def add_P2Xreceptors(self, compartment, time, g):
'''
Adds P2X3 receptors
Parameters
----------
compartment: section of NEURON cell
part of neuron
x: int
x - coordinate of ATP application
time: int (ms)
time of ATP application
g: float
receptor conductance
'''
x = [8300, 13485, 13485]
y = [0, 1800, -1800]
z = [0, 0, 0]
if self.fast_diff:
for i in range(len(x)):
diff = h.AtP_42(compartment(0.5))
# if i > 0:
# y = y*(-1)
diff.h = self.distance(compartment, x[i], y[i], z[i])
print(compartment)
print(diff.h)
diff.tx1 = time + i * self.dt
diff.Deff = 0.8
diff.c0cleft = 1
diff.k = 0.001
rec = h.p2x3(compartment(0.5))
rec.gmax = g
rec.Ev = 5
rec2 = h.p2x2(compartment(0.5))
rec2.gmax = 0
rec2.Ev = -7
h.setpointer(diff._ref_atp, 'patp', rec)
self.recs.append(rec)
h.setpointer(diff._ref_atp, 'patp', rec2)
self.recs.append(rec2)
self.diffs.append(diff)
else:
diff = h.AtP_slow(compartment(0.5))
diff.h = self.distance(compartment, x[0], y[0], z[0])
diff.tx1 = time + 0 + (diff.h / 1250) * 1000
diff.c0cleft = 100
# self.diffusions.update({diff: compartment})
rec = h.p2x3(compartment(0.5))
rec.gmax = g
rec.Ev = 5
h.setpointer(diff._ref_atp, 'patp', rec)
self.recs.append(rec)
self.diffs.append(diff)
def add_P2Xreceptors(self, compartment, time, g):
'''
Adds P2X3 receptors
Parameters
----------
compartment: section of NEURON cell
part of neuron
x: int
x - coordinate of ATP application
time: int (ms)
time of ATP application
g: float
receptor conductance
'''
if self.fast_diff:
diff = h.AtP_42(compartment(0.5))
diff.h = self.distances.get(compartment)
diff.tx1 = time
diff.Deff = 0.8
if self.numofmodel == 4 or self.numofmodel == 5:
diff.c0cleft = 10
else:
diff.c0cleft = 1
if self.numofmodel == 1:
diff.k = 0
elif self.numofmodel == 3:
diff.k = 0.6
else:
diff.k = 0.01
else:
diff = h.AtP_slow(compartment(0.5))
diff.h = self.distances.get(compartment)
diff.tx1 = time + 0 + (diff.h / 1250) * 1000
diff.c0cleft = 100
self.diffusions.update({diff: compartment})
rec = h.p2x3(compartment(0.5))
rec.gmax = g
rec.Ev = 5
if self.numofmodel == 4 or self.numofmodel == 5:
rec2 = h.p2x2(compartment(0.5))
rec2.Ev = -7
rec2.gmax = 1
h.setpointer(diff._ref_atp, 'patp', rec2)
self.recs.append(rec2)
if self.numofmodel == 4:
rec.gmax = 0
if self.numofmodel == 5:
rec.gmax = 0.2
rec2.gmax = 0.2
h.setpointer(diff._ref_atp, 'patp', rec)
self.recs.append(rec)
self.diffs.append(diff)
def add_P2Xreceptors(self, compartment, time, g):
'''
Adds P2X3 receptors
Parameters
----------
compartment: section of NEURON cell
part of neuron
x: int
x - coordinate of ATP application
time: int (ms)
time of ATP application
g: float
receptor conductance
'''
if self.fast_diff:
for i in range(10):
diff = h.AtP_42(compartment(0.5))
diff.h = self.distances.get(compartment)
diff.tx1 = time + i * 70
diff.Deff = 0.8
diff.c0cleft = 25
diff.k = 0.0 #1
rec = h.p2x3(compartment(0.5))
rec.gmax = g
rec.Ev = 2
rec2 = h.p2x2(compartment(0.5))
rec2.gmax = 0
rec2.Ev = -7
h.setpointer(diff._ref_atp, 'patp', rec)
self.recs.append(rec)
h.setpointer(diff._ref_atp, 'patp', rec2)
self.recs.append(rec2)
self.diffs.append(diff)
else:
diff = h.AtP_slow(compartment(0.5))
diff.h = self.distances.get(compartment)
diff.tx1 = time + 0 + (diff.h / 1250) * 1000
diff.c0cleft = 100
# self.diffusions.update({diff: compartment})
rec = h.p2x3(compartment(0.5))
rec.gmax = g
rec.Ev = 5
h.setpointer(diff._ref_atp, 'patp', rec)
self.recs.append(rec)
self.diffs.append(diff)
def define_biophysics(self):
'''
Adds channels and their parameters
'''
for sec in self.all: # 'all' defined in build_subsets
sec.Ra = 35 # Axial resistance in Ohm * cm
sec.cm = 1 # Membrane capacitance in micro Farads / cm^2
sec.insert('navv1p8')
sec.insert('extrapump')
sec.insert('koi')
sec.insert('naoi')
sec.insert('nakpump')
sec.insert('nattxs')
sec.insert('kdr')
sec.insert('iKCa')
sec.insert('kad')
sec.insert('kap')
sec.insert('leak')
sec.insert('Nav1_3')
sec.insert('iCaL')
sec.insert('CaIntraCellDyn')
sec.insert('extracellular')
ap_diff = h.AtP_slow(sec(0.5))
ap_diff.h = self.distances.get(sec)
ap_diff.tx1 = 1000 + 0 + (ap_diff.h / 1250) * 1000
ap_diff.c0cleft = 100
self.diffs.append(ap_diff)
for seg in sec:
h.setpointer(ap_diff._ref_atp, 'im', seg.kdr)
h.setpointer(ap_diff._ref_atp, 'im', seg.kad)
h.setpointer(ap_diff._ref_atp, 'im', seg.kap)
if self.numofmodel == 8 or self.numofmodel >= 11:
sec.gbar_navv1p8 = 0.2
elif self.numofmodel == 7:
sec.gbar_navv1p8 = 0.1
else:
sec.gbar_navv1p8 = 0
sec.gbar_kdr = 0.01
sec.gbar_kad = 0.1
sec.gbar_kap = 0.1
sec.gbar_iKCa = 0.0015
sec.depth_CaIntraCellDyn = 0.1
sec.cai_tau_CaIntraCellDyn = 2.0
sec.cai_inf_CaIntraCellDyn = 50.0e-6
sec.pcabar_iCaL = 0.0001
if self.numofmodel == 6:
sec.gbar_nattxs = 0.2
else:
sec.gbar_nattxs = 0.1
sec.gbar_Nav1_3 = 0.2
sec.smalla_nakpump = -0.0047891
sec.theta_naoi = 0.029
sec.theta_koi = 0.029
sec.celsiusT_nattxs = 37
sec.celsiusT_navv1p8 = 37
sec.celsiusT_nakpump = 37
for sec in self.stimsec:
if self.numofmodel == 13 or self.numofmodel == 14:
self.add_5HTreceptors(sec, 10, 1)
else:
self.add_P2Xreceptors(sec, 100, 3)