- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-11-17 10:26:39+13:00
- Desc:
- Using sympy for rational nullspace
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6cc/rawfile/959a1eab6b859e88de73c065526e3aff5828cd39/parameter_finder/kinetic_parameters_PKA.py
# PKA module
# 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.
# all reactions are reversible. no closed loops.
# cAMP binds to R subunit one at a time
num_cols = dims['num_cols']
num_rows = dims['num_rows']
bigNum = 1e3
fastKineticConstant = bigNum
smallReverse = fastKineticConstant/(pow(bigNum,2))
# [Ka, Kb, Kd, Kpki]
Km = [9.14, 1.64, 4.375, 2e-4]
N = len(Km)
kim = []
kip = []
for i in range(4):
kim.append(fastKineticConstant) # 1/s
kip.append(kim[i] / Km[i])
# repeat exct reactions for type I and type II holoenzymes
# No closed loop, so no detailed balance
k_kinetic = kip + kip + kim + kim
# CONSTRAINTS
N_cT = []
# # Reaction i: [PKA:PKI] = [C][PKI] at SS big error. Not isolated reaction
# repeat for type 1 and 2
if False:
N_cT[0][num_cols + 1] = 1
N_cT[0][num_cols + 5] = 1
N_cT[0][num_cols + 7] = -1
# Gibbs free energy of L + R binding **MED_ERROR**
if False:
N_cT[2][num_cols + 3] = 1 # ARC
N_cT[2][num_cols] = -1 # cAMP
N_cT[2][num_cols + 2] = -1 # RC
G_0_bind = -45.1872 # kJ/mol
R = 8.314
T = 310
K_bind = np.exp(G_0_bind/(R*T))*10^6
K_C = []
# volume vector
W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
return (k_kinetic, [N_cT], K_C, W)
