- 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.py
# Kr module, translated from Kernik19
# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
# Based on 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']
cKo = V['cKo']
G_GHK = 2.134709059004477e-08 # G_GHK [=] mA/mM
P_Kr = G_GHK/F * 1e12 # Unit pL/s .
x_Kr_channel = 143*414/N_A*1e15
x_Kr_channel = 3000/N_A*1e15
x_Kr_channel = V['numChannels']/N_A*1e15 # unit fmol
# load gate transition parameters
params_xr1 = [0.003702708442915483, 1.6149028778859738, 4.5365827167917646E-4, -1.3218634652232777]
params_xr2 = [0.01245000000189733, -1.0273976425216251, 0.4649999999963666, -0.18153135376657775]
alpha_xr1 = params_xr1[0]*1e3 # unit s ^ -1
beta_xr1 = params_xr1[2]*1e3 # unit s ^ -1
alpha_xr2 = params_xr2[0]*1e3 # unit s ^ -1
beta_xr2 = params_xr2[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
kf_Kr = [P_Kr / x_Kr_channel/np.sqrt(cKo), # R_GHK
alpha_xr1, # Rx1_0
alpha_xr1, # Rx1_1
alpha_xr2, # Rx2_0
alpha_xr2] # Rx2_1
kr_Kr = [P_Kr / x_Kr_channel/np.sqrt(cKo), # R_GHK
beta_xr1, # Rx1_0
beta_xr1, # Rx1_1
beta_xr2, # Rx2_0
beta_xr2] # Rx2_1
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)
