ecoli.processes.environment.diffusion_field

Diffusion Field

class ecoli.processes.environment.diffusion_field.DiffusionField(parameters=None)

Bases: Process

Diffusion in 2-dimensional fields of molecules with agent exchange

Agent uptake and secretion occurs at agent locations.

Notes:

• Diffusion constant of glucose in 0.5 and 1.5 percent agarose gel is around \(6 * 10^{-10} \frac{m^2}{s}\) (Weng et al. 2005. Transport of glucose and poly(ethylene glycol)s in agarose gels).

• Conversion to micrometers: \(6 * 10^{-10} \frac{m^2}{s}=600 \frac{micrometers^2}{s}\).

defaults: Dict[str, Any]

{   'bounds': [<Quantity(10, 'micrometer')>, <Quantity(10, 'micrometer')>],
    'depth': <Quantity(3000.0, 'micrometer')>,
    'diffusion': <Quantity(0.5, 'micrometer ** 2 / second')>,
    'exchanges_path': ('boundary', 'exchanges'),
    'external_path': ('boundary', 'external'),
    'gradient': {},
    'initial_state': {},
    'location_path': ('boundary', 'location'),
    'molecules': ['glc'],
    'n_bins': [10, 10],
    'time_step': 1}

diffuse(fields, timestep)

diffusion_delta(field, timestep)

calculate concentration changes cause by diffusion

get_bin_site(location)

get_local_environments(agents, fields)

get_single_local_environments(location, fields)

initial_state(config=None)

name = 'diffusion_field'

next_update(timestep, states)

ones_field()

ports_schema()

ecoli.processes.environment.diffusion_field.get_exponential_config()

ecoli.processes.environment.diffusion_field.get_gaussian_config()

ecoli.processes.environment.diffusion_field.get_random_field_config()

ecoli.processes.environment.diffusion_field.plot_fields(data, config, out_dir='out', filename='fields')

ecoli.processes.environment.diffusion_field.run_diffusion_field(config=None, total_time=100, filename='snapshots')