Recirculating bioreactors accumulate extracellular DNA. The cells lyse, release their genetic material into the medium, and the recirculation loop brings it back past the growing culture. The DNA isn't inert — it inhibits microbial growth, reducing productivity as it accumulates. The bioreactor's own waste product throttles its output.
The solution couples an electrophoretic filtration unit to the recirculation loop with model predictive control. An unscented Kalman filter estimates the real-time DNA concentration from indirect measurements. The MPC jointly optimizes two decisions: how fast to dilute the culture (adding fresh medium, washing out product and DNA together) and when to activate the electrophoretic filter (selectively removing DNA without removing product).
The joint optimization matters because the two controls interfere. Faster dilution removes DNA but also removes product and cells. More filtration removes DNA selectively but consumes energy and reduces flow rate. The MPC navigates this tradeoff by predicting the effect of each action over a rolling horizon, keeping DNA below the inhibition threshold while maximizing cumulative profit.
A simpler bang-bang controller — turn the filter on when DNA is high, off when DNA is low, with a lookup table for dilution rate — works but leaves money on the table. The MPC outperforms it under both normal and perturbed conditions because the predictive horizon lets it anticipate DNA buildup before it becomes inhibitory, activating the filter early at lower energy cost.
The bioreactor doesn't fail from lack of nutrients. It fails from accumulation of its own debris.