the linearized Poisson-Boltzmann equation with nonaffine parametrized boundary conditions using the reduced basis method
- Regularization of Poisson--Boltzmann Type Equations with Singular Source Terms Using the Range-Separated Tensor Format
- A Poisson-Nernst-Planck single ion channel model and its effective finite element solver
- An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
- A finite element iterative solver for a PNP ion channel model with Neumann boundary condition and membrane surface charge
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential
- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
- Title not available (Why is that?)
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