Roeland Merks

Leiden University is offering a fully funded PhD position in the broad area of theoretical and mathematical biology, computational physics, applied mathematics, or computational science. The project sits within the GreenTE (Green Tissue Engineering) Gravitation programme, a multidisciplinary consortium of seven Dutch universities studying how plants sense and respond to mechanical stimuli. The long-term goal is to use these mechanobiology insights to support engineering interventions that improve plant regeneration, seed longevity, and disease defense. The PhD researcher will develop and analyze two-dimensional and, later, three-dimensional models of plant development with mechanical feedback loops. The work focuses on how plant shape and size emerge from interactions between tissue- and organ-scale mechanics and cellular and molecular decision making. A major component is further development of the open-source VirtualLeaf package, which combines Hamiltonian descriptions of cell wall strain/stress and turgor pressure with biochemical ordinary differential equations. The models will use simulated data as well as 2D and 3D imaging data from model plants such as Arabidopsis thaliana and Ceratopteris. At a later stage, the project may extend to 3D using VirtualLeaf3D, being developed in parallel by a postdoctoral researcher. The position is embedded in the Multiscale Mathematical Biology team at Leiden University’s Faculty of Science and the Institute of Biology Leiden, and it is also connected to the qBioLeiden quantitative biology initiative. The successful candidate will work closely with experimental collaborators across the GreenTE consortium, including the group of Prof. dr. Dolf Weijers at Wageningen University, and will interact with PhD students performing mechanical interventions such as stretching, squeezing, and poking of embryos and roots. The role includes publishing in scientific journals, writing a PhD thesis, co-teaching relevant courses, and contributing to student supervision. Leiden University seeks candidates with a master’s degree in applied numerical mathematics, computational/theoretical physics, theoretical biology, computer science, or a related field. Applicants should have strong English writing and speaking skills, good scientific writing ability, the capacity to work independently in a multidisciplinary setting, and experience in numerical mathematical modeling such as vertex-based or Cellular Potts models, particle-based simulations, PDEs, or FBA. Programming skills in C++ or a related language are expected, together with a strong interest in plant cell and developmental biology. The appointment is initially for one year and, after a positive evaluation, can be extended for another three years. The salary is €3,204 to €4,051 gross per month for a full-time 38-hour appointment, plus a holiday allowance, end-of-year bonus, pension scheme, commuting reimbursement, flexible leave, and other employment benefits. Applications received before 15 September 2026 will be given full consideration. The planned start date is fall or winter 2026, with flexibility. To apply, candidates should use the application button on the Leiden University jobs page and upload a motivation letter, updated CV, MSc transcripts, a copy or draft of the master’s thesis, contact details for one or two former supervisors, and examples of previously written code. For further information about the position, prospective applicants may contact Prof. dr. Roeland Merks at [email protected].

This PhD position at Leiden University offers an exciting opportunity to join the EU PhotoMel project, a multidisciplinary consortium focused on decoding early-life UVA and skincare additive interactions that drive melanoma risk and progression in young adults. The research will be conducted within the Faculty of Science, specifically in the Mathematical Institute and the Institute of Biology, and is embedded in the Multiscale Mathematical Biology (MMB) team and the qBioLeiden initiative. The project aims to develop and interpret novel two-dimensional multiscale mathematical models of melanoma cell migration through complex networks of extracellular matrix (ECM) fibers, with the goal of understanding how UV and chemical-induced ECM changes affect cell migration, proliferation, and gene expression. As a PhD student, you will further develop simulation techniques for modeling the mechanochemical regulation of melanoma cell migration, integrating these into frameworks such as the Tissue Simulation Toolkit and other CPM platforms. You will design simulation experiments to reflect ECM modifications due to UV and skincare additives, guided by literature, consortium data, and advanced parameter identification methods. Collaboration with a postdoc and experimental biologists, including colleagues at the Medical University of Vienna, will allow you to extend modeling insights to three dimensions and validate models against experimental data from ex vivo human skin samples and organotypic models. The position is part of a vibrant, international research environment at Leiden’s Bio Science Park, one of Europe’s largest science parks. The Faculty of Science is renowned for its diverse research activities spanning mathematics, information science, astronomy, physics, chemistry, bio-pharmaceutical sciences, biology, and environmental sciences. The Mathematical Institute is internationally oriented and focuses on key research themes such as algebra, geometry, analysis, probability, statistics, and data science. The MMB team specializes in mechanobiology and mathematical biology, working closely with experimental collaborators. Applicants should have a Master’s degree in theoretical biology, applied mathematics, computational/theoretical physics, computer science, or a related discipline. Strong English proficiency, scientific writing skills, and the ability to work independently in a multidisciplinary environment are essential. Experience in numerical mathematical modeling (e.g., Cellular Potts modeling, particle-based simulations, PDEs, FBA) and programming skills in C++ or a related language are required. The position offers a competitive salary (€3059 - €3881 gross per month), holiday allowance, end-of-year bonus, pension scheme, reimbursement of public transport commuting costs, flexible working hours, generous leave days, home-working allowance, and a university-provided laptop. Applications are accepted until July 14th, 2026. To apply, submit a letter of motivation, CV, MSc transcripts, a copy or draft of your Master’s thesis, contact details of 1 or 2 former supervisors, and examples of previously written code via the application link. The starting date is flexible, with a preferred start in Fall 2026. For further information, contact Prof. dr. Roeland Merks at [email protected].

Leiden University is advertising a PhD position in Theoretical/Mathematical Biology focused on modeling cell migration in complex extracellular matrices (ECMs) to better understand the risk of young adult skin cancer / melanoma . The project is part of the EU consortium PhotoMel (Decoding Early-Life UVA and Skincare Additive Interactions Driving Melanoma Risk and Progression in Young Adults), a multidisciplinary collaboration of European universities and partners. The research aims to decode how chemical exposures and UVA-induced damage in early childhood affect ECM remodeling, skin cell mutations, and the melanoma niche. The successful PhD candidate will develop and extend two-dimensional models of melanoma cell migration in complex 2D ECMs. The work builds on a recent hybrid Cellular Potts model (hCPM) that couples cell migration and traction with molecular dynamics models of ECM fiber networks and PDE models for growth factors and ECM-modifying enzymes. Simulated data and imaging data of skin samples will be used to initialize and validate the models, with possible extension to 3D later in the project. Relevant study areas include theoretical biology, mathematical biology, computational science, computational physics, applied mathematics, biology, physics, computer science, biomedical engineering , and related quantitative fields. The post is embedded in an open, diverse, and interdisciplinary cancer research environment, and the student is expected to participate in PhotoMel events, training, and collaborations. Enquiries can be directed to Roeland Merks at [email protected] . The post links to the Leiden University careers page for full application details.