ACnet23 primary auditory cortex model (Beeman et al 2019)

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Accession:261423
These scripts were used to model a patch of layer 2/3 primary auditory cortex, making use of the the improvements to PGENESIS by Crone, et al. (2019). This single layer model contains a 48 x 48 grid of pyramidal cells (PCs) and a 24 x 24 grid of basket cells (BCs). The reduced PC models have 17 compartments with dimensions and passive properties that were fit to human cortical PC reconstructions. This parallel version of the simulation was used by Beeman, et al. (2019) to understand the effects of inhibition of PCs by BCs on auditory evoked potentials.
Reference:
1 . Beeman D, Yu A, Crone J (2019) Studying evoked potentials in large cortical networks with PGENESIS 2.4 BMC Neuroscience 20 Suppl 1:P46
2 . Crone JC, Vindiola MM, Yu AB, Boothe DL, Beeman D, Oie KS, Franaszczuk PJ (2019) Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator Frontiers in Neuroinformatics 13:69
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Auditory cortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell; Neocortex fast spiking (FS) interneuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: PGENESIS; GENESIS;
Model Concept(s):
Implementer(s): Beeman, Dave;
Search NeuronDB for information about:  Neocortex L2/3 pyramidal GLU cell; GabaA; AMPA; Gaba; Glutamate;
// genesis

/* FILE INFORMATION
     GENESIS implementation by D. Beeman of the channel models described in
     Alain Destexhe and Denis Par, Impact of network activity on the
     integrative properties of neocortical pyramidal neurons in vivo.
     Journal of Neurophysiology 81: 1531-1547, 1999

   Some adjustments were made to represent the model in

     Destexhe A, Rudolph M, Fellous JM and Sejnowski TJ.
     Fluctuating synaptic conductances recreate in-vivo-like activity in
     neocortical neurons. Neuroscience 107: 13-24, 2001.

   Based on the NEURON demonstration 'FLUCT' by Alain Destexhe.
   http://cns.iaf.cnrs-gif.fr
*/

// passive membrane parameters
float   CM
float   RA
float   RM

// channel equilibrium potentials (V)
float   EREST_ACT = -0.063  // value for vtraub in Destexhe et al. (2001)
// float   EREST_ACT = -0.058 // value for vtraub in Destexhe and Par (1999)
float   ENA       =  0.050
float   EK        = -0.090

/* These channels use the setupalpha function to create tabchannel tables
   to represent alpha and beta values in the form (A+B*V)/(C+exp((V+D)/F))
   The first 6 arguments are the coefficients for alpha, and the last 6
   are for beta
*/

//========================================================================
//                Tabchannel Hippocampal fast Na channel
// Based on Traub, R. D. and Miles, R.  Neuronal Networks of the hippocampus
// Cambridge University Press (1991)
//========================================================================

function make_Na_traub_mod
    str chanpath = "Na_traub_mod"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if (({exists {chanpath}}))
                return
    end

    create tabchannel {chanpath}
    setfield ^  \
        Ek      {ENA}   \               //      V
        Ik      0       \               //      A
        Gk      0       \               //      S
        Xpower  3       \
        Ypower  1       \
        Zpower  0

    setupalpha {chanpath} X  \
        {320e3  * (0.013 + EREST_ACT)}                 \
        -320e3 -1.0 {-1.0   * (0.013 + EREST_ACT)}     \
        -0.004                                          \
        {-280e3 * (0.040 + EREST_ACT)}                 \
        280e3                                           \
        -1.0                                            \
        {-1.0   * (0.040 + EREST_ACT)}                 \
        5.0e-3
    // Traub and Miles Na inactivation was shifted by Destexhe and Par
    // but this version uses no offset
    // float offset = -0.010 
    float offset = 0.0 
    setupalpha {chanpath} Y  \
        128.0                           \
        0.0                             \
        0.0                             \
        {-1.0 * (0.017 + EREST_ACT + offset)}    \
        0.018                           \
        4.0e3                           \
        0.0                             \
        1.0                             \
        {-1.0 * (0.040 + EREST_ACT + offset)}    \
        -5.0e-3
end

//========================================================================
//                Tabchannel K(DR) Hippocampal cell channel
// Based on Traub, R. D. and Miles, R.  Neuronal Networks of the hippocampus
// Cambridge University Press (1991)
//========================================================================
function make_K_traub_mod
    str chanpath = "K_traub_mod"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if (({exists {chanpath}}))
                return
    end

    create tabchannel {chanpath}
    setfield ^  \
        Ek      {EK}    \               //      V
        Ik      0       \               //      A
        Gk      0       \               //      S
        Xpower  4       \
        Ypower  0       \
        Zpower  0

    setupalpha {chanpath} X  \
        {32e3 * (0.015 + EREST_ACT)}    \
        -32e3                           \
        -1.0                            \
        {-1.0 * (0.015 + EREST_ACT) }   \
        -0.005                          \
        500                             \
        0.0                             \
        0.0                             \
        {-1.0 * (0.010 + EREST_ACT) }   \
        0.04
end