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AVAR_simulation_vclamp.py
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AVAR_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 AVA_simulation_vc(gAVA_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
surf=1121.79e-8 # surface in cm^2 form neuromorpho AVAL
vol=129.08e-12 # total volume
Fc=96485 #Faraday constant C/mol
Z=2 #Valence
alphan=surf/(Z*Fc*vol)
L=math.sqrt(surf/math.pi)
rsoma=L*1e4
cm_uFcm2=gAVA_scaled[6]
cm_pF=cm_uFcm2*1e6/surf
#fixed conductances
soma=h.Section(name="soma")
soma.L=rsoma
soma.diam=rsoma
soma.Ra=100
soma.cm=cm_uFcm2
h.psection(sec=soma)
soma.insert('irk')
soma.insert('leak')
soma.insert('egl19')
soma.insert('nca')
soma.insert('unc103')
for seg in soma:
seg.egl19.gbar=gAVA_scaled[0]
seg.leak.gbar=gAVA_scaled[1]
seg.irk.gbar=gAVA_scaled[2]
seg.nca.gbar=gAVA_scaled[3]
seg.unc103.gbar=gAVA_scaled[4]
seg.leak.e=gAVA_scaled[5]
seg.eca=60
seg.ek=-80
stim=h.VClamp(soma(0.5))
dir(stim)
simdur = 1500
stim.amp[0]=-30
stim.amp[2]=-30
stim.dur[0]=1007.8
stim.dur[1]=250
stim.dur[2]=242.2
ik_vec = h.Vector()
ica_vec=h.Vector()
inca_vec=h.Vector()
ileakAVA_vec=h.Vector()
t_vec = h.Vector()
inca_vec.record(soma(0.5)._ref_i_nca)
ik_vec.record(soma(0.5)._ref_ik)
ica_vec.record(soma(0.5)._ref_ica)
ileakAVA_vec.record(soma(0.5)._ref_i_leak)
t_vec.record(h._ref_t)
ref_ik=[]
ref_ica=[]
ref_inca=[]
ref_t=[]
ref_ileakAVA=[]
for i in numpy.linspace(start=vstart, stop=vstop, num=ns):
stim.amp[1]=i
h.tstop=simdur
h.dt=0.01
h.finitialize(-30)
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)
# NCA currents
ref_inca_vec=numpy.zeros_like(inca_vec)
inca_vec.to_python(ref_inca_vec)
ref_inca.append(ref_inca_vec)
#calcium currents
ref_ica_vec=numpy.zeros_like(ica_vec)
ica_vec.to_python(ref_ica_vec)
ref_ica.append(ref_ica_vec)
# LEAKAGE current
ref_ileakAVA_vec=numpy.zeros_like(ileakAVA_vec)
ileakAVA_vec.to_python(ref_ileakAVA_vec)
ref_ileakAVA.append(ref_ileakAVA_vec)
# total current calculation
itot=[]
itot=map(sum, zip(ref_ik,ref_ica,ref_inca,ref_ileakAVA))
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
## SS I-V CURVE
ind=numpy.where(numpy.logical_and(time[0]>=247, time[0]<=257))
ind_max=numpy.amax(ind)
ind_min=numpy.amin(ind)
iv=numpy.mean(itot_normalized[:,ind_min:ind_max],axis=1)
# PEAKS I-V CURVE
ind2=numpy.where(numpy.logical_and(time[0]>=7.8, time[0]<=17.8))
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