The electric potential of a macromolecule in a solvent: A fundamental approach

DOI10.1016/0021-9991(91)90043-KzbMath0743.65094MaRDI QIDQ1181936

André H. Juffer, Herman J. C. Berendsen, Eugen F. F. Botta, Bert A. M. van Keulen, Auke van der Ploeg

Publication date: 27 June 1992

Published in: Journal of Computational Physics (Search for Journal in Brave)

zbMATH Keywords

boundary element methodelectric potentialPoisson equationPoisson-Boltzmann equationmacromoleculeNumerical results

Mathematics Subject Classification ID

PDEs in connection with optics and electromagnetic theory (35Q60) Laplace operator, Helmholtz equation (reduced wave equation), Poisson equation (35J05) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Applications to the sciences (65Z05) Boundary element methods for boundary value problems involving PDEs (65N38) Electro- and magnetostatics (78A30)

Related Items (47)

Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery ⋮ Fast multipole method for 3-D Poisson-Boltzmann equation in layered electrolyte-dielectric media ⋮ Efficient calculation of fully resolved electrostatics around large biomolecules ⋮ A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation ⋮ Tikhonov type regularization method for the Cauchy problem of the modified Helmholtz equation ⋮ Nonlocal electrostatics in spherical geometries using eigenfunction expansions of boundary-integral operators ⋮ A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations ⋮ Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code ⋮ Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation ⋮ A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules ⋮ A boundary element formulation of protein electrostatics with explicit ions ⋮ On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics ⋮ A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation ⋮ A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation ⋮ A sixth-order image approximation to the ionic solvent induced reaction field ⋮ Multiscale molecular dynamics using the matched interface and boundary method ⋮ An integral equation method for the advection-diffusion equation on time-dependent domains in the plane ⋮ The de Rham-Hodge analysis and modeling of biomolecules ⋮ A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver ⋮ Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns ⋮ Fast and accurate solvers for simulating Janus particle suspensions in Stokes flow ⋮ A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids ⋮ An integral equation-based numerical method for the forced heat equation on complex domains ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems ⋮ A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver ⋮ A new boundary integral equation for molecular electrostatics with charges over whole space ⋮ ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems ⋮ A novel Trefftz method of the inverse Cauchy problem for 3D modified Helmholtz equation ⋮ Extending the fast multipole method for charges inside a dielectric sphere in an ionic solvent: high-order image approximations for reaction fields ⋮ A new version of the fast multipole method for screened Coulomb interactions in three dimensions ⋮ Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver ⋮ DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture ⋮ Harmonic Surface Mapping Algorithm for Electrostatic Potentials in an Atomistic/Continuum Hybrid Model for Electrolyte Solutions ⋮ A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers ⋮ A simulation method of combinding boundary element method with generalized Langevin dynamics ⋮ New versions of image approximations to the ionic solvent induced reaction field ⋮ FMM-Yukawa: an adaptive fast multipole method for screened Coulomb interactions ⋮ A regularization method for the cauchy problem of the modified Helmholtz equation ⋮ On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver ⋮ Quasi-reversibility and truncation methods to solve a Cauchy problem for the modified Helmholtz equation ⋮ An adaptive fast solver for the modified Helmholtz equation in two dimensions ⋮ A fast adaptive multipole algorithm for calculating screened Coulomb (Yukawa) interactions ⋮ Progress in developing Poisson-Boltzmann equation solvers ⋮ Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation ⋮ Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding ⋮ A quasi-reversibility regularization method for a Cauchy problem of the modified Helmholtz-type equation

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item

This page was built for publication: The electric potential of a macromolecule in a solvent: A fundamental approach