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;
// Cell parameter file for the reduced model of "cell 945" at 945 um below
// the surface, from Eyal et al. 2016 Fig 1c4.
// RM and Cm values are scaled by a ratio of the model segment area to
// that of same region of the reconstructed cell.
// These were obtained by parsing 2013_03_13_cell06_945_H42_05.CNG.swc
// to identify all terminal and non terminal branch intervals in regions
// at specified distances from the some

*relative
*cartesian
*asymmetric

// membrane constants (SI units) - scaled to give area corrections
*set_global        RM      3.10     // ohm*m^2
*set_global        RA      2.47      // ohm*m
*set_global        CM      0.0061    // farad/m^2
*set_global     EREST_ACT  -0.082     // volts (leakage potential)

// These include an additional scaling of RM and RA by 0.85 and CM by 1.18
// This gives another 15% increase in area, preserving  RM/RA ratio,
// resulting in better fit to 2 msec, 200pA injection pulse.

// Populate soma wih modified traub91 channels

soma    none  0  0 19 18.5   \
    Na_pyr             3000  \
    Kdr_pyr             1600  \
    Ca_hip_traub91      100  \
    Kahp_pyr             30  \
    Ca_conc            -7.769e12    \
    spike 0.0

*set_compt_param RA 1.24 // use average soma-apical0 Ra
apical0 soma       0   0  66    2.9  GABA_pyr 5.0 // apical trunk
*set_compt_param RA 2.47 // back to default
apical1 apical0    0   0  335   1.8  AMPA_pyr 5.0 // lower apical at 50 - 300 um

// For upper apical divide Rm and multiply CM by 2.08
// Apply additional spine area correction of 1.9
*set_compt_param RM 0.923
*set_compt_param CM 0.0206
apical2 apical1    0   0  267   2.3 GABA_pyr 5.0 // mid apical at 300 - 600 um
apical3 apical2    0   0  84    2.3 // apical tuft non-terminal > 600 um
apical4a apical3    -189   0  189   2.3 // terminal tuft btanches
apical4b apical3     189   0  189   2.3

// For oblique, scale by 3.7
// Apply additional spine area correction of 1.9*0.85
*set_compt_param RM 0.441
*set_compt_param CM 0.0432

oblique1 apical0 -34   0   0    4.9 //  AMPA_pyr 2.6526
oblique2a oblique1 -71   0  -71 2.3   GABA_pyr 2.6526
oblique2b oblique1 -71   0   71 2.3   AMPA_pyr 2.6526

// For basal0, scale factor is 2.78 - no spine correction, 0.85,1.18
*set_compt_param RM 1.116
*set_compt_param CM 0.0171
*set_compt_param RA 1.31 // use average soma-basal0 Ra
basal0  soma     0     0  -32   6.0  // GABA_pyr 2.6526
*set_compt_param RA 2.47// back to default

// Apply additional spine area correction of 1.9
// For basal1, scale factor is 5.0 (*0.85)
*set_compt_param RM 0.327
*set_compt_param CM 0.0583
basal1a  basal0 -22.0   0  -22.0 3.5
basal1b basal0   22.0   0 -22.0 3.5
// For basal2, scale factor is 3.22*1.9 (*0.85)
*set_compt_param RM 0.507
*set_compt_param CM 0.0375
basal2a basal1a -200    0  0    3.5
basal2b basal1a  0    0  -200   3.5   AMPA_pyr 5.0
basal2c basal1b  0    0  -200   3.5
basal2d basal1b  200    0  0   3.5