Vacancy number: 16603
Job type: PhD positions
Contract hours min: 38
Contract hours max: 38
Location: Leiden
Applying is possible until: 14 juli 2026
The Faculty of Science, the Mathematical Institute and the Institute of Biology are looking for a PhD Student in Theoretical or Mathematical Biology (1.0 FTE)
What you will do
The opening is for a research position within the field of computational science, mathematical or theoretical biology, computational physics, or applied mathematics. This PhD project is part of the EU project PhotoMel (Decoding Early-Life UVA and Skincare Additive Interactions Driving Melanoma Risk and Progression in Young Adults), a multidisciplinary consortium of 7 European universities and partners. Together, PhotoMel aims to prevent melanoma (skin cancer) onset in young adults by decoding the impact of chemical exposures on UVA-induced damage in early childhood, including ECM remodeling and skin cell mutations that shape the melanoma niche.
Your task will be to further develop two-dimensional models of melanoma cell migration in complex 2D ECMs. The goal will be to determine how UV/chemical-induced ECM changes affect melanoma cell migration, proliferation, and gene expression. We will build upon a recent hybrid Cellular Potts model (hCPM) of cell-ECM interactions, which couples CPMs of cell migration and cell traction with a molecular dynamics model of ECM fiber networks, and a PDE model describing growth factors and ECM-modifying enzymes. Models will be initiated with simulated data and imaging data of skin samples. At a later stage, the models can be extended to three dimensions using software developed concurrently by a postdoc in our team.
The successful applicant will be an integral member of the EU PhotoMel community, which offers an open, diverse and inspiring environment to engage in multidisciplinary cancer research at the intersection of biology, medicine and physics, and is expected to participate in EU PhotoMel events, training and collaborations.
- Develop and interpret novel two-dimensional multiscale mathematical models of cell migration through complex networks of ECM fibers, in close collaboration with members of the PhotoMel consortium.
- Further develop and adapt our two-dimensional simulation techniques to make them suitable for modeling the mechanochemical regulation of melanoma cell migration, in close collaboration with members of the PhotoMel consortium.
- Integrate the new techniques into the Tissue Simulation Toolkit (https://github.com/mathbioleiden/Tissue-Simulation-Toolkit ) and/or other CPM frameworks such as Morpheus or CompuCell3D.
- Design simulation experiments to reflect and interpret ECM modifications due to exposure to UV and skincare additives, based on data obtained elsewhere in the PhotoMel consortium
- Obtain detailed insights into the effects of UV and skincare additives on melanoma progression through simulation experiments guided by literature study, interactions with other participants of PhotoMel consortium and development of advanced distance measures and parameter identification.
- Collaborate with a postdoc working in our group, also within PhotoMel to extend your two-dimensional modeling insights to three dimensions and to validate these against experimental data produced elsewhere in the consortium
- Correct and improve your mathematical models in close collaboration with experimental biologists, including colleagues at the Medical University of Vienna who will image melanoma cell migration and cell-ECM interactions in ex vivo human skin samples and organotypic models
- Publication of the results in the scientific literature and writing a PhD thesis.
What you bring
- Master’s degree in theoretical biology, applied mathematics, computational/theoretical physics, computer science or a related discipline;
- Written and oral proficiency in English, strong scientific writing skills;
- Ability to work independently in a multidisciplinary environment;
- Fluent interdisciplinary communication skills with scientists in cell biology and mathematics;
- Keen interest in cell and developmental biology of cancer;
- Experience in (numerical) mathematical modeling (e.g., Cellular Potts modeling, particle-based simulations, PDEs, FBA);
- Suitable programming skills in C++ or a related language.
Where you will work
Research at our faculty
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.
The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2.300 staff and almost 5,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together.
For more information, see www.universiteitleiden.nl/en/science and http://workingat.leiden.edu/
The Mathematical Institute (MI) is one of the eight institutes within the Faculty of Science and has a strong international orientation. The institute's mission is to push the boundaries of scientific knowledge by developing and applying high-quality mathematics while offering a wide range of mathematical programs in a friendly and intellectually stimulating environment. We believe that mathematics is a fundamental part of human knowledge, and we take pride in our role as guardians of this rich scientific discipline. We are dedicated to expanding the frontiers of mathematical knowledge and applying our expertise to solve challenges in other sciences, society, and industry. Additionally, we actively promote mathematical literacy through various outreach activities.
The Mathematical Institute focuses on four key research themes: Algebra, Geometry, and Number Theory; Analysis and Dynamical Systems; Probability; and Statistics and Data Science. There is extensive collaboration between these themes. For more information about the Mathematical Institute, see https://www.universiteitleiden.nl/en/science/mathematics.
Multiscale Mathematical Biology - The work will be embedded in the interdisciplinary Multiscale Mathematical Biology (MMB) team at the Mathematical Institute and the Institute of Biology Leiden, both at the Faculty of Science at Leiden University, and is also part of the qBioLeiden initiative that unites research in quantitative biology at Leiden University. The MMB team carries out mathematical biology research in close interaction with its own experimental work and that of collaborators. The team focuses on the mechanobiology of animals and plants. More information about the group can be found on http://www.mathbioleiden.nl
What we offer
Our goal is to work together to create a transparent and inclusive work environment in which everyone feels welcome and appreciated. Our organisation is always evolving and we need your ideas for improvement and innovation to take us further. We want to devote attention to your personal development.
You can count on an enjoyable job within the socially relevant world of education and research. The University's challenging and international work environment is located just steps away from Leiden’s lively city centre or the bustling city centre of The Hague. We also want to work with you to devote attention to your health and vitality, for example with the fun activities we organise through Healthy University.
We also offer:
- An employment contract for the duration of one year with a view to permanent employment. This contract falls under the CLA of Dutch Universities;
- A salary between €3059 - €3881 gross per month, based on a full-time appointment (38 hours) (PhD student);
- A holiday allowance (8%), an end-of-year bonus (8,3%), and an attractive pension scheme at ABP;
- Full reimbursement of public transport commuting costs for home-to-work travel;
- Flexible working hours: as a standard, you are entitled to a minimum of 29 leave days on the basis of a full-time working week of 38 hours; you can also save for extra leave, for example by working 40 hours a week, and in this way accrue an extra 96 leave hours, or exchange 96 leave hours for a 36-hour week.
- Lots of options when it comes to secondary employment conditions; within our terms of employment individual choices model, you can exchange leave days and/or salary for benefits such as an advantageous sports subscription and bicycle scheme;
- A home-working allowance (day and internet allowance) and attention for good workplaces. The University will also provide you with a laptop.
For more information about employment conditions, see https://www.universiteitleiden.nl/en/working-at/job-application-procedure-and-employment-conditions
All our PhD candidates are embedded in the Leiden University Graduate School of Science.
What we value
Promoting an inclusive community is central to Leiden University’s values and vision. We strive to be an open community in which all students and staff members feel valued and respected, and are able to fully develop themselves. We consider an inclusive academic environment, where students and staff can share their experiences and viewpoints, to be essential for the development of talent.
Want to apply or find out more?
If you want to apply straight way, click the application button.
Please ensure that you join to your application the following documents:
- A letter of motivation
- An updated CV
- The transcripts of your MSc studies
- A copy of (a draft of ) your Master’s thesis
- Contact details of 1 or 2 former supervisors
- Examples of previously written code
Applications received before July 15th, 2026 will be given full consideration.
Starting date Fall 2026, flexible.
Enquiries about the position can be made to Prof. dr. Roeland Merks, [email protected]
