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Drybench Bioreactor.
Yeast fed-batch simulator: S. cerevisiae, glucose-limited
Simulate a glucose feed that keeps S. cerevisiae below the critical growth rate and within your vessel's oxygen supply, with sources and limits shown.
per hour
Change it to simulate this run again in your browser. Every other value is the preset's.
- Oxygen runs out
- Not within the run
- Lowest DO
- 45.5% air saturation
- Biomass at 24 h
- 15.6g/L
- Peak OUR
- 43.3mmol/L/h
The run
Show the data
| Time (h) | Dissolved oxygen (% air saturation) | Biomass (g/L) | Substrate (g/L) | Feed rate (L/h) | Event |
|---|---|---|---|---|---|
| 0.00 | 100.0 | 1.5 | 0.02 | 0.00435 | |
| 0.96 | 94.2 | 1.65 | 0.0196 | 0.00479 | |
| 1.92 | 93.6 | 1.82 | 0.0196 | 0.00527 | |
| 3.00 | 92.9 | 2.02 | 0.0196 | 0.00587 | |
| 3.96 | 92.2 | 2.22 | 0.0196 | 0.00646 | |
| 4.92 | 91.4 | 2.44 | 0.0196 | 0.00711 | |
| 6.00 | 90.5 | 2.72 | 0.0196 | 0.00792 | |
| 6.96 | 89.5 | 2.99 | 0.0196 | 0.00872 | |
| 7.92 | 88.5 | 3.29 | 0.0196 | 0.0096 | |
| 9.00 | 87.2 | 3.66 | 0.0196 | 0.0107 | |
| 9.96 | 85.9 | 4.02 | 0.0196 | 0.0118 | |
| 10.92 | 84.5 | 4.42 | 0.0196 | 0.013 | |
| 12.00 | 82.8 | 4.91 | 0.0196 | 0.0144 | |
| 12.96 | 81.1 | 5.39 | 0.0196 | 0.0159 | |
| 13.92 | 79.3 | 5.92 | 0.0196 | 0.0175 | |
| 15.00 | 77.0 | 6.58 | 0.0196 | 0.0195 | |
| 15.96 | 74.7 | 7.22 | 0.0196 | 0.0214 | |
| 16.92 | 72.2 | 7.93 | 0.0196 | 0.0236 | |
| 18.00 | 69.2 | 8.8 | 0.0196 | 0.0263 | |
| 18.96 | 66.2 | 9.65 | 0.0196 | 0.029 | |
| 19.92 | 63.0 | 10.6 | 0.0196 | 0.0319 | |
| 21.00 | 58.9 | 11.7 | 0.0196 | 0.0355 | |
| 21.96 | 55.0 | 12.8 | 0.0196 | 0.0391 | |
| 22.92 | 50.8 | 14.1 | 0.0196 | 0.043 | |
| 24.00 | 45.5 | 15.6 | 0.0196 | 0.0479 |
Where this run leaves the model
This run stays inside the model and the correlations' ranges.
Also as a chemostat: open this preset in the app as a chemostat. A dilution rate above 0.28 per hour, or a run short of oxygen, is flagged as outside this model. (Van Hoek et al. 1998) Open as a chemostat
Every value and where it comes from
| Parameter | Value | Source |
|---|---|---|
| Maximum specific growth rate, μmax | 0.28 per hour | CitedVan Hoek et al. 1998abstract: below D 0.28 per hour glucose metabolism was fully respiratory (DS28911, aerobic glucose-limited chemostats, 30 °C)Reported range 0.28 to 0.3 per hour (Van Hoek et al. 1998, Postma et al. 1989, abstracts; the critical dilution rate in two strains (DS28911; CBS 8066, 0.30)) |
| Substrate affinity, Ks | 0.034 g/L | Illustrativegives the 110 µM residual glucose Postma et al. measured at low dilution rates (Yeast 1989, abstract) at D 0.10 with this preset's growth rate, yield and maintenance; their residual did not change with D, so a value fitted at one D is arbitraryReported range 0.0034 to 0.34 g/L (Postma et al. 1989, abstract; the tenfold test's span)Illustrative: not a measured value. Changing it tenfold either way does not change biomass, DO, OUR, the time oxygen runs out or the rescue steps at the precision shown (see the verification page). |
| Substrate inhibition, Ki | none | Model choiceMonod: no substrate inhibition |
| True yield of biomass on substrate, Y | 0.5 g/g | Citedvan Hoek et al. 2000, as quoted by Vos et al. 2016aerobic glucose-limited chemostats of CEN.PK113-7DReported range 0.45 to 0.5 g/g (Van Hoek et al. 1998, Postma et al. 1989, Table 1; abstract; observed yields in respiratory glucose-limited chemostats (0.45 to 0.49; 0.50)) |
| Maintenance, ms | 0.00703 g/g/h | Cited, convertedVos et al. 2016Results: 0.039 ± 0.003 mmol glucose/g/h in aerobic retentostats (CEN.PK113-7D, 30 °C); 0.039 mmol/g/h × 0.180156 g/mmolReported range 0.00703 to 0.0176 g/g/h (Vos et al. 2016, Discussion; their retentostat value to their own chemostat estimate, 2.5-fold higher) |
