相关论文: Towards optimal boundary integral formulations of …
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…
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…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
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…
In this paper, we present a parallel higher-order 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 computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
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…
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…
In a continuum model of the solvation of charged molecules in an aqueous solvent, the classical Poisson-Boltzmann (PB) theory is generalized to include the solute point charges and the dielectric boundary that separates the high-dielectric…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
A widely used electrostatics model in the biomolecular modeling community, the nonlinear Poisson-Boltzmann equation, along with its finite element approximation, are analyzed in this paper. A regularized Poisson-Boltzmann equation is…
Modeling the chemical, electric, and thermal transport as well as phase transitions and the accompanying mesoscale microstructure evolution within a material in an electronic device setting involves the solution of partial differential…
This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular…
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…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We consider the simulation of electromagnetic scattering by single and multiple isotropic homogeneous dielectric particles using boundary integral equations. Galerkin discretizations of the classical Poggio-Miller-Chang-Harrington-Wu-Tsai…
This paper proposes a collocation boundary element method based on the Burton--Miller method for solving transmission problems, which is rapidly convergent within the Krylov subspace solver framework. Our study enhances Burton--Miller-type…
We introduce a neural-preconditioned iterative solver for Poisson equations with mixed boundary conditions. Typical Poisson discretizations yield large, ill-conditioned linear systems. Iterative solvers can be effective for these problems,…