ecoli.processes.environment.reaction_diffusion_field

Reaction Diffusion Field

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

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)[source]
diffusion_delta(field, timestep)[source]

calculate new concentrations resulting from diffusion

get_bin_site(location)[source]
get_local_environments(agents, fields)[source]
get_single_local_environments(location, fields)[source]
initial_state(config=None)[source]

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

name = 'reaction_diffusion'
next_update(timestep, states)[source]
ones_field()[source]
ports_schema()[source]
react(fields, timestep)[source]
zeros_field()[source]
ecoli.processes.environment.reaction_diffusion_field.main()[source]