Executable

Vivarium-chemotaxis

Eran Agmon + 1 other
v0.0.1MITAug 2026

Citation: A Multi-Scale Approach to Modeling E. coli Chemotaxis

The Chemotaxis Master Composite integrates metabolism, transport, transcription, translation, complexation, degradation, proton motive force, flagella activity, and chemoreceptor activity; this repository provides the CHE, FLG, and PMF processes while other processes are imported from vivarium-cell.

molecularcellular
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How this model is classified mathematically and dynamically.

Model class
agent-based modelstochastic modelmulti-scale model
Formalism
stochastic
Determinism
Stochastic
Time dynamics
Discrete
Spatial
Compartmental
Multiscale
Yes

Organisms, entities and processes this model represents.

Organisms
Escherichia coli
Infectious agents
Not recorded
Health conditions
Not recorded
Biological processes
chemotaxisflagellum-dependent cell motility
Molecular entities
MeAsp
Proteins / genes
Not recorded

The data this model consumes and produces when executed.

Parameters

NameDefaultUnitMeaning
initial_ligand5millimolarligand concentration
n_flagella4Not recordedNumber of flagella assigned to the cell.
time_step0.01secondSimulation update interval.
PMF-140millivoltInitial proton motive force.
initial_mass1339.0 fgfemtogramInitial cell mass for the expression composite.

Initial conditions

NameValueUnit
receptor_internal_staten_methyl=2.0; chemoreceptor_activity=1/3; CheR=0.00016 mM; CheB=0.00028 mM; CheB_P=0.0Not recorded
membrane_ions_and_temperatureinternal K=300, Na=10, Cl=10, PROTON=0; external K=5, Na=145, Cl=110, PROTON=0, T=310.15 Kkelvin

Data inputs

NameFormatRequiredPurpose
transport_metabolism.csvCSVOptionalReference timeseries used by the transport-metabolism test.
transport_metabolism_experiment.csvCSVOptionalReference experiment data shipped with the repository.

Outputs

NameQuantityUnitFormat
emitted timeseriesconcentrationNot recordedNot recorded
simulation plotsspatial positionNot recordedPNG
flat reference timeseriesFlattened timeseries written by the transport-metabolism test.Not recordedCSV

Experiment protocol

Vivarium experiments construct a Process or composite, optionally provide an initial state and ligand timeline, and emit state at a configured step.

Timestep
0.01 {'value': 'second', 'iri': None, 'ontology_label': None, 'ontology': 'uo', 'mapping_confidence': 'none'}
Observables
chemoreceptor_activityCheY_Pmotile_statePMFthrusttorque

Runtime environment, dependencies, and compute requirements.

Language
Python
Environment
pip

Vivarium advances fixed timesteps. Runnable modules were enumerated from __main__ blocks; imported vivarium-cell processes are not separate repository entry points.

Compute requirements

GPU
Not required
Parallelism
single

Dependencies

runtime
  • vivarium-cell ==0.0.23
  • vivarium-core ==0.0.34
  • pymunk ==5.6.0
  • numpy
  • scipy
  • matplotlib

Containers

  • · mismplatform/vivarium-chemotaxis:v0.0.2

Entry points

  • python chemotaxis/processes/chemoreceptor_cluster.py

    Run the chemoreceptor cluster pulse and exponential-random analyses.

  • python chemotaxis/processes/coarse_motor.py

    Run the coarse motor variable-receptor analysis.

  • python chemotaxis/processes/flagella_motor.py

    Run the stochastic variable-flagella motor simulation.

  • python chemotaxis/processes/membrane_potential.py

    Run the membrane-potential simulation.

  • python chemotaxis/composites/chemotaxis_flagella.py

    Run the variable-flagella or expression chemotaxis composite.

    --variable
    Run the variable-flagella branch; mutually exclusive with --expression.
    --expression
    Run the expression branch; mutually exclusive with --variable.
    --flagella
    Number of flagella.
  • python chemotaxis/composites/chemotaxis_master.py

    Run the Chemotaxis Master Composite or render its topology.

    --topology
    Render the compartment topology instead of running the simulation.
  • python chemotaxis/composites/chemotaxis_minimal.py

    Run the minimal receptor-and-motor chemotaxis composite.

  • python chemotaxis/composites/flagella_expression.py

    Run the flagella expression or expression-metabolism composite.

    --metabolism
    Run the expression-metabolism branch; mutually exclusive with --expression.
    --expression
    Run the expression branch.
  • python chemotaxis/composites/transport_metabolism.py

    Run the transport-metabolism expression composite.

    --shift
    Use the shifted minimal-media condition.
  • python chemotaxis/experiments/paper_experiments.py <experiment_id>

    Run a registered chemotaxis paper experiment by figure identifier.

    experiment_id
    Experiment id corresponding to a figure number from the chemotaxis paper.

Tests

pytestpytest

Artifacts stored with this model.

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Identifiers and integrity.

Contacts
Related
  • Is derived from
    url:https://www.mdpi.com/1099-4300/22/10/1101
External IDs
  • url:https://github.com/vivarium-collective/vivarium-chemotaxis