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