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AIY_simulation_vclamp.py
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AIY_simulation_vclamp.py
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# "Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families"
# M. Nicoletti et al. PloS ONE, 19(3): e0298105.
# https://doi.org/10.1371/journal.pone.0298105
def AIY_simulation_vc(gAIY_scaled,vstart,vstop,ns):
# voltage clamp per Minimizzazioni con canali calcio fissati e ottimizzazione sul potassio
#i valori delle conduttanze del calcio vengono dal set xpp DEFINITIVO.ode
#fissati anche i valori di irk, kcnl per fittare le code e di slo1 slo2
#libere anche le conduttanze di perdita
from neuron import h,gui
import numpy
import math
from matplotlib import pyplot
from operator import add
from neuron import h,gui
import numpy
import math
from matplotlib import pyplot
from operator import add
surf=65.89e-8 # surface in cm^2 form neuromorpho AIYL
vol=7.42e-12 # total volume
L=math.sqrt(surf/math.pi)
rsoma=L*1e4
cm_uFcm2=gAIY_scaled[8]
soma=h.Section(name="soma")
soma.L=rsoma
soma.diam=rsoma
soma.cm=cm_uFcm2
soma.Ra=100
h.psection(sec=soma)
soma.insert('egl19')
soma.insert('slo1egl19')
soma.insert('nca')
soma.insert('leak')
soma.insert('slo1iso')
soma.insert('kqt1')
soma.insert('shl1')
for seg in soma:
seg.leak.gbar = gAIY_scaled[0]
seg.slo1iso.gbar = gAIY_scaled[1]
seg.kqt1.gbar=gAIY_scaled[2]
seg.egl19.gbar=gAIY_scaled[3]
seg.slo1egl19.gbar = gAIY_scaled[4]
seg.nca.gbar = gAIY_scaled[5]
seg.shl1.gbar = gAIY_scaled[6]
seg.leak.e=gAIY_scaled[7]
seg.eca=60
seg.ek=-80
stim=h.VClamp(soma(0.5))
dir(stim)
simdur = 1700
stim.amp[0]=-60
stim.amp[2]=-60
stim.dur[0]=1100
stim.dur[1]=500
stim.dur[2]=100
ik_vec = h.Vector()
ica_vec=h.Vector()
inca_vec=h.Vector()
ileakAIY_vec=h.Vector()
t_vec = h.Vector()
ik_vec.record(soma(0.5)._ref_ik)
ica_vec.record(soma(0.5)._ref_ica)
inca_vec.record(soma(0.5)._ref_i_nca)
ileakAIY_vec.record(soma(0.5)._ref_i_leak)
t_vec.record(h._ref_t)
ref_ik=[]
ref_ica=[]
ref_t=[]
ref_inca=[]
ref_ileakAIY=[]
#ref_curr_shl1=[]
for i in numpy.linspace(start=vstart, stop=vstop, num=ns):
stim.amp[1]=i
h.tstop=simdur
h.dt=0.01
h.finitialize(-60)
h.run()
#time
ref_t_vec=numpy.zeros_like(t_vec)
t_vec.to_python(ref_t_vec)
ref_t.append(ref_t_vec)
# potassium current
ref_ik_vec=numpy.zeros_like(ik_vec)
ik_vec.to_python(ref_ik_vec)
ref_ik.append(ref_ik_vec)
#calcium currents
ref_ica_vec=numpy.zeros_like(ica_vec)
ica_vec.to_python(ref_ica_vec)
ref_ica.append(ref_ica_vec)
# NCA currents
ref_inca_vec=numpy.zeros_like(inca_vec)
inca_vec.to_python(ref_inca_vec)
ref_inca.append(ref_inca_vec)
# LEAKAGE current
ref_ileakAIY_vec=numpy.zeros_like(ileakAIY_vec)
ileakAIY_vec.to_python(ref_ileakAIY_vec)
ref_ileakAIY.append(ref_ileakAIY_vec)
# total current calculation
itot=[]
itot=map(sum, zip(ref_ik,ref_ica,ref_ileakAIY,ref_inca))
current=numpy.array(list(itot))
inorm=current*1e9*surf #total current in pA
#time array
time1=numpy.array(ref_t)
resc_ind=numpy.where(time1[1,:]>=1000)
resc_min=numpy.amin(resc_ind)
resc_max=numpy.amax(resc_ind)
itot_normalized=inorm[:,resc_min:resc_max]
time=time1[:,resc_min:resc_max]-1000
## CALCULATION OF STEADY-STATE CURRENT-VOLATGE RELATION
ind=numpy.where(numpy.logical_and(time[0]>=550, time[0]<=599))
ind_max=numpy.amax(ind)
ind_min=numpy.amin(ind)
iv=numpy.mean(itot_normalized[:,ind_min:ind_max],axis=1)
# CALCULATION OF PEAK CURRENT-VOLTAGE RELATION
ind2=numpy.where(numpy.logical_and(time[0]>=100, time[0]<=200))
ind2_max=numpy.amax(ind2)
ind2_min=numpy.amin(ind2)
iv_peak=numpy.amax(itot_normalized[:,ind2_min:ind2_max])
iv_peak=[]
for j in range(ns):
if j<=6:
peak=numpy.amin(itot_normalized[j,ind2_min:ind2_max])
else:
peak=numpy.amax(itot_normalized[j,ind2_min:ind2_max])
iv_peak.append(peak)
return itot_normalized, time, iv_peak, iv