PhD position Computational Modelling and Digital Twins

PhD position Computational Modelling and Digital Twins

Published Deadline Location
1 Dec 17 Dec Wageningen

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Job description

Are you a highly motivated researcher and enthusiastic about key enabling technologies for the circular bioeconomy? Are you interested in the industrial aspects and applications of biotechnology as well as the prospect of an interdisciplinary project on biomanufacturing? If you feel excited about microbial fermentations and advanced digital technologies, we would like to invite you to apply for this exciting, computational PhD position within our team!

The offered PhD position will be part of the EU-funded projects “BIOS” and “Bioindustry 4.0”, which aim to develop research infrastructures services to promote deep digitalization of Industrial Biotechnology in our way towards smart biomanufacturing. These services include: a data fabric, digital twins for bioprocess design, strain discovery tools and decision support systems, advanced process analytical technology devices, and digital twins for bioprocess control.

Your responsibilities as a PhD candidate encompass the following key tasks:
  • creating a Digital Twin that replicates cellular processes and bioproduction mechanisms by harmonizing artificial intelligence (AI) with empirical data;
  • develop, expand and adapt genome scale models of metabolism using empirical data;
  • mine biological resources and combine them with existing data for pathway discovery.

These models will be constructed using empirical data obtained from the 'wet' research team, including bioprospecting and pathway discovery efforts. Your contributions will deepen our understanding of metabolic processes and their practical applications within biomanufacturing contexts. In this collaborative environment, you will work closely with other experimental PhDs who will provide you with valuable bioreactor data to inform and validate your computational models.

We are looking for a PhD candidate who is keen to perform state-of-the-art, original, and collaborative research in the aforementioned project. The candidate is expected to publish the research findings in leading international academic journals, but must also communicate well across disciplines, project partners and stakeholders. The candidate will also be involved in the supervision of MSc and BSc students who perform their thesis research within the framework of the project.

The research is embedded within two chair groups: Bioprocess Engineering, and more specifically, the Biomanufacturing and Digital Twins team, which is led by Prof. Dr. Vitor Martins dos Santos ( ; Systems & Synthetic Biology, led by Prof. Dr. Maria Suarez Diez.


Wageningen University & Research


  • a successfully completed MSc degree in Bioinformatics, Computational Biology, Computational Chemical Engineering, Industrial Biotechnology, or a relevant field;
  • proficiency in computational modeling, with experience in Python and R;
  • knowledge of advanced statistics and machine learning methods;
  • familiar with query languages such as SPARQL is a plus;
  • familiar with dynamic or constraint-based metabolic modeling is a plus.

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognized Certificate of Proficiency in the English Language. More information can be found here.

Conditions of employment

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:
  • sabbatical leave, study leave, and partially paid parental leave;
  • working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
  • the option to accrue additional compensation / holiday hours by working more, up to 40 hours per week;
  • there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
  • a fixed December bonus of 8.3%;
  • excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.

The gross salary for the first year is € 2.770 ,– per month rising to € 3.539,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We offer a unique position in an international environment with a pleasant and open working atmosphere.

You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 18th consecutive time.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.

Feeling welcome also has everything to do with being well informed. Wageningen University & Research's International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about helping your partner to find a job, housing, schooling. For instance under the "30% rule", certain categories of international staff can receive tax exemption on approximately 30% of their gross salary.


Wageningen University & Research

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,200 employees (6,400 fte) and 13,200 students and over 150.000 participants to WUR’s Lifelong Learning, Wageningen University & Research is one of the leading organisation in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.

You will work here
Research in the ‘Biomanufacturing and Digital Twins’ team led by Prof. Vitor A. P. Martins dos Santos focuses on the exploration, development, and implementation of pioneering technologies in biotechnology to facilitate bio-based production, spanning a wide range of biomanufacturing, from bioplastics, chemical to pharmaceuticals. The Biomanufacturing and Digital Twins group is embedded in the Laboratory of Bioprocess Engineering, an international, multidisciplinary, and vibrant research group at Wageningen University.

Read 5 reasons why your future colleagues enjoy working at WUR and watch this video to get an idea of our green campus!

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.


  • PhD
  • Engineering
  • max. 38 hours per week
  • University graduate
  • P1361811-7


Wageningen University & Research

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Droevendaalsesteeg, 6708 PB, Wageningen

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