- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-27 16:29:14+12:00
- Desc:
- Update with Kernik values
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/833/rawfile/0e16e4545154914cfdb5059c256786c192c68920/parameter_finder/kinetic_parameters_pCa.py
# pCa (PMCA) module
# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
# Translated from 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']
# constants are stored in V
F = V['F']
R = V['R']
Cm = V['Cm']
N_A = V['N_A']
cKo = V['cKo']
# initial concentration of enzyme pCa
x_pCa_channel = 3*725e1 / N_A * 1e15 # unit fmol
x_pCa_channel = V['numChannels']/N_A*1e15 # unit fmol
E0 = x_pCa_channel/V['V_myo']
fkc = 1e6
smr = 1e-3
Km = 0.5e-3 # [ =] mM
Vmax_og = 0.2625 # 0.2625 Kernick91 # 1.15 (Clancy01) # [ =] uA / uF
Vmax = Vmax_og * Cm / (F * V['V_myo']) # [=] mM/s
kcat = Vmax/E0 # E0 is the initial conc of enzyme pCa. [=] 1/s
kap = fkc
kam = kap*Km - kcat
kbp = kcat
kbm = kcat*smr # (kap*kbp)/kam
k_kinetic = [kap, kbp, kam, kbm]
# 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'],V['V_myo'],V['V_myo']]
return (k_kinetic, N_cT, K_C, W)
