One of the major challenges mankind faces nowadays is combating climate change. A substantial fraction of greenhouse gases are released by industrial processes, as steelmaking, (oil)refinery and waste processing. Emissions from these processes can partly be prevented with a recently developed technology called gas fermentation. Within this process, synthesis gas – amixture containing CO, CO2 and H2 – is converted into ethanol and acetic acid by bacteria such as Clostridium autoethanogenum. These products could be used in a wide range of applications, like fuels, plastics and cosmetics. Whilst gas fermentation is already applied at commercial-scale, challenges in scale-up persists due to complex multi-scale interactions among the bioreactor, gas bubbles, and bacteria. The poor solubility of CO and H2 alongside gas bubble coalescence, leads to low gas-to-liquid mass transfer rates (typically denoted via kLa). Slow mixing in industrial bioreactors (500m3), and high gas conversion rates, result in large spatial variations in dissolved gas concentrations. Bacteria experiencing concentration fluctuations have often been related to decreased process performance... ... Read more

Bioprocesses exploit the versatility of microorganisms to produce bio-products from renewable feedstocks. However, industrial-scale implementation often suffers from the “scale-up effect,” manifesting as reduced yield or productivity due to environmental heterogeneity in large bioreactors. This thesis presents a model-based approach to quantitatively reproduce these heterogeneous conditions and predict their impact on microbial performance.

For Penicillium chrysogenum, a 9-pool metabolically structured kinetic model was developed and integrated with an Euler-Lagrange computational fluid dynamics (CFD) simulation of a 54 m³ industrial bioreactor. This coupled model captured glucose gradients, penicillin productivity loss, and enabled the design of scale-down systems to mitigate mixing limitations, achieving predicted reductions of productivity loss by up to 50%.

For Saccharomyces cerevisiae, a 7-pool kinetic model was extended to include glucose uptake mechanisms, storage carbohydrate dynamics, and ethanol/glycerol re-consumption. The model reproduced Crabtree and Pasteur effects and demonstrated stability under highly dynamic pilot-scale conditions. The updated model provides a compact yet predictive framework for full-scale CFD integration.

Finally, this work outlines the foundation for implementing the digital twin concept in bioprocessing, emphasizing model simplification, fitness-for-purpose, and integration with real-time simulation for smart biomanufacturing. The results demonstrate the potential of combined kinetic-CFD models to optimize industrial fermentations, predict scale-up effects, and guide future bioprocess development. ... Read more

Renewable energy plays a key role in the fight to reduce greenhouse gas emissions while providing for human well-being and economic development. However, despite environmental benefits in terms of carbon sequestration, largely promoted biorenewable resources such as sugarcane and corn starch, so-called 1st generation (1G) feedstocks, are associated with other types of social and environmental issues that highly contradict the notion of sustainability, such as the food versus fuel conflict and the contribution to impacts such as deforestation, soil degradation, loss of biodiversity and contamination of water resources. As reaction to these issues, a lot of effort has been put into the development of technologies to extract and convert useful energy from non-food crops and agro-industrial residues, such as sugarcane bagasse, corn stover, and wheat straw. These now called 2nd generation (2G) feedstocks offer an extra challenge since fermentable sugars are not readily available; nonetheless, myriad technologies have been (and are being) developed to convert 2G materials into fuels and chemicals, with perhaps the most representative product being ethanol, a widely employed engine fuel and gasoline additive. 2G or cellulosic ethanol can be produced via biochemical pathways, thermochemical pathways, or a third option that combines aspects of the other two, commonly called the thermo-biochemical, or hybrid, pathway. The latter is the focus of this thesis, which explores this pathway via process modeling, simulations, (multi-objective) optimization, and other strategies applied in order to determine which process choices and conditions lead to the best performance in terms of main sustainability aspects. While the thermochemical process of gasification enables the nearly full conversion of biomass without the need for complex and expensive stages of pretreatment and hydrolysis, the subsequent biological conversion (fermentation) of syngas might offer several advantages when compared to the traditional catalytic conversion, e.g. higher flexibility of H2:CO ratios and tolerance to gas contaminants . Although certain challenges may drawback the commercial competitiveness of syngas fermentation, such as the low productivity when compared to heterotrophic fermentation, intelligent choices of process integration and design parameters could substantially enhance the performance of the process. ... Read more

The broth in industrial scale fermentors may contain significant gradients in, for example, substrate concentration, dissolved oxygen and shear rates. From the perspective of microbes in this fermentor, these gradients translate to temporal variations in their environment that may affect their metabolic response. As a result, there may be differences in process yield between laboratory scale fermentations and their industrial counterpart. Rather than scaling-up bioprocesses based on equivalence, it is recommended to scale-down: mimic the large-scale environment in lab scale setups, to account for hydrodynamic-metabolic interaction from the start. In this thesis, the use of Euler-Lagrange computational fluid dynamics to capture the large-scale fermentation environment is explored. Lagrangian simulations offer to study processes from the microbial perspective (so-called “lifelines”), and enable coupling of metabolic models describing the response to external variations. With this, it is possible to take the history of the trajectory of the microbe into account, as organisms may not adapt to their surroundings instantaneously. Guidelines for the setup of fermentor simulations are presented, and several means for processing the lifelines are discussed. The obtained information is used to design lab-scale fermentations that mimic large-scale conditions. It is furthermore shown how coupled hydrodynamic-metabolic simulations can be used to predict yield-loss, assess process improvements, and study the onset of population heterogeneity in large-scale fermentors. Additionally, a more fundamental towards the role of the turbulent Schmidt number in multi-impeller mixing is included. ... Read more