Reaction-diffusion sims of Ca2+ signals in astrocytic branchlets at the nanoscale (Denizot et al 22)

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Reaction-Diffusion simulations are performed in geometries that were designed from the latest data available from super-resolution microscopy on astrocytes, published by Arizono et al., Nature Communications, 2020. The high spatial resolution of this model allows to propose plausible mechanisms by which astrocyte morphology at the nanoscale, notably shaft width, can influence local calcium dynamics and thus affect specialized neuron-astrocyte communication.
Model Information (Click on a link to find other models with that property)
Model Type: Glia;
Brain Region(s)/Organism:
Cell Type(s): Astrocyte;
Gap Junctions:
Receptor(s): IP3;
Simulation Environment: STEPS;
Model Concept(s): Reaction-diffusion;
Implementer(s): Denizot, Audrey [audrey.denizot at];
Search NeuronDB for information about:  IP3;
This is the README file for the script to perform simulations of the bleaching protocol from:

Denizot, A., M. Arizono, U. V. Nägerl, H. Berry, & E. De Schutter. Control of Ca2+ signals by astrocyte nanoscale morphology at tripartite synapses, Glia, Sep. 2022, doi: 10.1002/glia.24258

This model requires STEPS software, which is freely available at

First, you need to download STEPS at or directly at
Dependencies for STEPS are described on the README file at 

The model requires that the following packages are installed:
- numpy
- pickle
- sys
- pyqtgraph

The model is divided in 2 python files:

This file contains 2 functions:
- getModel(), that defines all molecules, reactions, reaction constants involved in the model
- gen_geom(), that imports the geometry from the meshes "5nodes_ratio1.inp", "5nodes_ratio1.inp" and "5nodes_ratio1.inp", which correspond to astrocytic branchlets with shaft width of d0, d0/2 and d0/3, respectively. 

This file sets initial conditions and runs the simulation while recording data in a file. Bleaching occurs at t=1000 ms.
To run this script, simply call the function with python with an integer i as an argument that will be the seed for the given simulation as well as the name of the mesh file 'filename'. The output file, out.filename.i', contains in each line the number of fluorescing ZSGreen molecules in the region to be bleached (left) and in the central node (right). Time between two lines corresponds to 3.6 ms, to fit experimental data, but can be manually changed by the user at line 12.

Example command:
python 1 5nodes_ratio3.inp

"5nodes_ratio1.inp", "5nodes_ratio1.inp" and "5nodes_ratio1.inp" correspond to astrocytic branchlets with shaft width of d0, d0/2 and d0/3