Location: BG_K_ATP @ 2486d4f8ecc2 / parameter_finder / kinetic_parameters_K_ATP.py

Author:

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

Date:

2024-11-06 13:48:55+13:00

Desc:

Adding sedml and exposure files

Permanent Source URI:

https://models.physiomeproject.org/workspace/83a/rawfile/2486d4f8ecc2e433682a321dbd9ead857b9c26d5/parameter_finder/kinetic_parameters_K_ATP.py

# 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']
    cKo = V['cKo']
    G_GHK = 2.406602454217436e-15    # Unit mA/mM
    P_KATP = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
    x_KATP_channel = 3700e5 / N_A * 1e15 # unit    fmol
    x_KATP_channel = V['numChannels']/N_A*1e15 # unit fmol

    # Calculate bond graph constants from kinetic parameters
    # Note: units of kappa are fmol/s, units of K are fmol^-1
    kf_KATP = [P_KATP/x_KATP_channel]
    kr_KATP = [P_KATP/x_KATP_channel]

    k_kinetic = kf_KATP + kr_KATP

    # 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)