A treecode-accelerated boundary integral Poisson–Boltzmann solver for electrostatics of solvated biomolecules
We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of
solvated biomolecules described by the linear Poisson–Boltzmann equation. The method …
solvated biomolecules described by the linear Poisson–Boltzmann equation. The method …
A two-component Matched Interface and Boundary (MIB) regularization for charge singularity in implicit solvation
We present a new Matched Interface and Boundary (MIB) regularization method for treating
charge singularity in solvated biomolecules whose electrostatics are described by the …
charge singularity in solvated biomolecules whose electrostatics are described by the …
Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
A significant challenge in numerical solution to the Poisson-Boltzmann equation is due to
singular charge sources in terms of Dirac delta functions. To overcome this difficulty, several …
singular charge sources in terms of Dirac delta functions. To overcome this difficulty, several …
Progress in developing Poisson-Boltzmann equation solvers
This review outlines the recent progress made in developing more accurate and efficient
solutions to model electrostatics in systems comprised of bio-macromolecules and …
solutions to model electrostatics in systems comprised of bio-macromolecules and …
Frontiers in biomolecular mesh generation and molecular visualization systems
With the development of biomolecular modeling and simulation, especially implicit solvent
modeling, higher requirements are set for the stability, efficiency and mesh quality of …
modeling, higher requirements are set for the stability, efficiency and mesh quality of …
An implicit boundary integral method for computing electric potential of macromolecules in solvent
A numerical method using implicit surface representations is proposed to solve the
linearized Poisson–Boltzmann equation that arises in mathematical models for the …
linearized Poisson–Boltzmann equation that arises in mathematical models for the …
On preconditioning the treecode-accelerated boundary integral (TABI) Poisson–Boltzmann solver
We recently developed a treecode-accelerated boundary integral (TABI) solver for solving
Poisson–Boltzmann (PB) equation [1]. The solver has combined advantages in accuracy …
Poisson–Boltzmann (PB) equation [1]. The solver has combined advantages in accuracy …
Computing protein pkas using the tabi Poisson–Boltzmann solver
A common approach to computing protein pKas uses a continuum dielectric model in which
the protein is a low dielectric medium with embedded atomic point charges, the solvent is a …
the protein is a low dielectric medium with embedded atomic point charges, the solvent is a …
A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
Abstract The Poisson-Boltzmann model is an effective and popular approach for modeling
solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we …
solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we …
Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces
We study the parallelization of a flexible order Cartesian treecode algorithm for evaluating
electrostatic potentials of charged particle systems in which N particles are located on the …
electrostatic potentials of charged particle systems in which N particles are located on the …