MSCA-DN-FAIROmics: Multiscale Modelling for Risk-averse Optimisation and Control of Plant-based Fermented Food Production

The vision of BioTeC+ (Chemical & Biochemical Process Technology & Control) (PI Prof. Jan F.M. Van Impe) is to consolidate and strengthen both its international research position and its societal impact by focusing on a carefully selected number of research areas and application domains in applied chemistry/chemical and biological process engineering.

At present, these application domains can be characterized by the keywords industrial biotechnology, closing the waste/water cycle, and public health. These constitute the pillars (columns) (bio)chemical reactions & reactors, (biological) waste(-water) treatment systems, and predictive microbiology/microbial risk assessment within BioTeC’s research matrix. This broad range of application domains is supported by our long standing systemic (systems and control) approach towards applied chemistry/chemical and biological process engineering. The research areas (i) systems theory, systems biology and analysis, process model identification (including optimal experimental design), (ii) process monitoring, and (iii) optimization and model based control characterize the transversal rows in the research matrix. These rows constitute the longstanding fundament of BioTeC’s research covering and underpinning all application domains (pillars).

KU Leuven/BioTeC+ runs a state-of-the-art L2 accredited laboratory for experimental predictive microbiology research, as well as highend computing facilities. Our 5 postdocs and 14 PhD researchers are involved in numerous international research projects and networks, including 6 ongoing EU projects. As a most international and inclusive team, we look forward to welcome you on our campus in the vibrant city of Gent, Belgium!

During the course of this Joint Doctorate, the candidate will spend 12 months at the I²SysBio Institute of the Spanish National Research Council CSIC. CSIC (Agencia Estatal Consejo Superior de Investigaciones Científicas) is an autonomous, multi-disciplinary public research body affiliated to the Spanish Ministry of Science and Innovation. CSIC has its own legal structure and is represented throughout the Spanish territory with a total of 105 centres/institutes. CSIC is the first Spanish organisation in the Framework Program of the European Union by number of projects and economic return. I²SysBio (PI Dr. Irene Otero-Muras) is a joint research institute involving Universitat de València (UV) and CSIC. I²SysBio Scientific Programs focus on research into the structure, function, dynamics, evolution, and manipulation of complex biological systems. Specifically, at CSIC-I2SysBio, the DC will benefit from the expertise in advanced mathematical analysis and control of biomolecular systems (including regulation, signalling and metabolism).

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Project

HORIZON-MSCA-DN Doctoral Network FAIROmics - FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods.

Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterized. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases, but not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims at developing doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities and social sciences.

• Doctoral Candidate DC8 to be recruited by KU Leuven/BioTeC+ will integrate genome scale metabolic network models developed within FAIROmics in a macroscopic structure using multiscale approaches. The flux balance analysis approach will be exploited to determine the free fluxes in the metabolic network. A main challenge in this context is the choice of the objective function. 
• The multiscale model will then be used in a model predictive control (MPC) framework to optimise the fermentation process. To ensure feasibility, the model will be reduced using biology driven state of the art tools. 
• Furthermore, the biological variability will be incorporated using a risk-averse MPC framework. Risk measures allow the use of partial information of probability distributions on uncertain variables in the control framework. 
• Incorporation of FBA in an MPC framework leads to a bilevel optimisation problem whose solution is not trivial. Thus, numerical methods to efficiently solve the MPC formulation will be developed.
• Analysis, control and optimization methods will be developed starting with available models and incorporating new knowledge as it is generated within FAIROmics.

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We are seeking highly motivated candidates that hold a master in Mathematical/Chemical/Control/Biological/Computer/... Engineering related subjects such as (Bio-)Process Modeling, Systems (Micro-)biology, and Applied Mathematics. 

Offer

• 3 years financial support to pursue a PhD (including Living, Mobility and Family Allowance according to HORIZON-MSCA-DN regulations) and many more benefits at KU Leuven;
• Being part of the dynamic KU Leuven/BioTeC+ research group (5 postdocs and about 14 PhD researchers), headed by Prof. Jan F.M. Van Impe; 
• Living in the beautiful and vibrant city of Gent, situated in the heart of Europe; 
• HORIZON-MSCA-DN FAIROmics doctoral network of 15 PhD students offering a unique environment for international academic/industrial collaboration;
• Secondment of 12 months at CSIC-I2SysBio (PI Dr. Irene Otero-Muras), Valencia, Spain; 
• Please note that this PhD position will lead to the award of a double diploma: KU Leuven/Arenberg Doctoral School for KU Leuven/BioTeC+ and UPV (Universitat Politècnica de València) for CSIC-I2SysBio.

HORIZON-MSCA-DN FAIROmics project
KU Leuven/BioTeC+
CSIC-I2SysBio

Interested?

For more information please contact Prof. dr. ir. Jan Van Impe, tel.: +32 477 256 172, mail: jan.vanimpe@kuleuven.be or Mrs. Monika Polanska, tel.: +32 9 310 27 39, mail: monika.polanska@kuleuven.be.

KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace diversity among individuals and groups as an asset. Open dialogue and differences in perspective are essential for an ambitious research and educational environment. In our commitment to equal opportunity, we recognize the consequences of historical inequalities. We do not accept any form of discrimination based on, but not limited to, gender identity and expression, sexual orientation, age, ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence, employment disability, health, or socioeconomic status. For questions about accessibility or support offered, we are happy to assist you at this email address.