#Granule cell model 2020 - Adapting.
#Authors: Stefano Masoli* 1, Marialuisa Tognolina* 1, Umberto Laforenza 2, Francesco Moccia 3, Egidio D'Angelo 1,4
#Author information: 1 Department of Brain and Behavioral Sciences, University of Pavia, Via Forlanini 6, I-27100, Pavia, Italy,
#2 Department of Molecular Medicine, University of Pavia, Via Forlanini 6, I-27100, Pavia, Italy,
#3 Department of Biology and Biotechnology, University of Pavia, Via Forlanini 6, I-27100, Pavia, Italy,
#4 Brain Connectivity Center, IRCCS Mondino Foundation, Via Mondino 2, I-27100, Pavia, Italy,
#* Co-Author
#Citation: Masoli S.*, Tognolina M.*, Laforenza U., Moccia F., D’Angelo E. Parameter tuning differentiates granule cell subtypes enriching transmission properties at the cerebellum input stage. Nature communication biology 2020.
#DOI: 10.1038/s42003-020-0953-x
from neuron import h
import math
from Syntype import Synapse_py3
import numpy as np
class Grc_accelerate:
def __repr__(self):
return 'Grc_regular_morph[{}]'.format(self._id)
def __init__(self, _id):
self._id = _id
h.load_file('stdlib.hoc')
h.load_file('import3d.hoc')
cell = h.Import3d_Neurolucida3()
cell.input('morphology/GrC2020.asc')
i3d = h.Import3d_GUI(cell,0)
i3d.instantiate(self)
#Soma channels
self.soma[0].nseg = 1 + (2 * int(self.soma[0].L / 40))
self.soma[0].Ra = 100
self.soma[0].cm = 2
self.soma[0].insert('Leak')
self.soma[0].gmax_Leak = 0.00029038073716
self.soma[0].e_Leak = -60
self.soma[0].insert('Kv3_4')
self.soma[0].gkbar_Kv3_4 = 0.00076192450951999995
self.soma[0].insert('Kv4_3')
self.soma[0].gkbar_Kv4_3 = 0.0028149683906099998
self.soma[0].ek = -88
self.soma[0].insert('Kir2_3')
self.soma[0].gkbar_Kir2_3 = 0.00074725514701999996
self.soma[0].insert('GRC_CA')
self.soma[0].gcabar_GRC_CA = 0.00060938071783999998
self.soma[0].insert('Kv1_1')
self.soma[0].gbar_Kv1_1 = 0.0056973826455499997
self.soma[0].insert('Kv1_5')
self.soma[0].gKur_Kv1_5 = 0.00083407556713999999
self.soma[0].insert('Kv2_2_0010')
self.soma[0].gKv2_2bar_Kv2_2_0010 = 1.203410852e-05
self.soma[0].insert('cdp5_CR_CAM')
self.soma[0].push()
self.soma[0].eca = 137.5
h.pop_section()
self.whatami = "GrC_2020_acc"
#DEND
for i in self.dend:
i.nseg = 1 + (2 * int(i.L / 40))
i.Ra = 100
i.cm = 2.5
i.insert('Leak')
i.gmax_Leak = 0.00025029700736999997
i.e_Leak = -60
i.insert('GRC_CA')
i.gcabar_GRC_CA = 0.0050012800845900002
i.insert('Kca1_1')
i.gbar_Kca1_1 = 0.010018074546510001
i.ek = -88
i.insert('Kv1_1')
i.gbar_Kv1_1 = 0.00381819207934
i.insert('Ubc_TRP')
i.gtrp_Ubc_TRP = 0.0005
i.insert('cdp5_CR_CAM')
i.push()
i.eca = 137.5
h.pop_section()
#Hilock
self.axon = h.Section(name = 'hilock', cell=self)
self.axon.L = 1
self.axon.nseg = 1
self.axon.diam = 1.5
self.axon.Ra = 100
self.axon.cm = 2
self.axon.insert('Leak')
self.axon.gmax_Leak = 0.00036958189720000001
self.axon.e_Leak = -60
self.axon.insert('GRC_NA_FHF')
self.axon.gnabar_GRC_NA_FHF = 0.0092880585146199995
self.axon.ena = 87.39
self.axon.insert('Kv3_4')
self.axon.gkbar_Kv3_4 = 0.020373463109149999
self.axon.ek = -88
self.axon.insert('GRC_CA')
self.axon.gcabar_GRC_CA = 0.00057726155447
self.axon.insert('cdp5_CR_CAM')
self.axon.push()
self.axon.eca = 137.5
h.pt3dadd(0.0, -5.62232, 0.0, self.axon.diam)
h.pt3dadd(0.0, -6.62232, 0.0, self.axon.diam)
h.pop_section()
self.axon.connect(self.soma[0],0,0)
#AIS
self.ais=h.Section(name = 'ais', cell=self)
self.ais.L = 10
self.ais.nseg = 1
self.ais.diam = 0.7
self.ais.Ra = 100
self.ais.cm = 1
self.ais.insert('GRC_NA_FHF')
self.ais.gnabar_GRC_NA_FHF = 1.28725006737226
self.ais.ena = 87.39
self.ais.insert('Kv3_4')
