vivarium.processes.diffusion_network module

class vivarium.processes.diffusion_network.DiffusionNetwork(initial_parameters=None)

Bases: vivarium.core.process.Process

defaults = {'channels': {}, 'concentrations': {}, 'diffusion': 0.01, 'initial_state': {}, 'membrane_composition': {}, 'molecules': ['glc'], 'network': {}}

diffusion_delta(locations, membrane, timestep)

name = 'diffusion_network'

next_update(timestep, states)

ports_schema()

vivarium.processes.diffusion_network.check_in_set(set_list, set)

vivarium.processes.diffusion_network.field_from_locations_series(locations_series, molecule_ids, n_bins, times)

vivarium.processes.diffusion_network.get_grid_config()

vivarium.processes.diffusion_network.get_two_compartment_config()

vivarium.processes.diffusion_network.make_location_network(n_bins)

vivarium.processes.diffusion_network.plot_diffusion_field_output(data, config, out_dir='out', filename='field')

vivarium.processes.diffusion_network.test_diffusion_network(config={'channels': {'porin': 0.05}, 'diffusion': 0.1, 'initial_state': {'concentrations': {'external': {'glc': 20.0}, 'internal': {'glc': 0.0}}, 'membrane_composition': {'porin': 5}}, 'molecules': ['glc'], 'network': {'edges': [('external', 'internal')], 'locations': ['external', 'internal'], 'membrane_edges': [('external', 'internal')], 'type': 'standard'}}, end_time=10)