- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-11-12 11:16:41+13:00
- Desc:
- Updating cellml and sedml
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/82d/rawfile/6ca9cbf971a30a2b5d74e93b0f3cdc816b065680/parameter_finder/kinetic_parameters_Ks.py
# Ks module, translated from Kernik 19
# 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 = 4.148559068672240e-10 # G_GHK [=] mA/mM
P_ks = G_GHK/F * 1e12 # Unit pL/s .
x_Ks_channel = 3000/N_A*1e15
x_Ks_channel = V['numChannels']/N_A*1e15 # unit fmol
# load gate transition parameters
params_xs = [0.00116560000000183, 0.000400323747581994, 0.000326899999998023, -1.41544821457997]
alpha_xs = params_xs[0]*1e3 # unit s ^ -1
beta_xs = params_xs[2]*1e3 # unit s ^ -1
# Calculate bond graph constants from kinetic parameters
# Note: units of kappa are fmol/s, units of K are fmol^-1
# gate particle is squared, so there are 4 reactions
kf_Ks = [P_ks / x_Ks_channel, # R_GHK
2*alpha_xs, # Rx0
alpha_xs] # Rx1
kr_Ks = [P_ks / x_Ks_channel, # R_GHK
beta_xs, # Rx0
2*beta_xs] # Rx1
k_kinetic = kf_Ks + kr_Ks
# 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)
