ecoli.processes.shape

Shape

Shape is used to calculate shape properties using 3D capsule geometry. Outputs length and `surface_area are determined from inputs volume and width. These variables are required to plug into a Lattice Environment

class ecoli.processes.shape.Shape(parameters=None)

Bases: Step

Shape Step

Derives cell length and surface area from width and volume.

Ports:

• cell_global: Should be given the agent’s boundary store. Contains variables: volume, width, length, and surface_area.

• periplasm_global: Contains the volume variable for the volume of the periplasm.

Parameters:

parameters (dict) –

A dictionary that can contain the following configuration options:

• width (float): Initial width of the cell in microns

defaults: Dict[str, Any]

{   'cytoplasm_fraction': 0.8,
    'initial_cell_volume': <Quantity(1.2, 'femtoliter')>,
    'initial_mass': <Quantity(1339, 'femtogram')>,
    'periplasm_fraction': 0.2,
    'width': <Quantity(1.0, 'micrometer')>}

initial_state(config=None)

name = 'ecoli-shape'

next_update(timestep, states)

ports_schema()

ecoli.processes.shape.length_from_volume(volume, width)

get cell length from volume, using the following equation for capsule volume, with V=volume, r=radius, a=length of cylinder without rounded caps, l=total length:

\(V = (4/3)*PI*r^3 + PI*r^2*a\) \(l = a + 2*r\)

ecoli.processes.shape.mmol_to_counts_from_volume(volume)

mmol_to_counts has units L/mmol

ecoli.processes.shape.surface_area_from_length(length, width)

get surface area from length and width, using 3D capsule geometry

\(SA = 4*PI*r^2 + 2*PI*r*a\)

ecoli.processes.shape.volume_from_length(length, width)

get volume from length and width, using 3D capsule geometry