Spikelet generation and AP initiation in a simplified pyr neuron (Michalikova et al. 2017) Fig 3

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Accession:206400
The article by Michalikova et al. (2017) explores the generation of spikelets in cortical pyramidal neurons. This package contains code for simulating the model with simplified morphology shown in Figs 3 and S2.
Reference:
1 . Michalikova M, Remme MW, Kempter R (2017) Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma. PLoS Comput Biol 13:e1005237 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s): I Na,t;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Action Potentials; Electrotonus; Action Potential Initiation; Axonal Action Potentials;
Implementer(s): Michalikova, Martina [tinka.michalikova at gmail.com];
Search NeuronDB for information about:  I Na,t;
from neuron import h

#--------------------- morphology --------------------------------------
# soma
L_soma = 40         
diam_soma = 20      
nseg_soma = 5  
   
# hill 
diam_hill = 1
nseg_hill = 5

# ais
L_ais = 30
diam_ais = 1
nseg_ais = 11

# axon
L_axon = 1000
diam_axon = 1
nseg_axon = 51

# dendrite
L_dend = 900     
diam_dend = 6
nseg_dend = 21

#--------------------- simulation control ------------------------------
h.dt = 0.025
tstop = 120
v_init = -70 

#-----------------------------------------------------------------------
#-----------------reversal potentials etc.------------------------------
#-----------------------------------------------------------------------
V_rest = v_init 
E_na   = 55  
E_k    =-90  
E_pas = v_init

temperature = 37.

#-------------------passive properties----------------------------------
r_a = 150      # Ohm*cm; 
c_m = 1   # microF/cm^2
r_m = 10000  # Ohm*cm^2
gpas = 1./r_m  # S/cm^2 

#---------------------active properties---------------------------------
# all conductance densities in S/cm^2 
#defaults
gna = 0.02 
gka = 0
gkdr =0.05

# soma
gna_soma =gna
gk_soma = gkdr

# dend
gna_dend = gna
gk_dend = gk_soma

# hill
gna_hill = 2*gna
gk_hill = 5*gkdr

# ais
gna_ais = 5 *gna
gk_ais = 5*gkdr

# axon
gna_axon = 2*gna
gk_axon = 2.5*gkdr

# VSHIFT of activation & inactivation curves
#somato-dendritic channels
na3_shm = 5
na3_shh = na3_shm
#axonal channels
nax_shm = -5
nax_shh = nax_shm

#----------------------- input -----------------------------------------
recording_location=0.5 
electrodeLocation = "soma(.5)"
delay = 100.
dur = 15
amp = 0