- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-11 14:53:16+12:00
- Desc:
- Changing method of number of channels present. Guess density. Using SA of human iPSC for Kernik. Updating volumes
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/83b/rawfile/0084fa749de7bc58ba31705633cf1a77e7eb0603/parameter_finder/kinetic_parameters_ns.py
# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
# Adapted 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 must be positive
G_GHK_Ca = 1.321393816363888e-14 # Unit mA/mM
G_GHK_Na = 3.504413071719025e-16
G_GHK_K = 3.587541555438427e-16
P_Ca = G_GHK_Ca/F * 1e12 # Unit pL/s . G_GHK_Ca [=] Amp/(mol/s)
P_Na = G_GHK_Na / F * 1e12
P_K = G_GHK_K / F * 1e12
x_ns = 5e3*2508 / N_A * 1e15 # unit fmol
x_ns = V['numChannels']/N_A*1e15 # unit fmol
# Calculate bond graph constants from kinetic parameters
# Note: units of kappa are fmol/s, units of K are fmol^-1
kf_ns = [P_Ca/x_ns, P_Na/x_ns, P_K/x_ns]
kr_ns = [P_Ca/x_ns, P_Na/x_ns, P_K/x_ns]
k_kinetic = kf_ns + kr_ns
# CONSTRAINTS
N_cT = []
K_C = []
# volume vector
# W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
W = [1] * num_cols + 3*[V['V_myo'], V['V_o']]
return (k_kinetic, N_cT, K_C, W)
