- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-07-06 16:25:32+12:00
- Desc:
- Updating to LRd 34.4 pL cell parameters
- Permanent Source URI:
- https://models.fieldml.org/workspace/82c/rawfile/f45e6de671edd766ff0cf3a153306d9ca117a209/parameter_finder/kinetic_parameters_Kr_clancy01.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 = 3.233669778973711e-09 # Unit mA/mM
P_Kr = G_GHK/F * 1e12 # Unit pL/s . G_GHK [=] Amp/(mol/s)
x_Kr_channel = 2*503e7/N_A*1e15 # fmol. From inferring whole cell conductance (Clancy) against single cell (10 Ps, Chinn)
x_Kr_channel = 5030/N_A*1e15
# load gate transition parameters
alpha = [28.523400884804747,
2.1719999886814705,
8.891319064613533,
655.999997020704,
8.891314046537206
]
beta = [2.3570011784259544,
1.0769999996074826,
2.9357019143027285,
243.8368647542509,
72.44770977217509
]
# Calculate bond graph constants from kinetic parameters
# Note: units of kappa are fmol/s, units of K are fmol^-1
kf_Kr = [P_Kr / x_Kr_channel] + alpha
kr_Kr = [P_Kr / x_Kr_channel] + beta
k_kinetic = kf_Kr + kr_Kr
# 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)
