ecoli.processes.spatiality.spatial_geometry

Spatial Geometry

SpatialGeometry Process calculates geometric parameters of nodes a nd edges utilized in diffusion_network.py. This process assumes E. coli is a spherocylinder with constant radius. This process is currently unfinished. This process assumes that there are properties of the nodes that specify which type of compartment it is such that the geometry rules below apply. This is not currently implemented in ecoli_spatial.py in vivarium-ecoli. Much of the geometry rules have been specified, however it should be checked to see if it leads to consistent results.

References

• width of 0.73 um: Cluzel et al., Nucleic Acids Research (2008)

• strain: K-12 Frag1

• periplasm width of 21 nm: Matias et al., J Bacteriology (2003)

• cell density of 1100 g/L (from WCM): Baldwin et al., Arch microbiol. (1995)

Warning

This process is unfinished.

class ecoli.processes.spatiality.spatial_geometry.SpatialGeometry(parameters=None)

Bases: Step

defaults: Dict[str, Any]

{   'density': 1100,
    'edges': {},
    'mw': {},
    'nodes': ['nucleoid', 'periplasm'],
    'width': 0.73}

initial_state(config=None)

name = 'spatial_geometry'

next_update(timestep, states)

ports_schema()

ecoli.processes.spatiality.spatial_geometry.main()

Simulate the process and plot results.

ecoli.processes.spatiality.spatial_geometry.run_spatial_geometry_process()

Run a simulation of the process.

Returns:

The simulation output.