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We present a new framework for expressing finite element methods on multiple intersecting meshes: multimesh finite element methods. The framework enables the use of separate meshes to discretize parts of a computational domain that are…
Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…
Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the…
Many immersed boundary methods solve for surface stresses that impose the velocity boundary conditions on an immersed body. These surface stresses may contain spurious oscillations that make them ill-suited for representing the physical…
This paper is devoted to the numerical validation of an explicit finite-difference scheme for the integration in time of Maxwell's equations in terms of the sole electric field, using standard linear finite elements for the space…
The standard Poisson-Boltzmann model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult…
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…
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…
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 accuracy of the free-surface lattice Boltzmann method (FSLBM) depends significantly on the boundary condition employed at the free interface. Ideally, the chosen boundary condition balances the forces exerted by the liquid and gas…
Future developments of lighter, more compact and powerful motors-driven by environmental and sustainability considerations in the transportation industry-involve higher stresses, currents and electromagnetic fields. Strong couplings between…
A procedure that allows study of unstable stability of a boundary layer between plasma and a magnetic field has been developed. Layer equilibrium for one reason or another is not set but follows from strict solution of kinetic equation with…
In this article we study adaptive finite element methods (AFEM) with inexact solvers for a class of semilinear elliptic interface problems. We are particularly interested in nonlinear problems with discontinuous diffusion coefficients, such…
For most finite element simulations, boundary-conforming meshes have significant advantages in terms of accuracy or efficiency. This is particularly true for complex domains. However, with increased complexity of the domain, generating a…
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…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…
This work develops an epsilon-uniform finite element method for singularly perturbed boundary value problems. A surprising and remarkable observation is illustrated: By moving one node arbitrarily in between its adjacent nodes, the new…
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-Nernst-Planck (PNP) equations are fundamental for modeling ion transport in electrochemical systems, capturing the intricate interplay of concentration gradients, electric fields, and ion fluxes essential for applications such…
We develop a fast method for computing the electrostatic energy and forces for a collection of charges in doubly-periodic slabs with jumps in the dielectric permittivity at the slab boundaries. Our method achieves spectral accuracy by using…