Location: BG_An01 @ 9e54fd92d505 / parameter_finder / kinetic_parameters_An01.py

Author:

Shelley Fong <sfon036@UoA.auckland.ac.nz>

Date:

2025-07-21 14:26:07+12:00

Desc:

Updating conc ICs

Permanent Source URI:

https://staging.physiomeproject.org/workspace/d51/rawfile/9e54fd92d5052fccd5aadcc23ee8822c3d1167bb/parameter_finder/kinetic_parameters_An01.py

# An01 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']

    # from MATLAB PSO for the channel
    G_GHK = 3.539462052865353e-12

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

    kf =[channel_Cl]
    kr =[channel_Cl]
    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)