- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-08-19 14:20:55+12:00
- Desc:
- Changing rdf link
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/b8b/rawfile/3750deed6e3853e3a563bf0b3833bbe59a16de5e/parameter_finder/kinetic_parameters_funny.py
# funny module, translated from Kernik19
# 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']
T = V['T']
N_A = V['N_A']
G_GHK_Na = 8.167940775713335e-10 # Unit mA/mM
G_GHK_K = 2.366168724266607e-09 # Unit mA/mM
P_f_Na = G_GHK_Na/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
P_f_K = G_GHK_K/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
x_fK_channel = 5000e3*6673/N_A*1e15 # unit fmol
x_fNa_channel = x_fK_channel/100 # for Na component
# load gate transition parameters
params_gate = [5.78970090430308e-07, -1.83090386964676, 0.0116300002850840, 0.787348904990578]
alpha = params_gate[0]*1e3 # unit s ^ -1
beta = params_gate[2]*1e3 # unit s ^ -1
kf = [P_f_Na / x_fNa_channel, # R_GHK
P_f_K / x_fK_channel, # R_GHK
alpha]
kr = [P_f_Na / x_fNa_channel, # R_GHK
P_f_K / x_fK_channel, # R_GHK
beta]
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'], V['V_myo'], V['V_o']] + [1] * (num_rows-4)
return (k_kinetic, N_cT, K_C, W)
