Ion channels are part of nature’s solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as large-scale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P³M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters.

中文翻译：

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具有各向异性介电常数的离子通道和纳米孔中的电荷传输模拟。

离子通道是自然调节生物环境解决方案的一部分。每个离子通道都由一串氨基酸组成，这些氨基酸带有强烈且变化剧烈的永久电荷，以这样一种方式折叠，以形成一个纳米级的水孔，跨越生物细胞的其他大部分不可渗透的膜。对于寻求了解此类纳米级系统如何实现类似设备功能的设备工程师来说，这些天然存在的蛋白质特别有趣。来自 X 射线晶体学的高分辨率结构信息以及大规模计算资源的可用性使得进行真实的离子通道模拟成为可能。一般而言，需要一系列模拟方法来研究生物系统的不同方面，如离子通道。生物学蒙特卡洛（BioMOCA），三维粗粒度粒子离子通道模拟器，为研究离子通道渗透提供了一种强大而通用的方法。BioMOCA 基于 Boltzmann Transport Monte Carlo (BTMC) 和 Particle-Particle-Particle-Mesh (P³ M) 伊利诺伊大学厄巴纳香槟分校开发的方法论。在本文中，我们简要讨论了生物物理学和工程界目前正在追求的模拟通道系统中离子流的各种方法，并展示了具有各向异性介电常数对通过具有不同有效直径的许多纳米孔的离子流的影响。