- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-11-12 10:57:09+13:00
- Desc:
- Updating cellml and sedml
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/82e/rawfile/1fb000a5cf2d6895c9c41e37dbe0565db663ea67/parameter_finder/kinetic_parameters_TO.py
# transient outward, translated from Kernik19 model
# 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 = 1.154140674723088e-08 # Unit mA/mM
P_to = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
x_to_channel = 8800e3/N_A*1e15 # unit fmol
x_to_channel = V['numChannels']/N_A*1e15 # unit fmol
# load gate transition parameters
params_r = [0.029380177124271,2.608456313221509,0.196830579136332,-0.101962639822750]
params_s = [3.977695957311321e-04,-1.352897405948804,0.037512325129369,1.404170222801920]
z_rf = params_r[1]
z_rr = params_r[3]
z_sf = params_s[1]
z_sr = params_s[3]
zf = [z_rf, z_sf]
zr = [z_rr, z_sr]
# unit s ^ -1
alpha_r_bg = params_r[0]*1e3 # unit s ^ -1
beta_r_bg = params_r[2]*1e3 # unit s ^ -1
alpha_s_bg = params_s[0]*1e3 # unit s ^ -1
beta_s_bg = params_s[2]*1e3 # unit s ^ -1
kf_to = [P_to / x_to_channel, # R_GHK
alpha_r_bg, # Rr_00
alpha_r_bg, # Rr_01
alpha_s_bg, # Rs_00
alpha_s_bg] # Rs_10
kr_to = [P_to / x_to_channel, # R_GHK
beta_r_bg, # Rr_00
beta_r_bg, # Rr_01
beta_s_bg, # Rs_00
beta_s_bg] # Rs_10
k_kinetic = kf_to + kr_to
# 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']] + [1] * (num_rows-2)
return (k_kinetic, N_cT, K_C, W)
