A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
DOI10.1016/J.JCP.2022.111340OpenAlexW4281763390WikidataQ113871686 ScholiaQ113871686MaRDI QIDQ2672786
Siwen Wang, Emil Alexov, Yuanzhen Shao, Shan Zhao
Publication date: 13 June 2022
Published in: Journal of Computational Physics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jcp.2022.111340
regularizationfinite-difference methodPoisson-Boltzmann equationelectrostatic free energysingular charge sourceGaussian dielectric model
Numerical methods for partial differential equations, boundary value problems (65Nxx) Partial differential equations of mathematical physics and other areas of application (35Qxx) Elliptic equations and elliptic systems (35Jxx)
Related Items (2)
Uses Software
Cites Work
- Unnamed Item
- Unnamed Item
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- Geometric and potential driving formation and evolution of biomolecular surfaces
- 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
- Convergence of phase-field free energy and boundary force for molecular solvation
- Accurate evaluation of electrostatics for macromolecules in solution
- On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
- Unified construction of Green's functions for Poisson's equation in inhomogeneous media with diffuse interfaces
- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
- Computational modeling of protein conformational changes -- application to the opening SARS-CoV-2 spike
- Efficient calculation of fully resolved electrostatics around large biomolecules
- Benchmarking electrostatic free energy of the nonlinear Poisson-Boltzmann model for the Kirkwood sphere
- Reproducing ensemble averaged electrostatics with super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes
- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces
- Range-separated tensor decomposition of the discretized Dirac delta and elliptic operator inverse
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- Potential Space Estimates for Green Potentials in Convex Domains
- Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation
- An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- Regularization of Poisson--Boltzmann Type Equations with Singular Source Terms Using the Range-Separated Tensor Format
This page was built for publication: A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions