- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-13 11:56:11+12:00
- Desc:
- Fixing equations
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/857/rawfile/764c22a661800aa2d3173388426c3b88d31ebc80/parameter_finder/kinetic_parameters_sGC.py
# cGS module, translated from Yang et al 2005
# 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):
num_cols = dims['num_cols']
num_rows = dims['num_rows']
fkc = 1e6
smr = 1e-3
E0 = 0.05 # [=] uM #GUESS for sum of sGC forms
# DIMENSIONALISE appropriate rates by multiplying by E0, the quantity used to nondimensionalise the model
k1p = 2e6*E0 # [=] 1/uM.s
k1m = 100 # [=] 1/s
k2p = 0.1 # [=] 1/s
k2m = smr # [=] 1/s
k3p = 0.003e6*E0 # [=] 1/uM.s
k3m = smr # [=] 1/s
k4p = 0.011 # [=] 1/s
k4m = smr # [=] 1/s
k_dno_p = 0.01 # [=] 1/s
k_dno_m = smr # [=] 1/s
# closed loop exists: recalculate parameter k4m (or k1m) using loop [1,2,4]. Then use update to recalculate k3m.
if False:
k4m = k1p*k2p*k4p/(k1m*k2m)
else:
k1m = k1p * k2p * k4p / (k4m * k2m)
k3m = k1p*k3p*k4p/(k1m*k4m)
# Calculate bond graph constants from kinetic parameters
# Note: units of kappa are fmol/s, units of K are fmol^-1
kf = [k1p,
k2p,
k3p,
k4p,
k_dno_p,
]
kr = [
k1m,
k2m,
k3m,
k4m,
k_dno_m,
]
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)
