- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-06 11:33:36+12:00
- Desc:
- trying to match channel density to Kernik19
- Permanent Source URI:
- https://models.cellml.org/workspace/82e/rawfile/c7069969c3a025bf83bc11624a29ca1c4e841896/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 = 3.736786048787426e-09 # Unit mA/mM
P_to = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
x_to_channel = 4406e7/N_A*1e15 # unit fmol. Fedida 91: 1175 Endocardium of rabbit myocyte
# load gate transition parameters
params_r = [0.0553600000096661, 2.28623234372134, 0.220839999993386, -0.131848324558065]
params_s = [0.000344200000005845, -1.51477720975217, 0.0642889999980204, 1.75042355789096]
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] # unit s ^ -1
beta_r_bg = params_r[2] # unit s ^ -1
alpha_s_bg = params_s[0] # unit s ^ -1
beta_s_bg = params_s[2] # 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)
