Location: BG_CO2_hydration @ c7db73a7fd05 / parameter_finder / kinetic_parameters_CO2_hyd.py

Author:

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

Date:

2022-05-24 13:05:09+12:00

Desc:

Init

Permanent Source URI:

http://models.cellml.org/workspace/886/rawfile/c7db73a7fd0546bc1cbff02d2e7ad5d3ca4e85fa/parameter_finder/kinetic_parameters_CO2_hyd.py

# Hydration of CO_2 by carbonic anhydrase to form bicarbonate and proton, taken from Crampin and Smith 2006

# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)

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']

    fkc = 1e6
    # dissociation constants for A+B>C where Kd = k-/k+
    # K_H is given as pK_H. K_H = 10^(-pK_H)
    kr = [0.365 ] # [=] 1/s
    kf = [0.48e6] # [=] 1/s

    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']]*num_rows

    return (k_kinetic, N_cT, K_C, W)