Přehled

Title: Adaptive control system for microbial cultivations

Study program: Biomedical Technology and Bioinformatics

Supervisor: doc. Mgr. Ing. Karel Sedlář, Ph.D.

Topic description:

In the last decade, several semi-automated and robotic platforms for cultivation of microorganisms have emerged. Although they are equipped with integrated sensing and control systems to enable reproducible and scalable experiments, the cultivation parameters need to be set up manually.

This PhD project focuses on expanding the sensory capabilities of small-scale bioreactor platforms, such as Chi.Bio or Pioreactor, and integrating these measurements into an automated, adaptive control system. By synthesizing real-time data with precise hardware control, the project provides a framework to optimize bacterial cultivation conditions during data-driven fed-batch or continuous mode. Ultimately, the research aims to orchestrate these cultivations through a fully cybernetic bioinformatics approach, enabling the autonomous triggering of metabolic switches to drive the production of valuable secondary metabolites.

The project will be conducted at the Department of Biomedical Engineering, with anticipated collaboration with national (Faculty of Chemistry, BUT; Masaryk University) and international partners (HES-SO Valais Wallis, Switzerland; Polytechnic University of Valencia, Spain).

Your task:

  • To develop a hardware solution for the cultivation of bacteria with a range of sensors to measure various signals.

  • To develop a unique software self-adapting intelligent technique to operate the hardware of small modular bioreactors to reveal cultivation conditions for various microbes.

  • To publish results in scientific journals and international conferences.

Requirements:

  • Master’s degree in a relevant field, e.g. microelectronics, biomedical engineering.

  • Strong programming skills, preferably Python or C++.

  • Familiarity with single-board computers and open hardware platforms.

  • Good communication skills in English.

  • A keen interest in modern biotechnology and bioinformatics.

We offer:

  • Collaboration within an active and interdisciplinary team – Bioinformatics and Systems Biology Lab (BioSys_BUT).

  • Project (Czech Science Foundation) co-funded position (financial support beyond the state scholarship).

  • Opportunities for professional development, including participation in international conferences, workshops, and specialized training.

Relevant publications:

https://doi.org/10.1021/acs.biochem.4c00149

https://doi.org/10.1016/j.crmeth.2025.101009

For more information about this topic please contact Karel Sedlar – sedlar@vut.cz.

Application portal: https://www.vut.cz/eprihlaska/

Application deadline: April 30, 2026

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