Efficient calculation of fully resolved electrostatics around large biomolecules
From MaRDI portal
Publication:2134490
DOI10.1016/j.jcp.2021.110718OpenAlexW3201940645MaRDI QIDQ2134490
Daniil Bochkov, Raphael Egan, Frédéric Gibou, Rochishnu Chowdhury
Publication date: 3 May 2022
Published in: Journal of Computational Physics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jcp.2021.110718
Numerical methods for partial differential equations, boundary value problems (65Nxx) Miscellaneous topics in partial differential equations (35Rxx) Elliptic equations and elliptic systems (35Jxx)
Related Items (3)
A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions ⋮ A kernel-free boundary integral method for the nonlinear Poisson-Boltzmann equation ⋮ Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential
Uses Software
Cites Work
- A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
- A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
- A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid
- A decomposed immersed interface method for variable coefficient elliptic equations with non-smooth and discontinuous solutions
- A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
- A Voronoi interface approach to cell aggregate electropermeabilization
- A fourth order accurate discretization for the Laplace and heat equations on arbitrary domains, with applications to the Stefan problem
- xGFM: recovering convergence of fluxes in the ghost fluid method
- A supra-convergent finite difference scheme for the variable coefficient Poisson equation on non-graded grids
- Piecewise-polynomial discretization and Krylov-accelerated multigrid for elliptic interface problems
- An efficient fluid-solid coupling algorithm for single-phase flows
- Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations
- The electric potential of a macromolecule in a solvent: A fundamental approach
- A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
- Tree methods for moving interfaces
- Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson-Boltzmann theory
- A second-order-accurate symmetric discretization of the Poisson equation on irregular domains
- A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
- A review of level-set methods and some recent applications
- A boundary condition capturing method for Poisson's equation on irregular domains
- Solving elliptic interface problems with jump conditions on Cartesian grids
- A parallel Voronoi-based approach for mesoscale simulations of cell aggregate electropermeabilization
- Solving Poisson-type equations with Robin boundary conditions on piecewise smooth interfaces
- Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
- Geometric integration over irregular domains with application to level-set methods
- High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
- Efficient symmetric discretization for the Poisson, heat and Stefan-type problems with Robin boundary conditions
- The Immersed Interface Method for Elliptic Equations with Discontinuous Coefficients and Singular Sources
- A Fast Iterative Algorithm for Elliptic Interface Problems
- An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations
- A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
- New Geometric Immersed Interface Multigrid Solvers
- A Comparison of Algebraic Multigrid and Geometric Immersed Interface Multigrid Methods for Interface Problems
- Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
- The Explicit-Jump Immersed Interface Method: Finite Difference Methods for PDEs with Piecewise Smooth Solutions
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- The Immersed Interface Method
- The Numerical Solution of Laplace's Equation
- Adaptive numerical treatment of elliptic systems on manifolds
This page was built for publication: Efficient calculation of fully resolved electrostatics around large biomolecules