On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
electrostatic free energyfinite element methodmolecular surfacePoisson-Boltzmann equationpseudo-time approachregularized Poisson-Boltzmann equation
Smoothness and regularity of solutions to PDEs (35B65) 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) Electro- and magnetostatics (78A30) Biological applications of optics and electromagnetic theory (78A70) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Biochemistry, molecular biology (92C40)
This paper is concerned with solving the Poisson-Boltzmann equation (PBE), a widely used implicit solvent model for the electrostatic analysis of solvated biomolecules. Some challenges of solving the PBE are that the equation has an exponential nonlinearity, complex interfaces between solute and solvent, and singular source terms. This paper develops a novel finite element method (FEM) in the pseudo-time framework for solving the PBE. By changing the time-independent problem into a time-dependent problem, the authors find that such a technique can completely suppress the nonlinear instability through the time splitting implementation. As for the singular charge sources, they investigate both the singular delta function method and the regularized delta function method. Using a body-fitted mesh, they find that the proposed pseudo-time FEM solvers are more accurate than existing pseudo-time finite difference solvers. Numerical results of several benchmark problems and free energy calculations of protein systems are presented to demonstrate the unconditional stability, accuracy, and robustness of the proposed PBE method.
- Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent
- Adaptive pseudo-time methods for the Poisson-Boltzmann equation with Eulerian solvent excluded surface
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- An effective parallel implemented for an stable method of Poisson-Boltzmann equation based on finite element method
- A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- 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
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
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- 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
- tabipb
- TetGen, a Delaunay-based quality tetrahedral mesh generator
- The electric potential of a macromolecule in a solvent: A fundamental approach
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
- On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
- Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
- Bio-inspired computing platform for reliable solution of Bratu-type equations arising in the modeling of electrically conducting solids
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- 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 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
- Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules
- Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
- Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
- An effective parallel implemented for an stable method of Poisson-Boltzmann equation based on finite element method
- Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential
- A method of boundary equations for nonlinear Poisson-Boltzmann equation arising in biomolecular systems
- A new numerical method for nonlocal electrostatics in biomolecular simulations
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