| Oxygen affinity, Ko | 0.01 mg/L | Illustrativeno source read gives yeast's oxygen affinity; set at the order of E. coli's measured value (Stolper et al. 2010, 121 nM, 0.004 mg/L), rounded upReported range 0.001 to 0.1 mg/L (Stolper et al. 2010, Results; the tenfold test's span)Illustrative: not a measured value. Changing it tenfold either way does not change biomass, DO, OUR, the time oxygen runs out or the rescue steps at the precision shown (see the verification page). |
| Substrate | glucose | Setting |
| Biomass carbon fraction | 0.4738 g C per g dry weight | CitedFolsom and Carlson 2015Table 2: E. coli MG1655, glucose-limited chemostats, mean 47.38 percentReported range 0.4706 to 0.4769 g C per g dry weight (Folsom and Carlson 2015, Table 2; the four glucose-limited dilution rates)Not species-specific |
| Biomass degree of reduction, γX | 4.17 per C-mol | Cited, convertedFolsom and Carlson 2015Table 2: E. coli, glucose-limited, mean formula CH1.725N0.23O0.4325; 4 + H − 2·O − 3·N, ammonium the nitrogen sourceReported range 4.14 to 4.2 per C-mol (Folsom and Carlson 2015, Table 2; the four glucose-limited dilution rates' formulas)Not species-specific |
| Growth-associated product, α | 0 g/g | Model choiceproduct off |
| Non-growth-associated product, β | 0 g/g/h | Model choiceproduct off |
| Starting biomass, X0 | 1.5 g/L | Setting |
| Starting substrate, S0 | 0.02 g/L | Setting |
| Starting volume, V0 | 7 L | Setting |
| Mode | fed-batch | Setting |
| Feed law | exponential | Setting |
| Feed starts at | 0 h | Setting |
| Substrate in the feed, Sf | 500 g/L | Setting |
| Set growth rate, μset | 0.1 per hour | Setting |
| The pump's limit, Fmax | 0.2 L/h | Setting |
| Working volume limit, Vmax | 10 L | Setting |
| Feed stops at | none | Setting |
| Temperature | 30 °C | Setting |
| Headspace pressure | 1 atm, absolute | Setting |
| Inlet O₂ | 20.95 % of the dry gas | Setting |
| Gas flow | 1 vvm | Setting |
| Agitation | 600 rpm | Setting |
| kLa from | value | Setting |
| kLa at these settings | 400 per hour | Setting |
| DO setpoint | 30 % air saturation | Setting |
| Vessel diameter, T | 0.22 m | Setting |
| Impeller diameter, D | 0.088 m | Setting |
| Rushton impellers | 1 | Setting |
| Broth, for the correlation | coalescing | Setting |
| Agitation limit | 900 rpm | Setting |
| Gas flow limit | 2 vvm | Setting |
| Inlet O₂ limit | 40 % | Setting |
| Gas-flow basis | actual | Model choiceLegacy vvm is actual dry-gas volume at reactor temperature and pressure, per current liquid volume. |
| Feed dissolved oxygen | 0 mg/L | Model choiceDefault feed is deoxygenated; change to the measured feed dissolved oxygen. |
Mass balance
Over the run, carbon closes within 10⁻⁸ and electrons within 10⁻⁸ of what went in, as a fraction of it: the substrate fed and taken up against the biomass, product, CO₂ and what the feed and draw-off carry.
Verification
This preset's run is one of the 33 scenarios the engine is checked against SciPy's Radau on (2026-10-07), and its golden run holds this published version still. The verification page lists the fixtures, their hashes and the tolerances.
Preset s-cerevisiae-fed-batch@1; model 2.0.0; solver 1.1.0. Computed when this page was built; the app recomputes it in your browser.
Draft until the independent bioprocess reviewer signs the equations, the presets and the fixtures (Q-19).
Limits
- Teaching and estimation model, not a validated process model.
- The rescue cascade stays within the agitation, gas-flow and oxygen-enrichment limits you enter, and ignores cooling capacity, vessel pressure and gas-safety limits. Oxygen enrichment near flammable solvents or vapours is a fire and explosion hazard. Do not run a vessel from these outputs without your own engineering review.