self.ais.gkbar_Kv3_4 = 0.0064959534065400001
self.ais.ek = -88
self.ais.insert('Leak')
self.ais.gmax_Leak = 0.00029276697557000002
self.ais.e_Leak = -60
self.ais.insert('GRC_CA')
self.ais.gcabar_GRC_CA = 0.00031198539471999999
self.ais.insert('GRC_KM')
self.ais.gkbar_GRC_KM = 0.00056671971737000002
self.ais.insert('cdp5_CR_CAM')
self.ais.push()
self.ais.eca = 137.5
h.pt3dadd(0.0, -6.62232, 0.0, self.ais.diam)
h.pt3dadd(0.0, -16.62232, 0.0, self.ais.diam)
h.pop_section()
lensec = 7
secnumber_aa = int(126/lensec)
secnumber_pf = int(1000/lensec)
self.ais.connect(self.axon,1,0)
len_initial = -16.62232
len_ending = 7
self.HD_aa = [h.Section(cell=self, name='aa_'+str(x)) for x in range(secnumber_aa)]
for b in self.HD_aa:
b.L = lensec
b.nseg = 1
b.diam = 0.3
b.Ra = 100
b.cm = 1
b.insert('GRC_NA')
b.gnabar_GRC_NA = 0.026301636815019999
b.ena = 87.39
b.insert('Kv3_4')
b.gkbar_Kv3_4 = 0.00237386061632
b.ek = -88
b.insert('Leak')
b.gmax_Leak = 9.3640921249999996e-05
b.e_Leak = -60
b.insert('GRC_CA')
b.gcabar_GRC_CA = 0.00068197420273000001
b.insert('cdp5_CR_CAM')
b.push()
b.eca = 137.5
h.pt3dadd(0.0, len_initial , 0.0, b.diam)
h.pt3dadd(0.0, len_initial - len_ending, 0.0, b.diam)
h.pop_section()
len_initial = len_initial - len_ending
self.HD_pf1 = [h.Section(cell=self, name='pf_'+str(x)) for x in range(secnumber_pf)]
len_initial = -142.62232
len_ending_pf = 7
for i in self.HD_pf1:
i.L = lensec
i.nseg = 1
i.diam = 0.15
i.Ra = 100
i.cm = 1
i.insert('GRC_NA')
i.gnabar_GRC_NA = 0.017718484492610001
i.ena = 87.39
i.insert('Kv3_4')
i.gkbar_Kv3_4 = 0.0081756804703699993
i.ek = -88
i.insert('Leak')
i.gmax_Leak = 3.5301616000000001e-07
i.e_Leak = -60
i.insert('GRC_CA')
i.gcabar_GRC_CA = 0.00020856833529999999
i.insert('cdp5_CR_CAM')
i.push()
i.eca = 137.5
h.pt3dadd(len_initial, len_initial , 0.0, i.diam)
h.pt3dadd(len_initial + len_ending_pf, len_initial , 0.0, i.diam)
h.pop_section()
len_initial = len_initial + len_ending_pf
self.HD_pf2 = [h.Section(cell=self, name='pf_'+str(x)) for x in range(secnumber_pf)]
for z in self.HD_pf2:
z.L = lensec
z.nseg = 1
z.diam = 0.15
z.Ra = 100
z.cm = 1
z.insert('GRC_NA')
z.gnabar_GRC_NA = 0.017718484492610001
z.ena = 87.39
z.insert('Kv3_4')
z.gkbar_Kv3_4 = 0.0081756804703699993
z.ek = -88
z.insert('Leak')
z.gmax_Leak = 1.4118927999999999e-07
z.e_Leak = -60
z.insert('GRC_CA')
z.gcabar_GRC_CA = 0.00020856833529999999
z.insert('cdp5_CR_CAM')
z.push()
z.eca = 137.5
h.pt3dadd(len_initial, len_initial , 0.0, i.diam)
h.pt3dadd(len_initial - len_ending_pf, len_initial , 0.0, i.diam)
h.pop_section()
len_initial = len_initial - len_ending_pf
#Connections
#AA
for j in range(secnumber_aa-1):
l = j+1
self.HD_aa[l].connect(self.HD_aa[j],1,0)
#PF
for i in range(secnumber_pf-1):
l = i+1
self.HD_pf1[l].connect(self.HD_pf1[i],1,0)
self.HD_pf2[l].connect(self.HD_pf2[i],1,0)
self.HD_pf1[0].connect(self.HD_aa[secnumber_aa-1],1,0)
self.HD_pf2[0].connect(self.HD_aa[secnumber_aa-1],1,0)
#Axon connection to the AIS
self.HD_aa[0].connect(self.ais,1,0)
#Time and Voltage vectors
self.time_vector = h.Vector()
self.time_vector.record(h._ref_t)
self.vm_soma = h.Vector()
self.vm_soma.record(self.soma[0](0.5)._ref_v)
#SYNAPSES
def createsyn(self, nsyn_MF_AMPA, nsyn_MF_NMDA, list_dend_AMPA, list_dend_NMDA):
self.MF_GrC = []
self.MF_GrC_mossy = []
#Mossy AMPA
for x in range(0,nsyn_MF_AMPA):
for z1 in list_dend_AMPA:
self.MF_GrC.append(Synapse_py3('mossy',self,self.dend[z1]))
#Mossy NMDA
for y in range(0,nsyn_MF_NMDA):
for z2 in list_dend_NMDA:
self.MF_GrC_mossy.append(Synapse_py3('mossynmda',self,self.dend[z2]))