ecoli.processes.environment.diffusion_field
Diffusion Field
- class ecoli.processes.environment.diffusion_field.DiffusionField(parameters=None)[source]
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}
- name = 'diffusion_field'