New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
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Cites work
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- scientific article; zbMATH DE number 5060482 (Why is no real title available?)
- 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
- A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces
- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- Accurate evaluation of electrostatics for macromolecules in solution
- An Interior Trust Region Approach for Nonlinear Minimization Subject to Bounds
- 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
- Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications
- Finite element methods and their convergence for elliptic and parabolic interface problems
- Line search algorithms with guaranteed sufficient decrease
- Minimization of Electrostatic Free Energy and the Poisson–Boltzmann Equation for Molecular Solvation with Implicit Solvent
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- Regularity results for elliptic equations in Lipschitz domains
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Cited in
(41)- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- Reduced basis method for the nonlinear Poisson-Boltzmann equation regularized by the range-separated canonical tensor format
- Regularization of Poisson-Boltzmann-type equations with singular source terms using the range-separated tensor format
- A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- Efficient generation of membrane and solvent tetrahedral meshes for ion channel finite element calculation
- On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
- A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation
- On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
- A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
- A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule
- Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent
- 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
- Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
- An Effective Finite Element Iterative Solver for a Poisson--Nernst--Planck Ion Channel Model with Periodic Boundary Conditions
- A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
- AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
- Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
- SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
- Benchmarking electrostatic free energy of the nonlinear Poisson-Boltzmann model for the Kirkwood sphere
- 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
- An efficient finite element solver for a nonuniform size-modified Poisson-Nernst-Planck ion channel model
- 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
- A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
- Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- An effective minimization protocol for solving a size-modified Poisson-Boltzmann equation for biomolecule in ionic solvent
- Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
- A Poisson-Nernst-Planck single ion channel model and its effective finite element solver
- Fast solution of the linearized Poisson-Boltzmann equation with nonaffine parametrized boundary conditions using the reduced basis method
- 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
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