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)