## Materials and Methods
### Control System
#### 2.2.2 Control System Realisation  
The adaptive control system for the batch bioreactor was developed based on the presented AMFC. To obtain high-quality milk products, the quantities of the fermentation process (concentrations of microorganisms, substrate, and product, temperature, etc.) must follow the prescribed reference values. One of the quantities which correlates well with all the important fermentation process quantities is CO\({}_{2}\) release. This means that it is possible to assure proper trajectories of the fermentation process quantities by means of the control system, which will assure the proper dynamic profile of the CO\({}_{2}\) release. A variable speed stirrer drive was used to assure the prescribed dynamic profile of the CO\({}_{2}\) release. The described enhanced mathematical model of the fermentation process in the bioreactor presented was used to determine the order of the reference model and the dimension of the adaptation mechanism. The reference trajectories (reference model) of the bioreactor's quantities were obtained empirically in such a way that the fermentation would be completed in a shorter time, that the final value of the product would be as high as possible, and that there would be no excessive and sudden changes in the growth of microorganisms during fermentation. The goal of the adaptive control system is to assure the prescribed dynamics of the quantities in the bioreactor in the case of an unknown batch bioreactor, various substrates, microorganisms, and disturbances.  
The developed concept presented requires the bioreactor to be equipped with a variable speed stirrer's drive and a measurement gauge for dissolved CO\({}_{2}\) concentration. The mentioned stirrer's system is capable of altering and maintaining a specified mixing speed in the bioreactor. The majority of contemporary commercial applications of batch bioreactors include the required components, or they are available as accessories. A control module, which would perform the developed control, is conceptualised as an external component (PLC, PC with an added AD/DA periphery, or a dedicated controller). In the case of realisation using the external controller, an application with signal transfer between a controlled plant (i.e., a batch bioreactor with the stirrer's system and the measurement gauge) and the controller is evidently necessary. An overview of the market was carried out by contacting representatives of producers, such as Metler Toledo. Existing commercial applications of batch bioreactors enable simple analogue signal transfer, with information on dissolved CO\({}_{2}\) concentration from the measurement gauge into the external controller (analogue input is necessary). Unfortunately, the existing stirrer's systems are not customised for setting up a reference value from the external controller. With existing commercial applications of batch bioreactors, a more comprehensive adaptation or upgrade of input-output interfaces is necessary (as was carried out in our case).  
A second option is the realisation of a control algorithm within the programme equipment of a batch controller. This option is far less expensive and simpler than the first one, though the second option requires a flexible enough program interface on the batch bioreactor, which would be suitable for the implementation of the adaptive controller.