APBS

swMATH5766WikidataQ65072984 ScholiaQ65072984MaRDI QIDQ17905FDOQ17905

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Official website: http://www.poissonboltzmann.org

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

Cited In (only showing first 100 items - show all)

• A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• 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
• 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
• Regularization of Poisson-Boltzmann-type equations with singular source terms using the range-separated tensor format
• A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
• 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
• 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
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• On the convergence of an optimal additive Schwarz method for parallel adaptive finite elements
• Poisson-Boltzmann equation boundary conditions for biological 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
• 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 domain decomposition method for the polarizable continuum model based on the solvent excluded surface
• A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation
• Two-scale finite element Green's function approximations with applications to electrostatic potential computation
• A finite difference method and analysis for 2D nonlinear Poisson-Boltzmann equations
• Lattice evolution solution for the nonlinear Poisson-Boltzmann equation in confined domains
• Quality meshing of implicit solvation models of biomolecular structures
• A reduced basis method for the nonlinear Poisson-Boltzmann equation
• 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
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• DelPhi
• Probabilistic interpretation and random walk on spheres algorithms for the Poisson-Boltzmann equation in molecular dynamics
• An optimal Schwarz preconditioner for a class of parallel adaptive finite elements
• A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
• Finite element modeling of biomolecular systems in ionic solution
• NanoShaper
• A posteriori analysis and efficient refinement strategies for the Poisson-Boltzmann equation
• Finite element approximation to a finite-size modified Poisson-Boltzmann equation
• 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
• A new boundary integral equation for molecular electrostatics with charges over whole space
• Physical modeling of aqueous solvation
• An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
• PNPSIC
• Fast molecular solvation energetics and forces computation
• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
• Iterative convex quadratic approximation for global optimization in protein docking
• qPIPSA
• FEM and BEM parallel processing: theory and applications – a bibliography (1996‐2002)
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
• Some random batch particle methods for the Poisson-Nernst-Planck and Poisson-Boltzmann equations
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• nuSMPBIC
• A stochastic solver of the generalized Born model
• Image charge methods for a three-dielectric-layer hybrid solvation model of biomolecules
• Radial basis collocation method and quasi-Newton iteration for nonlinear elliptic problems
• Geometry-guided computation of 3D electrostatics for large biomolecules
• 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
• Stability of a Cylindrical Solute-Solvent Interface: Effect of Geometry, Electrostatics, and Hydrodynamics
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• 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
• 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
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
• AMBER
• CHARMM
• PetFMM
• A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
• Delphi
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• Browndye
• FISHPAK
• Macrodox
• MIBPB
• SDA
• PIM
• UHBD
• AFMPB
• FFTSVD
• Fastcap
• LINCS
• PyMOL
• FEtk
• GAMER
• PHG
• F2Dock
• SETTLE
• MolEnergy
• PDB2PQR
• TexMol

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