Related papers: Efficient mesh refinement for the Poisson-Boltzman…
We study finite-difference approximations of both Poisson and Poisson-Boltzmann (PB) electrostatic energy functionals for periodic structures constrained by Gauss' law and a class of local algorithms for minimizing the finite-difference…
Electromagnetic simulations of complex geologic settings are computationally expensive. One reason for this is the fact that a fine mesh is required to accurately discretize the electrical conductivity model of a given setting. This…
Given a partial differential equation (PDE), goal-oriented error estimation allows us to understand how errors in a diagnostic quantity of interest (QoI), or goal, occur and accumulate in a numerical approximation, for example using the…
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…
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 nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…
Immersed boundary methods are high-order accurate computational tools used to model geometrically complex problems in computational mechanics. While traditional finite element methods require the construction of high-quality boundary-fitted…
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…
Models incorporating uncertain inputs, such as random forces or material parameters, have been of increasing interest in PDE-constrained optimization. In this paper, we focus on the efficient numerical minimization of a convex and smooth…
This paper considers the finite element solution of the boundary value problem of Poisson's equation and proposes a guaranteed em a posteriori local error estimation based on the hypercircle method. Compared to the existing literature on…
The finite element method can be viewed as a machine that automates the discretization of differential equations, taking as input a variational problem, a finite element and a mesh, and producing as output a system of discrete equations.…
The Stokes-Brinkman equations model flow in heterogeneous porous media by combining the Stokes and Darcy models of flow into a single system of equations. With suitable parameters, the equations can model either flow without detailed…
We present numerical experiments for geophysics electromagnetic (EM) modeling based upon high-order edge elements and supervised $h+p$ refinement approaches on massively parallel computers. Our high-order $h+p$ refinement strategy is based…
This work surveys an r-adaptive moving mesh finite element method for the numerical solution of premixed laminar flame problems. Since the model of chemically reacting flow involves many different modes with diverse length scales, the…
This paper introduces a new computational methodology for determining a-posteriori multi-objective error estimates for finite-element approximations, and for constructing corresponding (quasi-)optimal adaptive refinements of finite-element…
We present a novel energy-based numerical analysis of semilinear diffusion-reaction boundary value problems. Based on a suitable variational setting, the proposed computational scheme can be seen as an energy minimisation approach. More…
An adaptive regularization strategy for stabilizing Newton-like iterations on a coarse mesh is developed in the context of adaptive finite element methods for nonlinear PDE. Existence, uniqueness and approximation properties are known for…
We consider linear reaction-diffusion equations posed on unbounded domains, and discretized by adaptive Lagrange finite elements. To obtain finite-dimensional spaces, it is necessary to introduce a truncation boundary, whereby only a…
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…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…