Drybench Bioreactor product page
Drybench Bioreactor.
Chemostat washout simulator
An E. coli chemostat at a dilution rate you choose: the steady state, washout as D approaches the maximum growth rate, and the oxygen the culture needs.
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
- 38.3% air saturation
- Biomass at 24 h
- 3.79g/L
- Peak OUR
- 44.3mmol/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 | 3.79 | 0.0000255 | 1.75 | |
| 0.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 1.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 3.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 3.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 4.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 6.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 6.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 7.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 9.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 9.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 10.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 12.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 12.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 13.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 15.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 15.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 16.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 18.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 18.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 19.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 21.00 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 21.96 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 22.92 | 38.3 | 3.79 | 0.0000256 | 1.75 | |
| 24.00 | 38.3 | 3.79 | 0.0000256 | 1.75 |
Where this run leaves the model
This run stays inside the model and the correlations' ranges.
Every value and where it comes from
| Parameter | Value | Source |
|---|---|---|
| Maximum specific growth rate, μmax | 0.61 per hour | CitedHaverkorn van Rijsewijk et al. 2011Table 1: 0.61 ± 0.01 per hour, wild-type BW25113 in batch on glucose (M9, 37 °C)Reported range 0.54 to 1.23 per hour (Kovárová-Kovar and Egli 1998, Table 2, the 37 °C rows; strains and methods at 37 °C on glucose) |
| Substrate affinity, Ks | 0.000033 g/L | CitedKovárová et al. 1996, as quoted by Kovárová-Kovar and Egli 1998abstract: about 33 µg/L at every temperature from 17.4 to 40 °C (ML30, glucose-limited chemostats)Reported range 0.000033 to 0.00716 g/L (Kovárová-Kovar and Egli 1998, Table 2, the 37 °C rows; strains and methods at 37 °C on glucose) |
| Substrate inhibition, Ki | none | Model choiceMonod: no substrate inhibition |
| True yield of biomass on substrate, Y | 0.422 g/g | Cited, convertedNanchen et al. 2006Table 1: MG1655, glucose-limited chemostats, 37 °C; 76 ± 3 g dry weight per mol glucose ÷ 180.156 g/molReported range 0.422 to 0.572 g/g (Nanchen et al. 2006, Table 1; the strains listed there, 76 to 103 g/mol) |
| Maintenance, ms | 0.0667 g/g/h | Cited, convertedNanchen et al. 2006Table 1: MG1655, glucose-limited chemostats, 37 °C; 0.37 ± 0.09 mmol glucose/g/h × 0.180156 g/mmolReported range 0.0198 to 0.0685 g/g/h (Nanchen et al. 2006, Table 1; the strains listed there, 0.11 to 0.38 mmol/g/h) |
| Oxygen affinity, Ko | 0.00387 mg/L | Cited, convertedStolper et al. 2010Results: Ks for growth 121 ± 20 nM O₂ (K-12, on glycerol, 37 °C); 121 nM × 31.998 g/molReported range 0.000096 to 0.0064 mg/L (Stolper et al. 2010, Discussion; 3 to 200 nM, the Km of the cytochrome bd and bo oxidases quoted there) |
| Substrate | glucose | Setting |
| Biomass carbon fraction | 0.4738 g C per g dry weight | CitedFolsom and Carlson 2015Table 2: glucose-limited chemostats, D 0.1 to 0.4 per hour, mean 47.38 ± 0.74 percent (MG1655)Reported range 0.4706 to 0.4769 g C per g dry weight (Folsom and Carlson 2015, Table 2; the four glucose-limited dilution rates) |
| Biomass degree of reduction, γX | 4.17 per C-mol | Cited, convertedFolsom and Carlson 2015Table 2: glucose-limited chemostats, mean formula CH1.725N0.23O0.4325; 4 + H − 2·O − 3·N, ammonium the nitrogen source (the table's own degree of reduction, 4.86, counts nitrogen at oxidation state 0)Reported range 4.14 to 4.2 per C-mol (Folsom and Carlson 2015, Table 2; the four glucose-limited dilution rates' formulas) |
| 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 | 3.793 g/L | Derivedthe steady state at D 0.25 per hour: X* = D·(Sf − S*)/(D/Y + ms), oxygen not limiting |
| Starting substrate, S0 | 0.0000255 g/L | Derivedthe steady state at D 0.25 per hour: S* = Ks·(D + Y·ms)/(μmax − D), oxygen not limiting |
| Starting volume, V0 | 7 L | Setting |
| Mode | chemostat | Setting |
| Substrate in the feed, Sf | 10 g/L | Setting |
| Dilution rate, D | 0.25 per hour | Setting |
| Temperature | 37 °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 10⁻⁹ and electrons within 10⁻⁹ 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 chemostat@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.