ecoli.processes.chemotaxis.coarse_motor

Coarse Motor Processes

MotorActivity models E. coli coarse motor activity, without explicit flagella.

References

Based on the model described in:

Vladimirov, N., Lovdok, L., Lebiedz, D., & Sourjik, V. (2008). Dependence of bacterial chemotaxis on gradient shape and adaptation rate.

CheY phosphorylation model from:

Kollmann, M., Lovdok, L., Bartholome, K., Timmer, J., & Sourjik, V. (2005). Design principles of a bacterial signalling network. Nature.

Motor switching model from:

Scharf, B. E., Fahrner, K. A., Turner, L., and Berg, H. C. (1998). Control of direction of flagellar rotation in bacterial chemotaxis. PNAS.

An increase of attractant inhibits CheA activity (chemoreceptor_activity), but subsequent methylation returns CheA activity to its original level.

TODO – add CheB phosphorylation

class ecoli.processes.chemotaxis.coarse_motor.MotorActivity(parameters=None)

Bases: Process

Models changes to coarse motor activity, based on chemoreceptor_activity and current motor state.

Ports:

• internal: includes variables ccw_motor_bias, ccw_to_cw, motile_state, CheY_P

• external: includes variables thrust and torque

defaults: Dict[str, Any]

{   'adapt_precision': 3,
    'ccw_to_cw_leak': 0.25,
    'cw_to_ccw': 0.83,
    'gamma_Y': 0.1,
    'initial_state': {   'external': {'thrust': 0, 'torque': 0},
                         'internal': {   'CheA': 1.0,
                                         'CheY_P': 0.5,
                                         'CheY_tot': 9.7,
                                         'CheZ': 1.0,
                                         'ccw_motor_bias': 0.5,
                                         'ccw_to_cw': 0.5,
                                         'chemoreceptor_activity': 0.3333333333333333,
                                         'motile_state': 1}},
    'k_s': 0.45,
    'k_y': 100.0,
    'k_z': 30.0,
    'mb_0': 0.65,
    'n_motors': 5,
    'time_step': 0.1,
    'tumble_jitter': 120.0}

name = 'coarse_motor'

next_update(timestep, states)

ports_schema()

create internal and external ports

ecoli.processes.chemotaxis.coarse_motor.main()

ecoli.processes.chemotaxis.coarse_motor.plot_variable_receptor(output, out_dir='out', filename='motor_variable_receptor')

ecoli.processes.chemotaxis.coarse_motor.run()

ecoli.processes.chemotaxis.coarse_motor.tumble(tumble_jitter=120.0)