- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-03-14 14:59:25+13:00
- Desc:
- Adding z to Vnorm in param_finding calculations, and updating parameters
- Permanent Source URI:
- https://models.cellml.org/workspace/831/rawfile/1be12bb694fe0367462fc4827b5411dc9f7e96f7/parameter_finder/kinetic_parameters_TCC.py
# fast Na module
# 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 = 8.941484386828576E-7 # Unit mA/mM
P_TCC = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
x_TCC = 50000/N_A*1e15 # unit fmol
# load gate transition parameters
params_b = [132.51796137864406, 0.3429854720383411, 48.8728740902765, -0.2775102001007474]
params_g = [1.7731164468320164, -0.4500912005641351, 47.97994076098573, 0.375200850350315]
z_bf = params_b[1]
z_br = params_b[3]
z_gf = params_g[1]
z_gr = params_g[3]
zf = [z_bf, z_gf]
zr = [z_br, z_gr]
# unit s ^ -1
alpha_b = params_b[0] # unit s ^ -1
beta_b = params_b[2] # unit s ^ -1
alpha_g = params_g[0] # unit s ^ -1
beta_g = params_g[2] # unit s ^ -1
kf_Ca = [P_TCC / x_TCC, # R_GHK
2 * alpha_b, # Rb_00
2 * alpha_b, # Rb_01
alpha_b, # Rb_10
alpha_b, # Rb_11
alpha_g, # Rg_00
alpha_g, # Rg_10
alpha_g] # Rg_20
kr_Ca = [P_TCC / x_TCC, # R_GHK
beta_b, # Rb_00
beta_b, # Rb_01
2 * beta_b, # Rb_10
2 * beta_b, # Rb_11
beta_g, # Rg_00
beta_g, # Rg_10
beta_g] # Rg_20
k_kinetic = kf_Ca + kr_Ca
# 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)
