- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2023-09-19 11:39:47+12:00
- Desc:
- adding cellml file
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/b2d/rawfile/97a6fdbed3c34c2d218a49e7455a8a8df068bb7a/parameter_finder/kinetic_parameters_RTK.py
# Receptor tyrosine kinase
# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
import numpy as np
def kinetic_parameters(M, include_type2_reactions, dims, V):
# Set the kinetic rate constants.
# original model had reactions that omitted enzymes as substrates e.g. BARK
# convert unit from 1/s to 1/uM.s by dividing by conc of enzyme
# all reactions were irreversible, made reversible by letting kr ~= 0
num_cols = dims['num_cols']
num_rows = dims['num_rows']
bigNum = 1e6
fastKineticConstant = bigNum
smallReverse = 1/bigNum
medReverse = np.sqrt(smallReverse)
# Reaction 1: Ligand binds receptor, which phosphorylates receptor (L + K1 <=> K1P )
k_1p = 100 # guess
k_1m = smallReverse
# Reaction 2: autophosphorylation of RTK (K1P + K2 <=> K2P )
k_2p = fastKineticConstant
k_2m = smallReverse
k_kinetic = [
k_1p, k_2p,
k_1m,k_2m
]
# CONSTRAINTS
N_cT = []
K_C = []
# volume vector
W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
return (k_kinetic, [N_cT], K_C, W)
