ecoli.processes.environment.reaction_diffusion_field

Reaction Diffusion Field

class ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion(parameters=None)

Bases: Process

Reaction and Diffusion in 2-dimensional fields of molecules, with agent uptake and secretion at agent locations.

Parameters: TODO

defaults: Dict[str, Any]

{   'bounds': [<Quantity(10, 'micrometer')>, <Quantity(10, 'micrometer')>],
    'depth': <Quantity(3000.0, 'micrometer')>,
    'diffusion': <Quantity(600.0, 'micrometer ** 2 / second')>,
    'exchanges_path': ('boundary', 'exchanges'),
    'external_path': ('boundary', 'external'),
    'gradient': None,
    'internal_time_step': 1,
    'kinetic_parameters': {},
    'location_path': ('boundary', 'location'),
    'molecules': [],
    'n_bins': [10, 10],
    'reactions': {},
    'time_step': 1}

diffuse(fields, timestep)

diffusion_delta(field, timestep)

calculate new concentrations resulting from diffusion

get_bin_site(location)

get_local_environments(agents, fields)

get_single_local_environments(location, fields)

initial_state(config=None)

sets uniform initial state at the concentration provided for each the molecule_id in config

name = 'reaction_diffusion'

next_update(timestep, states)

ones_field()

ports_schema()

react(fields, timestep)

zeros_field()

ecoli.processes.environment.reaction_diffusion_field.main()