Location: BG_NMDA @ daf905e976c1 / parameter_finder / kinetic_parameters_NMDA.py

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2025-09-05 14:27:21+12:00
Desc:
Adding Cellml with params
Permanent Source URI:
https://staging.physiomeproject.org/workspace/d56/rawfile/daf905e976c1e5bb1b29f8c1035040da8f7fe659/parameter_finder/kinetic_parameters_NMDA.py
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# NMDA 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'] # numRxn
    num_rows = dims['num_rows'] # numSpecies

    # constants are stored in V

    fkc = 1e6 # fastkineticconstant, 1/s
    skc = 1e-6 # smallkineticconstant

    # Re_bind
    # Re_depol

    # kf = [fkc]*num_cols
    # kr = [skc]*num_cols

    # guess!
    kf = [fkc, 10]
    kr = [skc]*num_cols
    k_kinetic = kf + kr #[kf,    kr]

    # CONSTRAINTS
    N_cT = []
    K_C = []

    # volume vector
    # W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
    W = list([1,1, V['V_o']]) + list([V['V_myo']]*4) + list([V['V_o']]*3)


    return (k_kinetic, N_cT, K_C, W)