相关论文: Parallel Higher-order Boundary Integral Electrosta…
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
In this paper, we solve the linearized Poisson-Boltzmann equation, used to model the electric potential of macromolecules in a solvent. We derive a corrected trapezoidal rule with improved accuracy for a boundary integral formulation of the…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
Implicit-solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges, however, other force fields…
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
The Poisson-Boltzmann equation (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular systems immersed in electrolytic solutions. A conventional mean…
In this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…
We study the boundary layer solution to singular perturbation problems involving Poisson-Boltzmann (PB) type equations with a small parameter $\epsilon$ in general bounded smooth domains (including multiply connected domains) under the…
This work proposes a fast iterative method for local steric Poisson--Boltzmann (PB) theories, in which the electrostatic potential is governed by the Poisson's equation and ionic concentrations satisfy equilibrium conditions. To present the…