ModelDB is moving. Check out our new site at https://modeldb.science. The corresponding page is https://modeldb.science/267259.

Spreading Depolarization in Brain Slices (Kelley et al. 2022)

 Download zip file 
Help downloading and running models
Accession:267259
A tissue-scale model of spreading depolarization (SD) in brain slices. We used the NEURON simulator's reaction-diffusion framework to implement embed thousands of neurons (based on the the model from Wei et al. 2014) in the extracellular space of a brain slice, which is itself embedded in an bath solution. We initiate SD in the slice by elevating extracellular K+ in a spherical region at the center of the slice. Effects of hypoxia and propionate on the slice were modeled by appropriate changes to the volume fraction and tortuosity of the extracellular space and oxygen/chloride concentrations.
Reference:
1 . Kelley C, Newton AJH, Hrabetova S, McDougal RA, Lytton WW (2022) Multiscale Computer Modeling of Spreading Depolarization in Brain Slices eNeuro [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular; Neuron or other electrically excitable cell; Glia;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s): Na/K pump; NKCC1; KCC2; I Na, leak; I Cl, leak; I K,leak; I K; I Na,t;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Spreading depolarization; Spreading depression; Reaction-diffusion;
Implementer(s): Kelley, Craig; Newton, Adam J H [adam.newton at yale.edu]; Lytton, William [bill.lytton at downstate.edu]; McDougal, Robert [robert.mcdougal at yale.edu];
Search NeuronDB for information about:  I Na,t; I K; I K,leak; Na/K pump; I Cl, leak; I Na, leak; KCC2; NKCC1; 
from analysis import traceExamples, allSpeciesMov
import sys 

datadir = sys.argv[-1]

# plot example traces 
cell_inds = [0, 6, 8, 9, 10 ]
traceExamples(datadir, datadir + 'example_traces.png', iss=cell_inds)

# generate movie for all ions and o2 over time 
## movie params 
vmins = [3.5, 100.0, 30.0, 0.01] # [k, cl, na, o2]
vmaxes = [40.0, 130.0, 140.0, 0.10] 
dur = 2 # sim duration in seconds
extent= (-250, 250, -250, 250) # (xmin, xmax, ymin, ymax)
allSpeciesMov(datadir, datadir + '/movFigs/', vmins, vmaxes, 
                datadir + 'species_movie.mp4', dur=dur, extent=extent)

# v1.0 - generates basic plots for sim specified by its output data dir as cmd line arg

Loading data, please wait...