- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-20 10:22:46+12:00
- Desc:
- Adding exposure files
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/818/rawfile/a67177c16af102ea8ec4d69929c771407a9803c7/parameter_finder/kinetic_parameters_HaiMurphy.py
# Hai murphy module
# adapted to smooth muscle contraction module from Yang et al 2005, which have different rate constants to original Hai Murphy.
# Also dependence on Ca_i and cGMP
# return (k_kinetic, N_cT, K_C, W) 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.
num_cols = dims['num_cols']
num_rows = dims['num_rows']
bigNum = 1e6
fastKineticConstant = bigNum
smallReverse = fastKineticConstant/(pow(bigNum,2))
k1 = 1180 # [=] 1/s ( 1 on Yang paper)
k2 = 0.07128868*0.0327 + 0.0086 # [=] 1/s (not accounting for Pi)
k3 = 1.8 # [=] 1/s
k4 = 0.1 # [=] 1/s
k5 = k2 # [=] 1/s
k6 = k1 # [=] 1/s
k7 = 0.045 # [=] 1/s
# use detailed balance to find k8
if True:
k8 = k1*k3*k5*k7/(k2*k4*k6)
else:
k8 = smallReverse # [=] 1/s
k_kinetic = [
k1,k3,k5,k7,
k2,k4,k6,k8
]
# CONSTRAINTS
N_cT = [] # np.zeros(len(M[0]))
K_C = []
# volume vector
W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
return (k_kinetic, [N_cT], K_C, W)
