Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
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Publication:6112666
DOI10.1016/j.cpc.2023.108808arXiv2111.00834OpenAlexW4379141531MaRDI QIDQ6112666
Shenggao Zhou, Min-Hong Chen, Wei Dou
Publication date: 7 August 2023
Published in: Computer Physics Communications (Search for Journal in Brave)
Full work available at URL: https://arxiv.org/abs/2111.00834
high efficiencycounterion stratificationNewton iteration method with truncationprecomputing speed-up strategysteric Poisson-Boltzmann theory
Cites Work
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- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
- A mathematical model for the hard sphere repulsion in ionic solutions
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- A new approach to the Lennard-Jones potential and a new model: PNP-steric equations
- Positivity preserving finite difference methods for Poisson-Nernst-Planck equations with steric interactions: application to slit-shaped nanopore conductance
- Variational approach to concentration dependent dielectrics with the Bruggeman model: theory and numerics
- Ionic size effects: generalized Boltzmann distributions, counterion stratification and modified Debye length
- Progress in developing Poisson-Boltzmann equation solvers
- An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics
- Continuum electrostatics for ionic solutions with non-uniform ionic sizes
- DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes
- Analysis of the Mean Field Free Energy Functional of Electrolyte Solution with Nonhomogenous Boundary Conditions and the Generalized PB/PNP Equations with Inhomogeneous Dielectric Permittivity
- Variational implicit-solvent predictions of the dry–wet transition pathways for ligand–receptor binding and unbinding kinetics
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
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