[PDF][PDF] Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications

BZ Lu, YC Zhou, MJ Holst, JA McCammon - Commun Comput Phys, 2008 - Citeseer
Efficiency and accuracy are two major concerns in numerical solutions of the Poisson-
Boltzmann equation for applications in chemistry and biophysics. Recent developments in …

Electrodiffusion phenomena in neuroscience and the nernst–planck–poisson equations

JJ Jasielec - Electrochem, 2021 - mdpi.com
This work is aimed to give an electrochemical insight into the ionic transport phenomena in
the cellular environment of organized brain tissue. The Nernst–Planck–Poisson (NPP) …

Poisson–Nernst–Planck equations for simulating biomolecular diffusion–reaction processes I: Finite element solutions

B Lu, MJ Holst, JA McCammon, YC Zhou - Journal of computational physics, 2010 - Elsevier
In this paper we developed accurate finite element methods for solving 3-D Poisson–Nernst–
Planck (PNP) equations with singular permanent charges for simulating electrodiffusion in …

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: Size effects on ionic distributions and diffusion-reaction rates

B Lu, YC Zhou - Biophysical journal, 2011 - cell.com
The effects of finite particle size on electrostatics, density profiles, and diffusion have been a
long existing topic in the study of ionic solution. The previous size-modified Poisson …

Variational multiscale models for charge transport

GW Wei, Q Zheng, Z Chen, K **a - siam REVIEW, 2012 - SIAM
This work presents a few variational multiscale models for charge transport in complex
physical, chemical, and biological systems and engineering devices, such as fuel cells, solar …

Differential geometry based multiscale models

GW Wei - Bulletin of mathematical biology, 2010 - Springer
Large chemical and biological systems such as fuel cells, ion channels, molecular motors,
and viruses are of great importance to the scientific community and public health. Typically …

Error analysis of finite element method for Poisson–Nernst–Planck equations

Y Sun, P Sun, B Zheng, G Lin - Journal of Computational and Applied …, 2016 - Elsevier
In this paper we study the a priori error estimates of finite element method for the system of
time-dependent Poisson–Nernst–Planck equations, and for the first time, we obtain its …

A virtual element method for the steady-state Poisson-Nernst-Planck equations on polygonal meshes

Y Liu, S Shu, H Wei, Y Yang - Computers & Mathematics with Applications, 2021 - Elsevier
Abstract Poisson-Nernst-Planck equations are a nonlinear coupled system which are widely
used to describe electrodiffusion processes in biomolecular systems and semiconductors …

Monte Carlo Simulation of Electrolyte Solutions in biology: in and out of equilibrium

D Boda - Annual reports in computational chemistry, 2014 - Elsevier
A concise account is given about Monte Carlo (MC) simulation techniques for homogeneous
and inhomogeneous systems of electrolyte solutions at concentrations characteristic of …

A multigrid method for the Poisson–Nernst–Planck equations

SR Mathur, JY Murthy - International Journal of Heat and Mass Transfer, 2009 - Elsevier
A computational technique for solving the Poisson–Nernst–Planck (PNP) equations is
developed which overcomes the poor convergence rates of commonly used algorithms. The …