Related papers: Accurate boundary-integral formulations for the ca…
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…
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…
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…
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…
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…
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 structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
This paper provides a rigorous analysis of boundary element methods for the magnetic field integral equation on Lipschitz polyhedra. The magnetic field integral equation is widely used in practical applications to model electromagnetic…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
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 demonstrate how meshfree finite difference methods can be applied to solve vector Poisson problems with electric boundary conditions. In these, the tangential velocity and the incompressibility of the vector field are prescribed at the…
Computational modeling and simulation of fluid-structure interactions constitute a fundamental cornerstone for advancing aerospace engineering endeavors. This paper addresses the notion and implementation of the immersed boundary method for…
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…
A variational approach is used to develop a robust numerical procedure for solving the nonlinear Poisson-Boltzmann equation. Following Maggs et al., we construct an appropriate constrained free energy functional, such that its…
The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…
We define a finite element method for the coupling of Stokes and nonlinear Poisson--Boltzmann equations. The novelty in the formulation is that the coupling from the electric potential to the drag in the momentum balance is rewritten as a…
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…
In computational biochemistry and biophysics, understanding the role of electrostatic interactions is crucial for elucidating the structure, dynamics, and function of biomolecules. The Poisson-Boltzmann (PB) equation is a foundational tool…
An explicit solution of the stationary one dimensional half-space boundary value problem for the linear Boltzmann equation is presented in the presence of an arbitrarily high constant external field. The collision kernel is assumed to be…