cac_init = 1.e-4
ip3_init = 0.1
gip3r = 12040
gserca = 0.3913
gleak = 6.020
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000
h.CVode().active(1)
h.cvode.atol(1e-10)
# define the regions for the rxd
cyt = rxd.Region(h.allsec(),
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1))
er = rxd.Region(h.allsec(), geometry=rxd.FractionalVolume(fe))
cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.FixedPerimeter(1))
# the species and other states
ca = rxd.Species([cyt, er], d=caDiff, name='ca', charge=2, initial=cac_init)
ip3 = rxd.Species(cyt, d=ip3Diff, initial=ip3_init)
ip3r_gate_state = rxd.State(cyt_er_membrane, initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
# pumps and channels between ER and Cytosol
serca = rxd.MultiCompartmentReaction(ca[cyt] > ca[er],
gserca / ((kserca /
(1000. * ca[cyt]))**2 + 1),
membrane=cyt_er_membrane,
gleak = 6.020
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000.0
#These parameters where missing in the tutorial so arbitrary values were chosen
#any resemblance to experimental values is purely coincidental.
fc = 0.7
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(h.allsec(),
name='cyt',
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1))
er = rxd.Region(h.allsec(), name='er', geometry=rxd.FractionalVolume(fe / 2.))
cyt_er_membrane = rxd.Region(h.allsec(),
name='mem',
geometry=rxd.ScalableBorder(
1, on_cell_surface=False))
ca = rxd.Species([cyt, er], d=caDiff, name="ca", charge=2, initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
minf = ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] +
kact)
lX, lY, lZ, lctyID = [0], [0], [0], [
E2
] # E2 pyramidal cell - nothing particular about the E2
timevec, idvec = h.Vector(), h.Vector()
ncrec = h.NetCon(ce[-1].soma(0.5)._ref_v, None, sec=ce[-1].soma)
ncrec.record(timevec, idvec, 0)
ncrec.threshold = 0 # 10 mV is default, lower it
ltimevec.append(timevec)
lidvec.append(idvec)
lncrec.append(ncrec) # record the spikes at soma
rxd.options.use_reaction_contribution_to_jacobian = False # faster (checked a few days before 10/16/13)
fc, fe = 0.83, 0.17 # cytoplasmic, er volume fractions
cyt = rxd.Region(rxdsec,
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1))
er = rxd.Region(rxdsec, geometry=rxd.FractionalVolume(fe))
cyt_er_membrane = rxd.Region(rxdsec, geometry=rxd.ScalableBorder(1))
caDiff = 0.233
ca = rxd.Species([cyt, er],
d=caDiff,
name='ca',
charge=2,
initial=dconf['cacytinit'])
caexinit = dconf['caexinit']
caextrude = rxd.Rate(ca, (caexinit - ca[cyt]) / taurcada,
regions=cyt,
membrane_flux=False)
ip3 = rxd.Species(cyt, d=0.283, name='ip3', initial=0.0)
# action of IP3 receptor
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000.0
# These parameters where missing in the tutorial so arbitrary values were chosen
# any resemblance to experimental values is purely coincidental.
fc = 0.7
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(fc, surface_fraction=1),
)
er = rxd.Region(h.allsec(), name="er", geometry=rxd.FractionalVolume(fe / 2.0))
cyt_er_membrane = rxd.Region(h.allsec(),
name="mem",
geometry=rxd.DistributedBoundary(1))
ca = rxd.Species([cyt, er], d=caDiff, name="ca", charge=2, initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
minf = ip3[cyt] * 1000.0 * ca[cyt] / (ip3[cyt] + kip3) / (1000.0 * ca[cyt] +
kact)
