Ecology: ATP Pathway Cooperation
A microbial metabolic competition model. Two populations chase ATP via different strategies — high-yield oxidative phosphorylation versus low-yield but fast substrate-level phosphorylation — and the run reveals which strategy dominates as the shared substrate is drawn down.
What it simulates
- A shared substrate resource and two populations with different ATP-production strategies.
- High-yield strategy (N1): more ATP per substrate, slower growth.
- Low-yield strategy (N2): faster growth, wastes substrate.
- The classic cooperation–competition tradeoff in microbial ecology.
- Dynamics solved by Tellurium directly from the original SBML file.
Run it on the Hub
- Open the Pfeiffer2001 ATP-Pathway Cooperation-Competition Model Lab on the public Hub.
- Click Run. The default scenario runs for 75 time units.
Inputs you can tune
| Input | Meaning |
|---|---|
integration_step | ODE solver step size. Smaller is more precise but slower. |
model_path | Relative path to the SBML file. Usually leave at the default. |
Biological parameters (rate constants, initial concentrations, stoichiometry) live in the SBML file model/data/BIOMD0000000337.xml — edit it directly to change the chemistry.
What results to expect
- Trajectories: substrate (S), high-yield population (N1), and low-yield population (N2) over time. In the default run, N1 collapses as N2 expands.
- Strategy fractions: low-yield rises to 1.0 while high-yield falls to 0.0; resource-per-biomass ratio is also tracked.
- Summary table: final and extremal values for substrate, populations, and strategy fractions.
Reference
SBML wrapper for Pfeiffer et al. (2001), BioModels BIOMD0000000337.
Source on GitHub: models-ecology — pfeiffer2001-atp-pathway-cooperation.