disintegration. Journal of Theoretical Biology.
:doi:`10.1016/j.jtbi.2010.11.040` :pmid:`21130780`.
"""
from pysb import *
from earm import shared
from earm.shared import V
from scipy.constants import N_A
from earm import albeck_modules
from earm import shen_modules
import re
Model()
# Declare monomers
albeck_modules.ligand_to_c8_monomers()
shen_modules.momp_monomers()
albeck_modules.apaf1_to_parp_monomers()
# The specific MOMP model to use
shen_modules.howells(do_pore_assembly=True, do_pore_transport=True)
# Set initial condition for uncleaved Bid to 0.1uM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 0.1e-6 * N_A * V))
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# Declare common observables
shared.observables()
mtor_modules.mtor_monomers() mtor_modules.mtor_initial() mtor_modules.mtor_complex_formation() mtor_modules.mtorc1_signaling_monomers() mtor_modules.mtorc1_signaling_initial() mtor_modules.mtorc1_signaling() mtor_modules.mtorc2_signaling() mtor_modules.tsc2_monomers() mtor_modules.tsc2_initial() mtor_modules.tsc2_inhibition_by_akt() mtor_modules.tsc2_inhibition_by_erk() mtor_modules.tsc2_activation_by_erk() mtor_modules.tsc2_gap_function() # ## Apoptotic signaling albeck_modules.ligand_to_c8_monomers() apoptosis_modules.apoptosis_monomers() apoptosis_modules.apoptosis_initial() albeck_modules.apaf1_to_parp_monomers() lopez_modules.translocate_tBid_Bax_BclxL() lopez_modules.tBid_activates_Bax_and_Bak() lopez_modules.effector_auto_activation() lopez_modules.tBid_binds_all_anti_apoptotics() lopez_modules.effectors_bind_anti_apoptotics() lopez_modules.sensitizers_bind_anti_apoptotics() lopez_modules.lopez_pore_formation() apoptosis_modules.apoptosis_sensitizer_translocation() apoptosis_modules.apoptosis_bim_and_puma_bind_anti_apoptotics() apoptosis_modules.apoptosis_bim_activate_bax() albeck_modules.pore_to_parp()