def axon_replenish(rs=[0.1, 0.5, 1.0]):
data = []
for r in rs:
syn = Synapse(verbose=args.verbose)
axon = syn.create_axon(
replenish_rate=r,
reuptake_rate=0.0,
verbose=args.verbose)
axon.set_concentration(0.0)
axon_recording = []
for _ in xrange(50):
axon_recording.append(axon.get_concentration())
axon.replenish()
axon_recording.append(axon.get_concentration())
data.append(("replenish %s" % str(r), axon_recording))
if not args.silent: plot(data, title="Replenish (replenish rate)")
def axon_reuptake(rs=[0.1, 0.5, 1.0], print_synaptic_cleft=False):
data = []
for r in rs:
syn = Synapse(verbose=args.verbose)
syn.synaptic_cleft.add_concentration(0.5)
axon = syn.create_axon(
replenish_rate=0.0,
reuptake_rate=r,
verbose=args.verbose)
axon.set_concentration(0.0)
record_components = [("reuptake %s" % str(r), axon)]
if print_synaptic_cleft:
record_components.append((
"synaptic cleft %s" % str(r),
syn.synaptic_cleft))
data += simulate_synapse(syn,
record_components = record_components,
iterations = 100)
if not args.silent: plot(data, title="Reuptake (reuptake rate)")
def create_synapse(presynaptic, postsynaptic, active_molecules=None,
transporter=Transporters.GLUTAMATE, receptor=Receptors.AMPA,
enzyme_concentration=1.0,
axon_delay=0, dendrite_strength=0.0015):
synapse = Synapse(
postsynaptic_id=postsynaptic.neuron_id,
initial_enzyme_concentration=enzyme_concentration,
active_molecules=active_molecules)
axon = synapse.create_axon(
transporter=transporter,
replenish_rate=0.1,
reuptake_rate=0.5,
capacity=1.0,
delay=axon_delay)
dendrite = synapse.create_dendrite(
receptor=receptor,
density=0.25,
strength=dendrite_strength)
presynaptic.axons.append(axon)
presynaptic.synapses.append(synapse)
presynaptic.synapses_stable.append(True)
postsynaptic.dendrites.append(dendrite)
return synapse