def setUp(self):
reactor = aggsim.Reactor(volume_uL=1e-9 * 45, temperature_C=40)
self.reactor = reactor
n_monomers = aggsim.numberOfMolecules(1e-15 * 45, 1e-6 * 10)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
self.monomer = monomers
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble',
monomers,
1.0,
packing_fraction=sp.pi /
(3 * sp.sqrt(2)))
self.ens = ensemble
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction(
'monomer', 'ensemble', 1e-13 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(nuc_reaction)
# Nucleation
denuc_reaction = aggsim.EnsembleDenucleationReaction(
'monomer', 'ensemble', 1e-3 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(denuc_reaction)
# Assembly
asmb_reaction = aggsim.SphericalAssemblyReaction(
'monomer', 'ensemble', 1e-8 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(asmb_reaction)
# Disassembly
disasmb_reaction = aggsim.SphericalDisassemblyReaction(
'monomer', 'ensemble', 1e-6 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(disasmb_reaction)
def setUp(self):
reactor = aggsim.Reactor(volume_uL=1e-9*45, temperature_C=40)
self.reactor = reactor
n_monomers = aggsim.numberOfMolecules(1e-15 * 45, 1e-6 * 10)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
self.monomer = monomers
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble', monomers, 1.0, packing_fraction=sp.pi/(3*sp.sqrt(2)))
self.ens = ensemble
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction('monomer','ensemble', 1e-13 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(nuc_reaction)
# Nucleation
denuc_reaction = aggsim.EnsembleDenucleationReaction('monomer','ensemble', 1e-3 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(denuc_reaction)
# Assembly
asmb_reaction = aggsim.SphericalAssemblyReaction('monomer','ensemble', 1e-8 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(asmb_reaction)
# Disassembly
disasmb_reaction = aggsim.SphericalDisassemblyReaction('monomer','ensemble', 1e-6 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(disasmb_reaction)
data_outs.addStream(sys.stdout)
# Write out parameters
data_outs.write("# Run started {}\n".format(util.timestamp()))
data_outs.write("# Command: {}\n".format(' '.join(sys.argv)))
data_outs.write("# Parameters:\n")
optdict = vars(options)
for (k,v) in optdict.items():
data_outs.write("#\t{k}: {v}\n".format(k=k, v=v))
# Set seed
sp.random.seed(options.random_seed)
# Set up reaction
reactor = aggsim.Reactor(volume_uL=1e-9*options.volume_fL, temperature_C=options.initial_temperature_C)
n_monomers = aggsim.numberOfMolecules(1e-15 * options.volume_fL, 1e-6 * options.initial_concentration_uM)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble', monomers, options.monomer_radius_nm, packing_fraction=sp.pi/(3*sp.sqrt(2)))
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction('monomer','ensemble', options.k_nucleation * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(nuc_reaction)
# Nucleation
denuc_reaction = aggsim.EnsembleDenucleationReaction('monomer','ensemble', options.k_denucleation * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(denuc_reaction)
# Assembly
asmb_reaction = aggsim.SphericalAssemblyReaction('monomer','ensemble', options.k_assembly * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(asmb_reaction)
# Disassembly
# Write out parameters
data_outs.write("# Run started {}\n".format(util.timestamp()))
data_outs.write("# Command: {}\n".format(' '.join(sys.argv)))
data_outs.write("# Parameters:\n")
optdict = vars(options)
for (k, v) in optdict.items():
data_outs.write("#\t{k}: {v}\n".format(k=k, v=v))
# Set seed
sp.random.seed(options.random_seed)
# Set up reaction
reactor = aggsim.Reactor(volume_uL=1e-9 * options.volume_fL,
temperature_C=options.initial_temperature_C)
n_monomers = aggsim.numberOfMolecules(
1e-15 * options.volume_fL, 1e-6 * options.initial_concentration_uM)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble',
monomers,
options.monomer_radius_nm,
packing_fraction=sp.pi /
(3 * sp.sqrt(2)))
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction(
'monomer', 'ensemble',
options.k_nucleation * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(nuc_reaction)
# Nucleation