Location: BG_CHE @ 643da5843ae8 / parameter_finder / kinetic_parameters_CHE.py

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-07-13 15:33:31+12:00
Desc:
Moving channel initial moles to main environment from channel component
Permanent Source URI:
https://models.physiomeproject.org/workspace/881/rawfile/643da5843ae88d97209514900c59e512a040a7b6/parameter_finder/kinetic_parameters_CHE.py

# Chloride-hydroxide exchanger, based on 6 state transporter by 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)
    pK_OH = 14 - 7.95
    K_OH = pow(10, -pK_OH)
    K_Cl = 18e3 # [=] mM
    kp = [4.29, 68.1] # [=] 1/s
    km = [250, 1.17] # [=] 1/s

    kf =[kp[0], fkc*K_OH, fkc, kp[1], fkc*K_Cl, fkc]
    kr =[km[0], fkc, fkc*K_Cl, km[1], fkc, fkc*K_OH]

    # detailed bal? They said they did it already
    kr[5] = np.product(kf)/(np.product(kr[0:4]))

    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']]*2 + [1]*len(kf)

    return (k_kinetic, N_cT, K_C, W)