Location: BG_Kr @ 73d6bc1016ed / parameter_finder / kinetic_parameters_Kr_channel.py

Author:

Shelley Fong <s.fong@auckland.ac.nz>

Date:

2022-03-03 09:58:16+13:00

Desc:

Changing Xi to X_i, and adding python param finder code

Permanent Source URI:

https://models.physiomeproject.org/workspace/82c/rawfile/73d6bc1016edb1be3ceadf6cccc4aa05ef251e58/parameter_finder/kinetic_parameters_Kr_channel.py

# 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']
    R = V['R']
    T = V['T']
    N_A = V['N_A']

    G_GHK = 1.7335734047388342E-8    # Unit mA/mM
    P_Kr = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
    x_Kr_channel = 5369/N_A*1e15 # unit    fmol

    # load gate transition parameters
    alpha = [28.523400884804747,
         2.1719999886814705,
         8.891319064613533,
         655.999997020704,
         8.891314046537206
         ]
    beta = [2.3570011784259544,
            1.0769999996074826,
            2.9357019143027285,
            243.8368647542509,
            72.44770977217509
            ]

    # Calculate bond graph constants from kinetic parameters
    # Note: units of kappa are fmol/s, units of K are fmol^-1

    kf_Kr = [P_Kr / x_Kr_channel] + alpha

    kr_Kr = [P_Kr / x_Kr_channel] + beta

    k_kinetic = kf_Kr + kr_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']] + [1] * (num_rows-2)

    return (k_kinetic, N_cT, K_C, W)