Vivarium-chemotaxis
Citation: A Multi-Scale Approach to Modeling E. coli Chemotaxis
The repository implements Vivarium processes and composites for Escherichia coli chemotaxis, including chemoreceptor activity, flagella activity, proton motive force, and integrated metabolism, transport, transcription, translation, complexation, degradation, and division processes.
How this model is classified mathematically and dynamically.
- Formalism
- Determinism
- Stochastic
- Time dynamics
- Discrete
- Spatial
- Compartmental
- Multiscale
- Yes
Organisms, entities and processes this model represents.
- Organisms
- Infectious agents
- Not recorded
- Health conditions
- Not recorded
- Biological processes
- Molecular entities
- Not recorded
- Proteins / genes
- Not recorded
The data this model consumes and produces when executed.
Parameters
| Name | Default | Unit | Meaning |
|---|---|---|---|
| initial_ligand | 5 | millimolar | Initial ligand concentration used to initialize the chemoreceptor cluster. |
| n_Tar | 6 | Not recorded | Number of Tar receptors in a chemoreceptor cluster. |
| n_Tsr | 12 | Not recorded | Number of Tsr receptors in a chemoreceptor cluster. |
| k_meth | 0.0625 | per second | Catalytic rate of receptor methylation. |
| k_demeth | 0.0714 | per second | Catalytic rate of receptor demethylation. |
| time_step | 0.01 | second | Vivarium process integration timestep. |
| n_flagella | 4 | Not recorded | Expected or initial number of flagella. |
| expected_pmf | -140 | Not recorded | Expected proton motive force used to scale motile thrust. |
Initial conditions
| Name | Value | Unit |
|---|---|---|
| chemoreceptor_internal_state | n_methyl=2.0; chemoreceptor_activity=1/3; CheR=0.00016 mM; CheB=0.00028 mM; CheB_P=0.0 | Not recorded |
| flagella_motor_internal_state | CheY=2.59 uM; CheY_P=2.59 uM; CheZ=1.0 uM; CheA=1.0 uM; chemoreceptor_activity=1/3; motile_state=1 | Not recorded |
Data inputs
| Name | Format | Required | Purpose |
|---|---|---|---|
| flagella_expression_metabolism.csv | CSV | Optional | Reference data used by the flagella expression/metabolism composite. |
| transport_metabolism.csv | CSV | Optional | Reference data used by the transport/metabolism composite. |
Outputs
| Name | Quantity | Unit | Format |
|---|---|---|---|
| Vivarium timeseries | concentration | Not recorded | Not recorded |
| simulation plots | PNG or other plot files generated by process, composite, and experiment plotting functions. | Not recorded | Not recorded |
Experiment protocol
Typical runs use Vivarium fixed-step simulation; the master composite uses a Brownian ligand timeline and emits a timeseries.
- Timestep
- 0.01 second
- Duration
- 500 second
- Observables
- chemoreceptor_activityn_methylCheY_Pmotile_statethrusttorque
Runtime environment, dependencies, and compute requirements.
- Language
- Python >=3.6,<3.9
- Environment
- pip
Vivarium legacy Generator composites use fixed-step simulation helpers. MongoDB is required for some larger experiments using database emitters.
Compute requirements
- GPU
- Not required
- Parallelism
- single
Dependencies
- runtime
- vivarium-cell ==0.0.23
- vivarium-core ==0.0.34
- pymunk ==5.6.0
Containers
- docker · mismplatform/vivarium-chemotaxis:v0.0.2
Entry points
python chemotaxis/composites/chemotaxis_flagella.pyRun the flagella chemotaxis composite in variable or expression mode.
- --variable
- Run variable flagella mode; mutually exclusive in intent with --expression.
- --expression
- Run expression mode; mutually exclusive in intent with --variable.
- --flagella
- Number of flagella.
python chemotaxis/composites/chemotaxis_master.pyRun the complete chemotaxis master composite or save its topology.
- --topology
- Save the compartment topology instead of running the simulation.
python chemotaxis/composites/chemotaxis_minimal.pyRun the minimal chemotaxis composite.
python chemotaxis/composites/flagella_expression.pyRun flagella expression, with an optional metabolism mode.
- --metabolism
- Run expression metabolism mode.
- --expression
- Expression mode flag.
python chemotaxis/composites/transport_metabolism.pyRun the transport and metabolism composite.
- --shift
- Run the shifted transport/metabolism condition.
python chemotaxis/experiments/paper_experiments.py <experiment_id>Run one of the paper experiments selected by figure identifier.
- experiment_id
- Experiment identifier corresponding to a paper figure.
python chemotaxis/processes/chemoreceptor_cluster.pyRun the chemoreceptor cluster process pulse and exponential-random analyses.
python chemotaxis/processes/coarse_motor.pyRun the coarse motor process analysis.
python chemotaxis/processes/flagella_motor.pyRun the flagella motor process with variable flagella.
python chemotaxis/processes/membrane_potential.pyRun the membrane potential process analysis.
Tests
pytestpytest
Artifacts stored with this model.
Identifiers and integrity.
- Metadata review
- Approved · 1da614bf-946a-4400-a0be-4fd0f1d00f74 · Oct 2026
- Contacts
- Eran Agmon · eagmon@stanford.edu
- Ryan Spangler · ryan.spangler@gmail.com
- External IDs
- url:https://github.com/vivarium-collective/vivarium-chemotaxis