- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-26 11:12:23+12:00
- Desc:
- Adding readme on stoich of H, and updating n values
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/880/rawfile/5f3e6c35b4cf5efea1c9ff43106535fba63c11ce/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
kf =[kp[0], fkc*K_H, fkc, kp[1], fkc*K_Na, fkc]
kr =[km[0], fkc, fkc*K_Na, km[1], fkc, fkc*K_H]
# detailed bal? They said they did it already
kr[5] = np.product(kf)/(np.product(kr[0:4]))
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 + [V['V_myo']]*len(kf)
return (k_kinetic, N_cT, K_C, W)
