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Simulation · Beard Lab / Randall et al.

QAMAS

Simulate mitochondrial ATP synthesis, oxygen consumption and membrane potential.

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What QAMAS is

Quantitative analysis of mitochondrial ATP synthesis (QAMAS) couples the respiratory chain, ATP synthase, adenine nucleotide and phosphate transport, and proton leak. Run the published isolated-mitochondria model or the cellular model with healthy or heart-failure metabolite pools and creatine kinase. Corollary integrates the repository's corrected-stoichiometry Antimony models with CVODE and returns concentration and flux time courses with explicit units. The cellular runtime corrects an upstream creatine species name to conserve the creatine pool; each result documents this correction. Oxygen, pH and cation concentrations remain fixed during each run. These are mechanistic research simulations, not patient-specific predictions; a finite-duration endpoint is not proof of steady state.

Run it here

No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.

Runs on On-demand CPU

Runs on our servers with on-demand compute. A first run needs time to load the model; active capacity can be reused and scales down when idle.

Run this model

QAMAS

Model

up to 7 credits · ~10s typical

Inputs and outputs

You provide

  • Modeloptional

  • ATP demand (% of baseline)optional

    100% = 3 µmol/s/L buffer in vitro, or 0.5 mmol/s/L cell in the cellular model. Demand stays constant during the simulation.

  • Initial buffer phosphate (mM)optional

    In vitro only; use 1 or 5 mM for the published phosphate comparison. Cellular phosphate is derived from the selected metabolite pools.

  • Oxygen partial pressure (mmHg)optional

    Held fixed throughout the run. The published baseline is 25 mmHg.

  • Duration (s)optional

    The upstream experiments integrate for 3000 s in vitro and 5000 s in the cellular model.

  • Output time pointsoptional

You get back

  • Time (s), ATP/ADP/phosphate (mM), membrane potential (mV), redox fractions and ATP synthesis / oxygen consumption fluxes (mmol/s/L mitochondria).

  • ATP, membrane potential, redox state and fluxes over time.

  • Parameters, units, initial pools, solver settings and pinned upstream source.

Licence

Commercial use permitted · MIT

MIT-licensed QAMAS model definitions; upstream copyright and license are retained with the bundled source.

Questions

Can I use QAMAS commercially?

Commercial use permitted. MIT-licensed QAMAS model definitions; upstream copyright and license are retained with the bundled source.

How do I run QAMAS without installing anything?

Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers, typically in 10s, and a run costs about 3 credits. Visitors without an account get 1,000 credits a month.

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