- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-07-13 15:51:00+12:00
- Desc:
- Moving channel initial moles to main environment from channel component
- Permanent Source URI:
- https://models.fieldml.org/workspace/87f/rawfile/9663cef135e064889113d2338e877c6a0f4244e0/parameter_finder/kinetic_parameters_NBC.py
# Na-HCO3 cotransporter, 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 = 1e4
# dissociation constants for A+B>C where Kd = k-/k+
K_Na = 4.87e3 # [=] mM
K_HCO3 = 8.02e-3 # [=] mM
kp = [9.97, 8.53e-2] # [=] 1/s
km = [5.6e1, 4.87e6] # [=] 1/s
pKi = 6.738
pKo = 7.185
ni = 2.91
no = 2.18
Kd_pHi = pow(pow(10, -pKi), -ni)
Kd_pHo = pow(pow(10, -pKo), no)
kf_1 =[kp[0], fkc, fkc, kp[1], fkc*K_HCO3, fkc*K_Na]
kr_1 =[km[0], fkc*K_Na, fkc*K_HCO3, km[1], fkc, fkc]
# pH_dependent reactions
kf_pHi = fkc
kr_pHi = kf_pHi*Kd_pHi
kf_2 = [kf_pHi]*6
kr_2 = [kr_pHi]*6
kf_pHo = fkc
kr_pHo = kf_pHo*Kd_pHo
kf_3 = [kf_pHo]*6
kr_3 = [kr_pHo]*6
# detailed bal? They said they did it already
# kr[5] = np.product(kf)/(np.product(kr[0:4]))
# total kf and kr
kf = kf_1 #+ kf_2 + kf_3
kr = kr_1 #+ kr_2 + kr_3
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)
