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thalamocortical2

Large-scale thalamocortical network model for simulating physiological and paroxysmal brain rhythms (4-7 Hz spike and wave discharges) described in articles:

Dervinis M, Crunelli V. Sleep waves in a large-scale corticothalamic model constrained by activities intrinsic to neocortical networks and single thalamic neurons. CNS Neurosci Ther. 2024; 30:e14206. https://doi:10.1111/cns.14206

Dervinis M, Crunelli V. Spike-and-wave discharges of absence seizures in a sleep waves-constrained corticothalamic model. CNS Neurosci Ther. 2024; 30:e14204. https://doi:10.1111/cns.14204

The main file is init.hoc

Language: Neuron

Major points:

  • To run the model in the serial manner, type in the terminal:
nrnivmodl && nrngui init.hoc

To run the model in a parallel manner (recommended), you have to set up Neuron to run with MPI (read more about this in the Neuron documentation). Once set up, type in this line:

nrnivmodl && mpiexec -np 16 nrniv -mpi init.hoc
  • Executing the init.hoc file on Neuron with all the parameters set up as it is currently, would produce 20 minutes of simulated neural activity resembling wakefulness. The data is saved in DAT files corresponding to individual cell models in the network. The files contain time, voltage, and synaptic current data.
  • In order to obtain simulations of physiological network sleep oscillations, adjust the state variable in the file init.hoc.
  • To get pure cortical simulations, set variables isFO and isHO to zero in the file ThCxprocs.hoc.
  • To obtain SWDs induced by the hyperpolarisation of thalamocortical (TC) cells, set the state variable inside the init.hoc file to 'SWDs_long'.
  • To obtain SWDs induced by tonic GABAa inhibition of TC cells, set the state variable inside the init.hoc file to 'awake_long' and adjust variable GABAfullsyn.gbar_c on line 698 inside the TCcell.hoc file.
  • To obtain SWDs induced by the decrease in the cortical GABAa current, set the state variable inside the init.hoc file to 'awake_long' and adjust variable GABAsyn.gbar_a on line 693 inside the Cx3cell.hoc file.
  • To obtain SWDs induced by the increase in the cortical AMPA current, set the state variable inside the init.hoc file to 'awake_long' and adjust variable GLUsyn.gbar_a on line 622 inside the Cx3cell.hoc file.
  • To obtain SWDs induced following the introduction of strongly intrinsically bursting cells in deep cortical layers, set the state variable inside the init.hoc file to 'awake_long', comment out lines 12 and 15, and uncomment lines 13 and 16 in the file Cx.hoc.
  • To obtain SWDs induced by the increase in the T-type calcium current in NRT cells, set the state variable inside the init.hoc file to 'awake_long' and adjust variable gcabar_its on line 333 inside the NRTcell.hoc file.
  • To obtain SWDs induced by the increase in the T-type calcium current in the higher order TC cells, set the state variable inside the init.hoc file to 'awake_long' and adjust variable gcabar_it on line 236 inside the TCcell.hoc file.
  • The repository also contains Matlab files used to analyse the simulated data. The main files are coherenceAnalysis.m, coherenceAnalysis2.m, coherenceAnalysis4.m, compareSync.m, summaryFigs.m, and frFractions.m.
  • For other issues, consult the articles.