vivarium.processes.derive_globals module

class vivarium.processes.derive_globals.DeriveGlobals(initial_parameters=None)

Bases: vivarium.core.process.Deriver

Process for deriving volume, mmol_to_counts, and shape from the cell mass

defaults = {'initial_mass': <Quantity(1339, 'femtogram')>, 'periplasm_volume_fraction': 0.3, 'width': 1}

name = 'globals_deriver'

next_update(timestep, states)

ports_schema()

vivarium.processes.derive_globals.get_default_global_state()

vivarium.processes.derive_globals.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

vivarium.processes.derive_globals.surface_area_from_length(length, width)

SA = 3*PI*r^2 + 2*PI*r*a

vivarium.processes.derive_globals.test_deriver(total_time=10)

vivarium.processes.derive_globals.volume_from_length(length, width)

inverse of length_from_volume