- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-25 14:19:21+12:00
- Desc:
- Fixing n_o in cellml
- Permanent Source URI:
- http://models.cellml.org/workspace/87f/rawfile/7d72968ae64a468d04e0487a5d88a8a8485c5e14/parameter_finder/kinetic_parameters_NBC.py
# Na-HCO3 cotransporter, 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_Na = 4.87e3 # [=] mM
K_HCO3 = 8.02e-3 # [=] mM
kp = [9.97, 8.53e-2] # [=] 1/s
km = [5.6e1, 4.87e6] # [=] 1/s
kf =[kp[0], fkc, fkc, kp[1], fkc*K_HCO3, fkc*K_Na]
kr =[km[0], fkc*K_Na, fkc*K_HCO3, km[1], fkc, fkc]
# 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 + [V['V_myo']]*len(kf) + [V['V_myo'], V['V_o']]
return (k_kinetic, N_cT, K_C, W)
