ecoli.processes.environment.lysis

Lysis

class ecoli.processes.environment.lysis.Lysis(parameters=None)

Bases: Step

defaults: Dict[str, Any]

{'bin_volume': <Quantity(1e-06, 'liter')>, 'secreted_molecules': []}

name = 'lysis'

next_update(timestep, states)

ports_schema()

class ecoli.processes.environment.lysis.LysisAgent(config=None)

Bases: Composer

Agent that uptakes a molecule from a lattice environment, bursts upon reaching a set mass, and spills the molecules back into the environment

Base class for composer classes.

Composers generate composites.

All composer classes must inherit from this class.

Parameters:

config (dict | None) – Dictionary of configuration options that can override the class defaults.

defaults: Dict[str, Any]

{   'agents_path': ('..', '..', 'agents'),
    'boundary_path': ('boundary',),
    'dimensions_path': ('..', '..', 'dimensions'),
    'fields_path': ('..', '..', 'fields'),
    'local_field': {},
    'lysis': {'secreted_molecules': ['GLC']},
    'transport_burst': {   'burst_mass': <Quantity(2000, 'femtogram')>,
                           'molecular_weights': {   'GLC': <Quantity(1e+22, 'femtogram / mole')>},
                           'uptake_rate': {'GLC': 2}}}

generate_flow(config)

generate_processes(config)

generate_steps(config)

generate_topology(config)

class ecoli.processes.environment.lysis.ToyTransportBurst(parameters=None)

Bases: Process

Toy process for testing Lysis. Uptakes a molecule from a field, and triggers lysis.

defaults: Dict[str, Any]

{   'burst_mass': <Quantity(2000, 'femtogram')>,
    'molecular_weights': {'GLC': <Quantity(1.0, 'femtogram / mole')>},
    'uptake_rate': {'GLC': 1}}

next_update(timestep, states)

ports_schema()

ecoli.processes.environment.lysis.main()

ecoli.processes.environment.lysis.mass_from_count(count, mw)