A Coupled 3-D PNP/ECP Model for Ion Transport in Biological Ion Channels
A Coupled 3-D PNP/ECP Model for Ion Transport in Biological Ion Channels
复制标题
生物离子通道中离子传输的耦合 3-D PNP/ECP 模型
DOI：
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发表时间：
2004
期刊：
影响因子：
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通讯作者：
Yang Liu
中科院分区：
文献类型：
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作者：
Zhicheng Yang;T. A. Van;Der Straaten;Umberto Ravaioli;Yang Liu
Poisson-Nernst-Planck（PNP）或漂移扩散理论可用于以有效的方式计算离子通道中的宏观电流。标准PNP理论的主要缺点是它基于电荷流的连续模型，因此它将离子建模为点粒子的气体。水也没有被明确地模拟，而是作为具有给定介电常数的背景介质引入。PNP模型可以通过在标准模型中包括校正项过量化学势（ECP）来修改，以包括有限离子尺寸和水占用的影响。吉莱斯皮等人[1]开发了一种基于密度泛函理论的ECP校正模型，该模型被引入到使用数值计算平台PROPHET实现的生物离子通道中离子传输的现有3-D PNP求解器中。由于将ECP校正直接纳入PNP矩阵公式不是一件容易的事，为了演示的目的，我们开发了一个相对简单的解耦松弛迭代算法。初步测试进行了理想化的通道几何形状，显示如何采用ECP校正模型改变显着的离子密度内的通道从传统的PNP理论单独预测。
The Poisson-Nernst-Planck (PNP) or Drift-Diffusion theory can be used to compute macroscopic current in ion channels in an efficient manner. The major drawback of the standard PNP theory is that it is based on a continuum model for the charge flow, therefore it models ions as a gas of point particles. Water is also not simulated explicitly, but introduced as a background medium with a given permittivity. The PNP model can be modified to include effects of finite ion size and water occupation by including a correction term, the Excess Chemical Potential (ECP), in the standard model. Gillespie et al. [1] developed a model for ECP correction, based on Density Functional theory, which is introduced in an existing 3-D PNP solver for ion transport in biological ion channels realized using the numerical computational platform PROPHET. Since incorporation of the ECP correction directly into the PNP matrix formulation is not an easy task, for demonstration purposes we developed a relatively simple decoupled relaxed iteration algorithm. Preliminary tests were conducted on idealized channel geometries, showing how the adopted ECP correction model alters significantly the ion densities inside the channel from those predicted by the conventional PNP theory alone.
影响因子：
5.6
作者：
Im, W;Roux, B
通讯作者：
Roux, B