gl = 0.0003 * scale ukcc2 = 0.3 * mM / sec unkcc1 = 0.1 * mM / sec p_max = 0.8 * mM / sec alpha = 5.3 epsilon = 0.17 * sec * (10**-1) g_gliamax = 5.0 * mM / sec e_kmax = 0.25 * sec * (10**-1) oa_bath = 32.0 / alpha o_bath = 32.0 * mM beta_o = 5 avo = rxd.constants.NA() q10 = 3.0**((h.celsius - 6.3) / 10.0) # sodium activation 'm' alpha_m = (0.32 * (v + 54.0)) / (1.0 - exp(-(v + 54.0) / 4.0)) beta_m = (0.28 * (v + 27.0)) / (exp((v + 27.0) / 5.0) - 1.0) mtau = 1.0 / (q10 * (alpha_m + beta_m)) minf = alpha_m / (alpha_m + beta_m) # sodium inactivation 'h' alpha_h = 0.128 * exp(-(v + 50.0) / 18.0) beta_h = 4.0 / (1.0 + exp(-(v + 27.0) / 5.0)) htau = 1.0 / (q10 * (alpha_h + beta_h)) hinf = alpha_h / (alpha_h + beta_h) # potassium activation 'n' alpha_n = (0.032 * (v + 52.0)) / (1.0 - exp(-(v + 52.0) / 5.0)) beta_n = 0.5 * exp(-(v + 57.0) / 40.0) ntau = 1.0 / (q10 * (alpha_n + beta_n)) ninf = alpha_n / (alpha_n + beta_n)
from matplotlib import pyplot
h.load_file('stdrun.hoc')
# parameters
h.celsius = 6.3
e = 1.60217662e-19
scale = 1e-14 / e
gnabar = 0.12 * scale # molecules/um2 ms mV
gkbar = 0.036 * scale
gl = 0.0003 * scale
el = -54.3
q10 = 3.0**((h.celsius - 6.3) / 10.0)
# sodium activation 'm'
alpha = 0.1 * vtrap(-(v + 40.0), 10)
beta = 4.0 * exp(-(v + 65) / 18.0)
mtau = 1.0 / (q10 * (alpha + beta))
minf = alpha / (alpha + beta)
# sodium inactivation 'h'
alpha = 0.07 * exp(-(v + 65.0) / 20.0)
beta = 1.0 / (exp(-(v + 35.0) / 10.0) + 1.0)
htau = 1.0 / (q10 * (alpha + beta))
hinf = alpha / (alpha + beta)
# potassium activation 'n'
alpha = 0.01 * vtrap(-(v + 55.0), 10.0)
beta = 0.125 * exp(-(v + 65.0) / 80.0)
ntau = 1.0 / (q10 * (alpha + beta))
ninf = alpha / (alpha + beta)
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else 3.5,
ecs_boundary_conditions=3.5)
na = rxd.Species(ecs,
name='na',
d=1.78,
charge=1,
initial=133.574,
ecs_boundary_conditions=133.574)
if args.buffer:
# Additional species are used for a phenomenological model of astrocytic
# buffering
kb = 0.0008
kth = 15.0
kf = kb / (1.0 + rxdmath.exp(-(k - kth) / 1.15))
Bmax = 10
A = rxd.Species(ecs,
name='buffer',
charge=1,
d=0,
initial=lambda nd: 0
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else Bmax)
AK = rxd.Species(ecs,
name='bound',
charge=1,
d=0,
initial=lambda nd: Bmax
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else 0)