cell2.nseg = 11
cell2.insert("pump")
# Where?
# the intracellular spaces
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(0.9, surface_fraction=1.0),
)
org = rxd.Region(h.allsec(), name="org", geometry=rxd.FractionalVolume(0.1))
cyt_org_membrane = rxd.Region(
h.allsec(), name="mem", geometry=rxd.ScalableBorder(pi / 2.0, on_cell_surface=False)
)
# the extracellular space
ecs = rxd.Extracellular(
-55, -55, -55, 55, 55, 55, dx=10, volume_fraction=0.2, tortuosity=1.6
)
# Who?
x = rxd.Species([cyt, org, cyt_org_membrane, ecs], name="x", d=1.0, charge=1, initial=0)
Xcyt = x[cyt]
Xorg = x[org]
# What? - produce X in cell 1
cell2.pt3dadd(20, 0, 0, 10)
cell2.nseg = 11
# Where?
# the intracellular spaces
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(0.9, surface_fraction=1.0),
)
org = rxd.Region(h.allsec(), name="org", geometry=rxd.FractionalVolume(0.1))
cyt_org_membrane = rxd.Region(h.allsec(),
name="mem",
geometry=rxd.ScalableBorder(
pi / 2.0, on_cell_surface=False))
cyt_ecs_membrane = rxd.Region(h.allsec(),
name="cell_mem",
geometry=rxd.membrane())
# the extracellular space
ecs = rxd.Extracellular(-55,
-55,
-55,
55,
55,
55,
dx=10,
volume_fraction=0.2,
tortuosity=1.6)
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] serca = rxd.MultiCompartmentReaction(ca[cyt],ca[er], gserca/((kserca / (1000. * ca[cyt])) ** 2 + 1), membrane=cyt_er_membrane, custom_dynamics=True) leak = rxd.MultiCompartmentReaction(ca[cyt],ca[er], gleak, gleak, membrane=cyt_er_membrane) minf = ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) k = gip3r * (minf * h_gate) ** 3 ip3r = rxd.MultiCompartmentReaction(ca[er],ca[cyt], k, k, membrane=cyt_er_membrane)