- Presets combine literature values and operating choices from multiple conditions; they are teaching scenarios, not validated strain/process parameter sets. Quantitative process use requires measured parameters and specialist validation.
- Literature growth-fitted Ks is not interchangeable with the uptake Ks used here. Without product/inhibition and with excess oxygen, growth half-saturation is Ks × (1 + 2Yms/μmax). Presets are not silently transformed without refitting.
- Nominal Rushton Np=5 assumes standard baffled turbulent geometry (Re above 10⁴, Kaiser et al. 2017); the app does not compute Reynolds number or broth rheology. Vessel geometry, multiple impellers and real-broth transfer need measurement.
- An unstructured uptake/Monod model with mixed literature parameters has not been quantitatively validated for a given strain or process. Reported parameter ranges do not establish predictive uncertainty for these composite presets.
- The Crabtree effect is not modelled; the S. cerevisiae preset stays glucose-limited, and a run that leaves glucose limitation or runs short of oxygen is flagged.
- The acetate onset is MG1655's; other strains differ.
- CHO and other sparged mammalian cultures are not modelled for oxygen limitation.
- The DO setpoint is a process margin, not a kinetic threshold.
- The gas phase is taken at steady state (no hold-up). Feed oxygen enters dC/dt through (Fin/V)(Cfeed−C); zero feed DO is the default. The chart shows oxygen in the liquid; a DO probe's reading lags it by the probe's response time, which is not modelled.
- Excursions past a limit that last less than about 3 minutes are not flagged: the model leaves out the gas phase's hold-up and the DO probe's response, which act over about a minute.
- Gas flow has an explicit actual or reference basis, including reference temperature and absolute pressure. The same ideal dry-inlet-gas conversion supplies molar flow, superficial velocity and gassed power. Gas-flow humidification and hydrostatic expansion are not modelled; freshwater solubility includes its water-vapour correction, but broth salinity and composition require measurement. Vvm is per current liquid volume; flow rises during feeding while kLa is held between aeration changes.
- Van 't Riet's empirical correlation supplies no validated prediction interval for your vessel or broth. Yawalkar et al. 2002 report substantial deviations for some conditions; use measured kLa when available.
- Real broths fall anywhere between the coalescing form used by default and the non-coalescing form; enter a measured kLa if you have one.
- The presets' 10 L vessel sits at the lower edge of the tank sizes Hughmark's correlation was fitted on (0.21 to 3.33 m).
- kLa is taken at the volume where the aeration is set, at the start or at a rescue step, and held as the volume grows.
- The product is biomass-equivalent for substrate yield, carbon fraction and degree of reduction. Product-enabled OUR, CER and RQ are approximate for chemically different products.
- When uptake falls below maintenance, nothing grows and nothing decays: death and endogenous decay are not modelled.
- The CO₂ evolution rate is the CO₂ produced: dissolved CO₂ and bicarbonate are not modelled.
- No heat transfer, pH control, parameter fitting or Monte Carlo.
- Scale-up assumes geometrically similar vessels with the same impellers, Np and gas flow per volume; constant P/V holds ungassed power, so gassed P/V differs between scales. It ignores cooling, mixing time and shear. Every kLa is the correlation's, flagged outside its fitted range, with no prediction interval.
- The yield check refuses only what the carbon and electron balances forbid; a feasible yield is not thereby a likely one.
- The model's feed law; pump calibration, line dead volume and feed density at temperature are yours to check.
- A complex medium is context; the model simulates one declared substrate; delivery is not verified.
- Matched by exact compound identity against a short ruled list; names are not read; glucose monohydrate is converted to anhydrous glucose by formula mass, assuming the exact monohydrate.
- An apparent ln(response) slope over your window; not the model's μmax; no OD-to-biomass conversion; no interval.
- Elapsed time from a declared event is not physiological equivalence; responses are not converted or overlaid on one axis; a simulation reference is context only.
- Estimates one parameter, conditional on every other value as entered; a wrong fixed value biases it without warning.
- Needs measured biomass as mass concentration and measured substrate; optical density alone is refused.
- No confidence interval; a profile is a numerical diagnostic.
- Values marked “Unverified” have not yet been checked against their sources; each is checked, or removed, before this app leaves preview.
- A link carries the preset and every parameter you changed, never results; a run you keep stays in this browser. No account needed.
- No offline use: the pages are served by the site, and nothing is installed.
A simulation, not a forecast. Every output follows from the model equations and the parameters you entered. It is a teaching and estimation model, not a validated process model, and not a prediction for any real strain, vessel or process.
Open in the appThe app shows the run in full, with its flags, and every value you can change.