Location: BG_K1_uterine @ 8149f79fbadb / parameter_finder / kinetic_parameters_K1_uterine.py

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2025-08-14 12:38:38+12:00
Desc:
Has gating. adding sedml
Permanent Source URI:
https://staging.physiomeproject.org/workspace/d57/rawfile/8149f79fbadba355a1ec74bb683355a04bba2ddc/parameter_finder/kinetic_parameters_K1_uterine.py
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# K1 module from Tong 2011

# 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']

    # from MATLAB PSO for the channel
    G_GHK = 3.25970736700753e-11

    # convert    to    permeability
    P = G_GHK / F * 1e12 #Unit    pL / s
    channel_K1 = P

    kf =[channel_K1]
    kr =[channel_K1]
    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)