On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
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finite element methodelectrostatic free energyPoisson-Boltzmann equationmolecular surfacepseudo-time approachregularized Poisson-Boltzmann equation
Biochemistry, molecular biology (92C40) Smoothness and regularity of solutions to PDEs (35B65) Electro- and magnetostatics (78A30) Biological applications of optics and electromagnetic theory (78A70) Boltzmann equations (35Q20) PDEs in connection with optics and electromagnetic theory (35Q60) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Stability and convergence of numerical methods for initial value and initial-boundary value problems involving PDEs (65M12) Mesh generation, refinement, and adaptive methods for boundary value problems involving PDEs (65N50) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10)
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Cites work
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- scientific article; zbMATH DE number 1480202 (Why is no real title available?)
- scientific article; zbMATH DE number 5179816 (Why is no real title available?)
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- Accurate evaluation of electrostatics for macromolecules in solution
- Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
- An iterative discontinuous Galerkin method for solving the nonlinear Poisson Boltzmann equation
- 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
- Discontinuous Galerkin method for the linear Poisson-Boltzmann equation
- Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
- Geometric and potential driving formation and evolution of biomolecular surfaces
- High-Order Methods for Incompressible Fluid Flow
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
- Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
- SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
- Spectral methods on triangles and other domains
- TetGen, a Delaunay-based quality tetrahedral mesh generator
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- The electric potential of a macromolecule in a solvent: A fundamental approach
- Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
- tabipb
Cited in
(17)- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
- Bio-inspired computing platform for reliable solution of Bratu-type equations arising in the modeling of electrically conducting solids
- Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent
- A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule
- Adaptive pseudo-time methods for the Poisson-Boltzmann equation with Eulerian solvent excluded surface
- A new numerical method for nonlocal electrostatics in biomolecular simulations
- An effective parallel implemented for an stable method of Poisson-Boltzmann equation based on finite element method
- A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
- Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation
- Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
- On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
- A method of boundary equations for nonlinear Poisson-Boltzmann equation arising in biomolecular systems
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
- Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential
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