Reduction of Dimensionality in Monte Carlo Simulation of Diffusion in Extracellular Space Surrounding Cubic Cells

  • Charles NicholsonEmail author
  • Padideh Kamali-Zare
Original Paper


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.


Extracellular space Volume fraction Tortuosity Monte Carlo Real-time iontophoresis 



Supported in part by National Institutes of Health Grant R01-NS28642 from the National Institute of Neurological Disorders and Stroke.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Neuroscience and PhysiologyNew York University School of MedicineNew YorkUSA
  2. 2.Darmiyan IncSan FranciscoUSA

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