1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
import pytest
from .testutils import compare_data, tol
@pytest.fixture
def model_pump(neuron_instance):
"""A simple rxd implementation of the sodium-potassium pump"""
h, rxd, data, save_path = neuron_instance
dend = h.Section(name="dend")
dend.diam = 2
dend.nseg = 101
dend.L = 100
cyt = rxd.Region(dend, name="cyt", nrn_region="i")
ecs = rxd.Region(dend, name="ecs", nrn_region="o")
mem = rxd.Region(dend, name="mem", geometry=rxd.membrane())
na = rxd.Species(
[cyt, ecs],
name="na",
charge=1,
initial=lambda nd: 18 if nd.region == cyt else 144,
)
k = rxd.Species(
[cyt, ecs],
name="k",
charge=1,
initial=lambda nd: 140 if nd.region == cyt else 3,
)
nai, nao, ki, ko = na[cyt], na[ecs], k[cyt], k[ecs]
exp = rxd.rxdmath.exp
pump = (0.8 / (1.0 + exp((25.0 - nai) / 3.0))) * (1.0 / (1.0 + exp(3.5 - ko)))
volume_scale = 1e-18 * rxd.constants.NA() * (dend.diam / 4.0)
pump_current = rxd.MultiCompartmentReaction(
2 * ko + 3 * nai,
2 * ki + 3 * nao,
pump * volume_scale,
mass_action=False,
membrane=mem,
membrane_flux=True,
)
model = (
dend,
cyt,
ecs,
mem,
na,
k,
nai,
nao,
ki,
ko,
pump,
volume_scale,
pump_current,
)
yield (neuron_instance, model)
def test_currents(model_pump):
"""Test currents generated by a Na/K-pump fixed step integration."""
neuron_instance, model = model_pump
h, rxd, data, save_path = neuron_instance
# check changing the units after initialization
h.nrnunit_use_legacy(False)
h.finitialize(-65)
h.nrnunit_use_legacy(True)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_currents_cvode(model_pump):
"""Test currents generated by a Na/K-pump variable step integration."""
neuron_instance, model = model_pump
h, rxd, data, save_path = neuron_instance
# check changing the units after initialization
h.CVode().active(True)
h.nrnunit_use_legacy(False)
h.finitialize(-65)
h.nrnunit_use_legacy(True)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
|
