- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-07-13 15:53:23+12:00
- Desc:
- Moving channel initial moles to main environment from channel component
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/880/rawfile/0da16207fa7d5d11e7940e4625a1f6ac30c58671/parameter_finder/kinetic_parameters_NHE.py
# Na-hydrogen exchanger, 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_H is given as pK_H. K_H = 10^(-pK_H)
pK_H = 6.783
K_H = pow(10, -pK_H)
K_Na = 33.6 # [=] mM
kp = [1.21e1, 7.33e-1] # [=] 1/s
km = [3.29, 2.69] # [=] 1/s
pKi = 6.464
ni = 3.18
Kd_pHi = pow(pow(10, -pKi), -ni)
kf_1 =[kp[0], fkc*K_H, fkc, kp[1], fkc*K_Na, fkc]
kr_1 =[km[0], fkc, fkc*K_Na, km[1], fkc, fkc*K_H]
# pH_dependent reactions
kf_pHi = fkc
kr_pHi = kf_pHi*Kd_pHi
kf_2 = [kf_pHi]*6
kr_2 = [kr_pHi]*6
# detailed bal? They said they did it already
# kr_1[5] = np.product(kf_1)/(np.product(kr_1[0:4]))
# kr_2[5] = np.product(kf_2)/(np.product(kr_2[0:4]))
# total kf and kr
kf = kf_1 #+ kf_2
kr = kr_1 #+ kr_2
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 + [1]*6
return (k_kinetic, N_cT, K_C, W)
