arXiv subjects

Xiulei Cao

Publications and source records attributed to Xiulei Cao.

3 recordsLinked to original sources

arXiv2019

On the selectivity of KcsA potassium channel: asymptotic analysis and computation

Potassium (K$^+$) channels regulate the flux of K$^+$ ions through cell membranes and plays significant roles in many physiological functions. This work studies the KcsA potassium channel, including the selectivity and current-voltage (IV) relations. A modified Poisson-Nernst-Planck system is employed, which include the size effect by Bikerman model and solvation energy by Born model. The selectivity of KcsA for various ions (K$^+$, Na$^+$, Cl$^-$, Ca$^{2+}$ and Ba$^{2+}$) is studied analytically, and the profiles of concentrations and electric potential are provided. The selectivity is mainly influenced by permanent negative charges in filter of channel and the ion sizes. K$^+$ is always selected compared with Na$^+$ (or Cl$^-$), as smaller ion size of Na$^+$ causes larger solvation energy. There is a transition for selectivity among K$^+$ and divalent ions (Ca$^{2+}$ and Ba$^{2+}$), when negative charge in filter exceeds a critical value determined by ion size. This explains why divalent ions can block the KcsA channel. The profiles and IV relations are studied by analytical, numerical and hybrid methods, and are cross-validated. The results show the selectivity of the channel and also the saturation of IV curve. A simple strategy is given to compute IV relations analytically, as first approximation. The numerical method deals with general structure or parameters, but the limitations and difficulties of pure numerical simulation are also pointed out. The hybrid method provides IV relations most effectively for comparison. The reason for saturation of IV relation is illustrated, and the IV curve shows agreement with the profile and scale of experimental results.

physics.bio-ph↗

arXiv2018

Electro-Neutral Models for dynamic Poisson-Nernst-Planck System: 2D Case

The Poisson-Nernst-Planck (PNP) system is a standard model for describing ion transport. In many applications, e.g., ions in biological tissues, the presence of thin boundary layers poses both modelling and computational challenges. In a previous paper, we derived simplified electro-neutral (EN) models in one dimensional space where the thin boundary layers are replaced by effective boundary conditions. In this paper, we extend our analysis to the two dimensional case where the EN model enjoys even greater advantages. First of all, it is much cheaper to solve the EN models numerically. Secondly, EN models are easier to deal with compared with the original PNP system, therefore it is also easier to derive macroscopic models for cellular structures using EN models. The multi-ion case with general boundary is considered, for a variety of boundary conditions including either Dirichlet or flux boundary conditions. Using systematic asymptotic analysis, we derive a variety of effective boundary conditions directly applicable to the EN system for the bulk region. To validate the EN models, numerical computations are carried out for both the EN and original PNP system, including the propagation of action potential for both myelinated and unmyelinated axons. Our results show that solving the EN models is much more efficient than the original PNP system.

physics.bio-ph↗

arXiv2017

Electro-Neutral Models for Dynamic Poisson-Nernst-Planck System

The Poisson-Nernst-Planck (PNP) system is a standard model for describing ion transport. In many applications, e.g., ions in biological tissues, the presence of thin boundary layers poses both modelling and computational challenges. In this paper, we derive simplified electro-neutral (EN) models where the thin boundary layers are replaced by effective boundary conditions. There are two major advantages of EN models. First of all, it is much cheaper to solve them numerically. Secondly, EN models are easier to deal with compared with the original PNP, therefore it is also easier to derive macroscopic models for cellular structures using EN models. Even though the approach is applicable to higher dimensional cases, this paper mainly focuses on the one-dimensional system, including the general multi-ion case. Using systematic asymptotic analysis, we derive a variety of effective boundary conditions directly applicable to EN system for the bulk region. This EN system can be solved directly and efficiently without computing the solution in the boundary layer. The derivation is based on matched asymptotics, and the key idea is to bring back higher order contributions into effective boundary conditions. For Dirichlet boundary conditions, the higher order terms can be neglected and classical results (continuity of electrochemical potential) are recovered. For flux boundary conditions, however, neglecting higher contribution leads to physically incorrect solutions since they account for accumulation of ions in boundary layer. The validity of our EN model is verified by several examples and numerical computation. In particular, our EN model is much more efficient than the original PNP model when applied to the computation of membrane potential.

physics.bio-ph↗