- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-06-30 14:25:17+12:00
- Desc:
- Renaming Siekmann files to nondefault; using DeYoung instead
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/8ab/rawfile/e96fcf69494a24946ba1e4aad50ee4991d8e92e9/parameter_finder/kinetic_parameters_IPR.py
# PLC module, translated from Bhalla and Iyengar 1999
# 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']
fkc = 1e6
smr = 1e-3
# transitions in the park/drive model
# q_12 and q_21 are rates in opposite direction of each other
# ORDER [q_IPR q_12 q_23 q_24 q_26 q_45] # kf
# [q_IPR q_21 q_32 q_42 q_62 q_54] # kr
# with average values for q_24 and q_42
kf = [1240, 3, 150, 10500, 11] # [=] 1/s
kr = [88, 69, 1e-4, 4010, 3330] # [=] 1/s
k_IPR_main = [0.05, 0.05] # [=] 1/s I think
k_kinetic = [k_IPR_main[0]] + kf + [k_IPR_main[1]] + 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']]*3 + [1]*(num_rows-3)
return (k_kinetic, N_cT, K_C, W)