Location: BG_Na_background @ 7bd2583315a0 / parameter_finder / kinetic_parameters_NaB.py

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-29 08:31:39+13:00
Desc:
Fixing units in cellml, and therefore channel density
Permanent Source URI:
https://models.cellml.org/workspace/82b/rawfile/7bd2583315a0a0f34cae507f0e4dbf4b3799dbe5/parameter_finder/kinetic_parameters_NaB.py
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# fast Na module

# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)

# Translated from Pan 2018 cardiac AP 

import numpy as np

def kinetic_parameters(M, include_type2_reactions, dims, V):
    # Set the kinetic rate constants

    num_cols = dims['num_cols']
    num_rows = dims['num_rows']

    # constants are stored in V
    F = V['F']
    N_A = V['N_A']

    x_Nab_channel = 10000*725 / N_A * 1e15 #unit    fmol
    x_Nab_channel = 2e0*10000*725 / N_A * 1e15 #unit    fmol

    G_GHK = 2.352272352716130e-10

    # convert    to    permeability
    P_Cab = G_GHK / F * 1e12 #Unit    pL / s
    channel_k = P_Cab / x_Nab_channel

    kf =[channel_k]
    kr =[channel_k]
    k_kinetic = kf + kr

    # CONSTRAINTS
    N_cT = []
    K_C = []

    # volume vector
    # W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
    W = [1] * num_cols + [V['V_myo'], V['V_o']]

    return (k_kinetic, N_cT, K_C, W)