- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-05-02 13:21:42+12:00
- Desc:
- Making exposure files
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/848/rawfile/5065a066ecead2260e7b91da029b4eac898d2f68/parameter_finder/kinetic_parameters_PLC.py
# PLC module, translated from Bhalla and Iyengar 1999
# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
# Based on 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']
num_rows = dims['num_rows']
fkc = 1e6
smr = 1e-3
# constants for reaction2 and reaction3 which are Michaelis-Menten
Km = [5, 19.84166667] # [=] mM
Vmax = [48, 10] # [=] 1/s
E0 = [0.25, 1] # [=] mM #from cellML kinetic file
kcat = [Vmax[i]/E0[i] for i in range(2)]
k0p = 0.15 # R0 [=] 1/s
k1p = 2.5 # R1 [=] 1/s
k2ap = fkc # R2a [=] 1/mM.s
k2bp = kcat[0] # R2b [=] 1/s
k3ap = fkc # R3a [=] 1/mM.s
k3bp = kcat[1] # R3b [=] 1/s
k4p = 0.000005 # R4 [=] 1/mM.s
k5p = 0.0000042 # R5 [=] 1/mM.s
k6p = 0.00005 # R6 [=] 1/mM.s
k7m = 0.000042 # R7 [=] 1/s # reaction is reversed in kinetic version, so swap km and kp
k8p = 0.0133 # R8 [=] 1/s
k0m = smr # R0 [=] 1/s
k1m = smr # R1 [=] 1/s
k2am = (k2ap*Km[0]) - kcat[0] # R2a [=] 1/s
k2bm = k2ap*kcat[0]/k2am # R2b [=] 1/mM2.s
k3am = (k3ap*Km[1]) - kcat[1] # R3a [=] 1/s
k3bm = k3ap*kcat[1]/k3am # R3b [=] 1/mM2.s
k4m = 1 # R4 [=] 1/s
k5m = 1 # R5 [=] 1/s
k6m = 1 # R6 [=] 1/s
k7p = 1 # R7 [=] 1/mM.s
k8m = smr # R8 [=] 1/s
# rate constants for reactions 0 - 8
# note: closed loop present, but parameters are adjusted from kinetic model to meet detailed balance
# closed loop for k7m and k8m. Different sign on k4 to make loop anticlockwise
# k7p = k4m*k5p*k6p*k7m/(k4p*k5m*k6m) # error is ~zero when this commented out
k8m = k4m*k5p*k6p*k8p/(k4p*k5m*k6m)
# Calculate bond graph constants from kinetic parameters
# Note: units of kappa are fmol/s, units of K are fmol^-1
kf = [k0p, # R0 [=] 1/s
k1p, # R1 [=] 1/s
k2ap, # R2a [=] 1/mM.s
k2bp, # R2b [=] 1/s
k3ap, # R3a [=] 1/mM.s
k3bp, # R3b [=] 1/s
k4p, # R4 [=] 1/mM.s
k5p, # R5 [=] 1/mM.s
k6p, # R6 [=] 1/mM.s
k7p, # R7 [=] 1/mM.s
k8p, # R8 [=] 1/s
]
kr = [
k0m,
k1m,
k2am,
k2bm,
k3am,
k3bm,
k4m, # R4 [=] 1/s
k5m, # R5 [=] 1/s
k6m, # R6 [=] 1/s
k7m, # R7 [=] 1/s
k8m # R8 [=] 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)
