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Reduction of Dimensionality in Monte Carlo Simulation of Diffusion in Extracellular Space Surrounding Cubic Cells
Neurochemical Research ( IF 4.4 ) Pub Date : 2019-04-16 , DOI: 10.1007/s11064-019-02793-6
Charles Nicholson , Padideh Kamali-Zare

The real-time iontophoretic method has measured volume fraction and tortuosity of the interstitial component of extracellular space in many regions and under different conditions. To interpret these data computer models of the interstitial space (ISS) of the brain are constructed by representing cells as Basic Cellular Structures (BCS) surrounded by a layer of ISS and replicating this combination to make a 3D ensemble that approximates brain tissue with a specified volume fraction. Tortuosity in such models is measured by releasing molecules of zero size into the ISS and allowing them to execute random walks in the ISS of the ensemble using a Monte Carlo algorithm. The required computational resources for such simulations may be high and here we show that in many situations the 3D problem may be reduced to a quasi-1D problem with consequent reduction in resources. We take the simplest BCS in the form of cubes and use MCell software to perform the Monte Carlo simulations but the analysis described here may be extended in principle to more complex BCS and an ISS that has a defined viscosity and an extracellular matrix that interacts with diffusing molecules. In the course of this study we found that the original analytical description of the relation between volume fraction and tortuosity for an ensemble of cubes may require a small correction.



中文翻译:

多维立方体周围细胞外空间扩散的蒙特卡罗模拟中的降维

实时离子电渗方法在许多区域和不同条件下测量了细胞外空间间隙成分的体积分数和曲折度。为了解释这些数据,通过将细胞表示为被一层ISS包围的基本细胞结构(BCS),然后复制此组合以形成一个3D集合来近似大脑的组织,从而构造出大脑的间隙空间(ISS)的计算机模型体积分数。通过将零大小的分子释放到ISS中并允许它们使用Monte Carlo算法在集合的ISS中执行随机游走,来测量此类模型中的曲折度。这种模拟所需的计算资源可能很高,在这里我们表明,在许多情况下,3D问题可以简化为准1D问题,从而减少了资源。我们采用立方体形式的最简单的BCS,并使用MCell软件执行蒙特卡洛模拟,但此处描述的分析原则上可以扩展到更复杂的BCS和具有确定粘度的ISS和与扩散相互作用的细胞外基质分子。在本研究过程中,我们发现对于一组立方体,体积分数与曲折度之间关系的原始分析描述可能需要进行少量校正。我们采用立方体形式的最简单的BCS,并使用MCell软件执行蒙特卡洛模拟,但此处描述的分析原则上可以扩展到更复杂的BCS和具有确定粘度的ISS和与扩散相互作用的细胞外基质分子。在本研究过程中,我们发现对于一组立方体,体积分数与曲折度之间关系的原始分析描述可能需要进行少量校正。我们采用立方体形式的最简单的BCS,并使用MCell软件执行蒙特卡洛模拟,但此处描述的分析原则上可以扩展到更复杂的BCS和具有确定粘度的ISS和与扩散相互作用的细胞外基质分子。在本研究过程中,我们发现对于一组立方体,体积分数与曲折度之间关系的原始分析描述可能需要进行少量校正。

更新日期:2019-04-16
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