Progress in developing Poisson-Boltzmann equation solvers
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Publication:2863922
Poisson-Boltzmann equationdielectric constantmolecular surfacenumerical techniquescontinuum electrostatics
Biochemistry, molecular biology (92C40) Finite difference methods for boundary value problems involving PDEs (65N06) Boundary element methods for boundary value problems involving PDEs (65N38) Parallel algorithms in computer science (68W10) Computational methods for problems pertaining to biology (92-08) Biophysics (92C05)
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- scientific article; zbMATH DE number 5669486
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Cites work
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- A fast, high-order algorithm for the solution of surface scattering problems: Basic implementation, tests, and applications
- A general formulation of alternating direction methods. I: Parabolic and hyperbolic problems
- A generalized Douglas ADI method for solving three‐dimensional parabolic differential equations on multilayers
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- A new paradigm for parallel adaptive meshing algorithms
- A new version of the fast multipole method for screened Coulomb interactions in three dimensions
- A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
- AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
- Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
- Adaptive numerical treatment of elliptic systems on manifolds
- An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations
- An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
- Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution
- Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
- Differential geometry based solvation model. I: Eulerian formulation
- Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
- High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
- Monte Carlo Methods for Calculating Some Physical Properties of Large Molecules
- Multiscale Bases for the Sparse Representation of Boundary Integral Operators on Complex Geometry
- On the fast matrix multiplication in the boundary element method by panel clustering
- On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method
- Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions
- Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
- Solution of acoustic scattering problems by means of second kind integral equations
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- The electric potential of a macromolecule in a solvent: A fundamental approach
- The geometry behind numerical solvers of the Poisson-Boltzmann equation
- Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities
Cited in
(10)- Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- Computational electrostatics for biological applications. Geometric and numerical approaches to the description of electrostatic interaction between macromolecules. Proceedings of the CEBA international meeting, Genova, Italy, July 1--3, 2013
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- Computational modeling of protein conformational changes -- application to the opening SARS-CoV-2 spike
- Poisson-Boltzmann equation boundary conditions for biological applications
- Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
- Progress in the development of a new lattice Boltzmann method
- Solving fluctuation-enhanced Poisson-Boltzmann equations
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
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