- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-23 13:19:19+12:00
- Desc:
- Move channel state calculations to channel component
- Permanent Source URI:
- https://models.fieldml.org/workspace/881/rawfile/611538ed9fe9c2672c6d8f932d27b2f7612686e6/parameter_finder/kinetic_parameters_CHE.py
# Chloride-hydroxide 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_OH = 14 - 7.95
K_OH = pow(10, -pK_OH)
K_Cl = 18e3 # [=] mM
kp = [4.29, 68.1] # [=] 1/s
km = [250, 1.17] # [=] 1/s
kf =[kp[0], fkc*K_OH, fkc, kp[1], fkc*K_Cl, fkc]
kr =[km[0], fkc, fkc*K_Cl, km[1], fkc, fkc*K_OH]
# 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)
