Section: Scientific Foundations
Identifying, controlling and optimizing bioprocesses
The dynamics of the microbial models possess specificities that do not allow the application of the popular methods of the theory of automatic control, such as linear control, feedback linearization or canonical forms.
 
positivity constraints. State variables, as well as control inputs, have to stay nonnegative (input flow pump cannot be reversed because of contamination issues).
 
nonlinearity. Several models have noncontrollable or nonobservable linearizations when inhibition effects are present (i.e. change of monotonicity in the growth curves).
 
model and measurement uncertainties. In biology, it is rarely relevant to consider model uncertainties as additive Gaussian or finite energy signals.
Software sensors and identification
Sensors in biology are often poor and do not provide the measurements of all the state variables of the models: substrate, strain and product concentrations. In addition, measurements are often spoilt by errors. For instance optical density measurements give an indirect measure of the biomass, influenced by abiotic factors that share the same medium.
Analytical techniques are well suited to ODE models of small dimension, such as:
 
guaranteed setmembership observers, when the system is non observable or in presence of unknown inputs,
 
(nonlinear) changes of coordinates, when the system is observable but not in a canonical form for the construction of observers with exponential convergence.
Software sensors can be also derived with the help of simulation based approaches like particle filtering techniques. This method is suited to diffusion models that approximate birth and death processes. They will allow us to investigate the different sources of randomness: demography, environment, but mainly imprecision of the sensors.
Similarly, identification techniques for constant parameters are based on sensor models as well as demography and environmental randomness models. In this case, Bayesian and nonBayesian statistical techniques can be used.
Bioprocess stabilization
In bioprocesses, the most efficient bacterial species at steady state are often inhibited by too large concentrations of substrates (this corresponds to assuming that the growth function $S\mapsto \mu \left(S\right)$ in the classical chemostat model is nonmonotonic). This implies that the washout equilibrium (i.e. disappearance of the biomass) can be attractive, making the bioprocess bistable.
A common way to globally stabilize the dynamics toward the efficient equilibrium is to manipulate the dilution rate $D$. But a diminution of the input flow rate for the stabilization requires to have enough room for an upstream storage, which is an expensive solution especially for developing countries that need to be equipped with new installations.
Alternative ways are proposed to stabilize bioprocesses without restricting the input flow rate:
 
either by physical means, in terms of recirculation and bypass loops, or membranes as a selective way to keep bacteria and their aggregates inside the tank and improve its efficiency.
 
either by biological means. The biological control consists in adding a small quantity another species with particular growth characteristics, that will help the other species to win the competition in the end.
Optimal control of bioreactors
The filling stage of bioreactors, or “fedbatch”, is often time consuming because the quantity of initial biomass is small and consequently the population growth is slow. The minimal time is a typical criterion for designing a filling strategy, but the optimal feedback synthesis is non trivial and may present singular arcs when the growth function is nonmonotonic.
Recent progress have been made in the consideration of
 
multispecies in sequential reactors (having more than one strain makes significantly more difficult to analyze singular arcs because of the higher dimensions of the state space, and there is little literature on the subject),
 
energy consumption of flow pumps and the value of byproducts of the biological reactions such as biogas in the criterion (instead of minimal time or as penalties). Recent concerns about sustainable development encourage engineers to look for compromises between those objectives under constraints on output concentrations.
Plant design and optimization
We distinguish two kind of setups:

The industrial setup. A research question, largely open today, is to identify networks of interconnections of bioreactors that are the most relevant for industrial applications in terms of the following objectives:

reasonably simple configurations (i.e. with a limited number of tanks and connections),

significant improvement of the residence time at steady state over single or simpler configurations, or shapes of the reservoirs such that the total volume required for a given desired conversion factor at steady state is reduced.


The bioremediation setup. Typically, the concentration of pollutant in a natural reservoir is solution of a transportdiffusion PDE, but the optimal control of the transport term is almost not studied in the literature.
An approach consists in finding satisfactory approximations of the solutions of transportdiffusionreaction PDE (for which the Eulerian speed of the fluid is determined by the Navier & Stokes equation), in terms of a network of ODEs, that makes effective the application of the Pontryagin Maximum Principe.