相关论文: Adaptive and Iterative Methods for Simulations of …
This work presents a finite element method for a modified Poisson-Nernst-Planck/Navier-Stokes (PNP/NS) model under the mechanical equilibrium, developed for compressible electrolytes. Another key contribution of this work is the reduction…
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…
In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the…
In this paper, we develop an adaptive finite element method for the nonlinear steady-state Poisson-Nernst-Planck equations, where the spatial adaptivity for geometrical singularities and boundary layer effects are mainly considered. As a…
The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological…
Electrokinetic phenomena in nanopore sensors and microfluidic devices require accurate simulation of coupled fluid-electrostatic interactions in geometrically complex domains with irregular boundaries and adaptive mesh refinement. We…
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing…
The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, have been developed to account for ionic size effects and…
In this paper, a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) model is presented as a nonlinear system of an electrostatic potential and multiple ionic concentrations. It mixes nonlinear algebraic equations with a…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
This work proposes a new stabilized $P_1\times P_0$ finite element method for solving the incompressible Navier--Stokes equations. The numerical scheme is based on a reduced Bernardi--Raugel element with statically condensed face bubbles…
This paper presents an efficient finite element iterative method for solving a nonuniform size-modified Poisson-Nernst-Planck ion channel (SMPNPIC) model, along with a SMPNPIC program package that works for an ion channel protein with a…
We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle…
We present a spectral element model for general-purpose simulation of non-overturning nonlinear water waves using the incompressible Navier-Stokes equations (INSE) with a free surface. The numerical implementation of the spectral element…
In this paper, we propose and analyze a second order accurate (in both time and space) numerical scheme for the Poisson-Nernst-Planck-Navier-Stokes system, which describes the ion electro-diffusion in fluids. In particular, the…
We consider in this paper random batch interacting particle methods for solving the Poisson-Nernst-Planck (PNP) equations, and thus the Poisson-Boltzmann (PB) equation as the equilibrium, in the external unbounded domain. To justify the…
The Poisson-Nernst-Planck equations with generalized Frumkin-Butler-Volmer boundary conditions (PNP-FBV) describe ion transport with Faradaic reactions, and have applications in a number of fields. In this article, we develop an adaptive…
We present an adaptive finite element method for the incompressible Navier--Stokes equations based on a standard splitting scheme (the incremental pressure correction scheme). The presented method combines the efficiency and simplicity of a…
We develop numerical methods to simulate the fluid-mechanical erosion of many bodies in two-dimensional Stokes flow. The broad aim is to simulate the erosion of a porous medium (e.g. groundwater flow) with grain-scale resolution. Our fluid…
Motivated by the need for efficient and accurate simulation of the dynamics of the polar ice sheets, we design high-order finite element discretizations and scalable solvers for the solution of nonlinear incompressible Stokes equations. We…