Related papers: Systematic Study of the Boundary Composition in Po…
We present an extension to the Poisson-Boltzmann model where the dipolar features of solvent molecules are taken explicitly into account. The formulation is derived at mean-field level and can be extended to any order in a systematic…
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…
We give a complete description of the boundary behaviour of the Poisson kernel and the harmonic Bergman kernel of a bounded domain with smooth boundary, which in some sense is an analogue of the similar description for the usual Bergman…
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…
The Poisson-Boltzmann equation (PBE) models the electrostatic interactions of charged bodies such as molecules and proteins in an electrolyte solvent. The PBE is a challenging equation to solve numerically due to the presence of…
We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a…
Consider the Poisson equation with the Dirichlet boundary condition on a three-dimensional polyhedral domain. For singular solutions from the non-smoothness of the domain boundary, we propose new anisotropic tetrahedral mesh refinement…
We analyze a new framework for expressing finite element methods on arbitrarily many intersecting meshes: multimesh finite element methods. The multimesh finite element method, first presented in [40], enables the use of separate meshes to…
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…
An algorithm for sequential calculation of non-isotropic matrix elements of the collision integral which are necessary for the solution of the non-linear Boltzmann equation by moment method is proposed. Isotropic matrix elements that we…
We present a method of CutFEM type for the Poisson problem with either Dirichlet or Neumann boundary conditions. The computational mesh is obtained from a background (typically uniform Cartesian) mesh by retaining only the elements…
We consider a class of nonlinear elliptic problems associated with models in biophysics, which are described by the Poisson-Boltzmann equation (PBE). We prove mathematical correctness of the problem, study a suitable class of…
The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we…
The $P_1$--nonconforming quadrilateral finite element space with periodic boundary condition is investigated. The dimension and basis for the space are characterized with the concept of minimally essential discrete boundary conditions. We…
A new approach of implementing initial and boundary conditions for the lattice Boltzmann method is presented. The new approach is based on an extended collision operator that uses the gradients of the fluid velocity. The numerical…
The Poisson boundary of a group G with a probability measure \mu is the space of ergodic components of the time shift in the path space of the associated random walk. Via a generalization of the classical Poisson formula it gives an…
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…
Poisson boundary is a measurable $\Gamma$-space canonically associated with a group $\Gamma$ and a probability measure $\mu$ on it. The collection of all measurable $\Gamma$-equivariant quotients, known as $\mu$-boundaries, of the Poisson…
We consider the problem of numerically approximating the solutions to a partial differential equation (PDE) when there is insufficient information to determine a unique solution. Our main example is the Poisson boundary value problem, when…
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…