APBS

swMATH5766WikidataQ65072984 ScholiaQ65072984MaRDI QIDQ17905FDOQ17905

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Source code repository: https://github.com/Electrostatics/electrostatics.github.io

Cited In (95)

• Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions
• Modeling electrokinetic flows by the smoothed profile method
• Radial basis collocation method and quasi-Newton iteration for nonlinear elliptic problems
• A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid
• Browndye: A software package for Brownian dynamics
• The de Rham-Hodge analysis and modeling of biomolecules
• Geometry-guided computation of 3D electrostatics for large biomolecules
• A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
• An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics
• A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
• Title not available (Why is that?)
• Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules
• Progress in developing Poisson-Boltzmann equation solvers
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• A Reduced Basis Method for the Nonlinear Poisson-Boltzmann Equation
• Fast Molecular Solvation Energetics and Forces Computation
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Stability of a Cylindrical Solute-Solvent Interface: Effect of Geometry, Electrostatics, and Hydrodynamics
• Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• On the convergence of an optimal additive Schwarz method for parallel adaptive finite elements
• Poisson-Boltzmann equation boundary conditions for biological applications
• ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
• Title not available (Why is that?)
• Efficient calculation of fully resolved electrostatics around large biomolecules
• A boundary element formulation of protein electrostatics with explicit ions
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
• A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
• 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
• Two-scale finite element Green's function approximations with applications to electrostatic potential computation
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• A finite difference method and analysis for 2D nonlinear Poisson-Boltzmann equations
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• Lattice evolution solution for the nonlinear Poisson-Boltzmann equation in confined domains
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
• Quality meshing of implicit solvation models of biomolecular structures
• Multiscale geometric modeling of macromolecules. I: Cartesian representation
• Title not available (Why is that?)
• A class of difference schemes with flexible local approximation
• A finite element recovery approach to Green's function approximations with applications to electrostatic potential computation
• Probabilistic interpretation and random walk on spheres algorithms for the Poisson-Boltzmann equation in molecular dynamics
• Multiscale molecular dynamics using the matched interface and boundary method
• Title not available (Why is that?)
• Adaptive numerical treatment of elliptic systems on manifolds
• On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
• A fast variational method for the construction of resolution adaptive \(C^2\)-smooth molecular surfaces
• Symmetry reduced dynamics of charged molecular strands
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• On variational iterative methods for semilinear problems
• Finite element approximation to a finite-size modified Poisson-Boltzmann equation
• A rapid boundary integral equation technique for protein electrostatics
• A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
• Accurate evaluation of electrostatics for macromolecules in solution
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• A new boundary integral equation for molecular electrostatics with charges over whole space
• Physical modeling of aqueous solvation
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• Local and parallel finite element algorithms for eigenvalue problems
• Iterative convex quadratic approximation for global optimization in protein docking
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
• Some Random Batch Particle Methods for the Poisson-Nernst-Planck and Poisson-Boltzmann Equations
• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• Model reduction-based initialization methods for solving the Poisson-Nernst-Planck equations in three-dimensional ion channel simulations
• A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
• FEM and BEM parallel processing: theory and applications – a bibliography (1996‐2002)
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• The calculus of boundary variations and the dielectric boundary force in the Poisson-Boltzmann theory for molecular solvation
• Finite Element Modeling of Biomolecular Systems in Ionic Solution
• A Posteriori Analysis and Efficient Refinement Strategies for the Poisson--Boltzmann Equation
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
• Local averaging based a posteriori finite element error control for quasilinear elliptic problems with application to electrical potential computation
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• An optimal Schwarz preconditioner for a class of parallel adaptive finite elements
• A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms
• A new approach to constrained total variation solvation models and the study of solute-solvent interface profiles
• Regularization of Poisson--Boltzmann Type Equations with Singular Source Terms Using the Range-Separated Tensor Format
• A stochastic solver of the generalized Born model
• An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery

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