- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-20 13:09:53+12:00
- Desc:
- Update comments
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/877/rawfile/3c9af7ee56cf16d37fad2f58c2d53640adf45870/parameter_finder/kinetic_parameters_AE1.py
# AE1 model based on Weinstein 2000
# 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
Kc = 50 # [=] mM
Kb = 198 # [=] mM
Pc = [562, 61]
Pb = [1247, 135]
# rxn order
# 1 X' + Cl > Cl.X'
# 2 Cl.X' > Cl.X''
# 3 Cl.X'' > X'' + Cl
# 4 B + X'' > B.X''
# 5 B.X'' > B.X'
# 6 B.X' > B + X'
# detailed bal is already satisfied in kinetic model
kf =[fkc, Pc[0], fkc*Kc, fkc, Pb[1], fkc*Kb]
kr =[fkc*Kc, Pc[1], fkc, fkc*Kb, Pb[0], fkc]
# 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']]*int(num_rows/2)
return (k_kinetic, N_cT, K_C, W)
