Postdoc: 3D simulation models of cell migration to decode the risk for young adult skin cancer

The Faculty of Science, the Mathematical Institute and the Institute of Biology of Leiden University are looking for a Postdoctoral Researcher in Computational Science or Mathematical Biology (1.0 FTE for three years)

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 postdoc 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 remodelling and skin cell mutations that shape the melanoma niche. Your task will be to develop a three-dimensional (3D) model of melanoma cell migration in complex 3D 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 3D extension of a hybrid Cellular Potts model (hCPM) of cell-ECM interaction, 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 3D imaging data of skin samples.

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.

Key responsibilities 

• Develop novel, three-dimensional simulation techniques 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 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 PhD student working in our group, also within PhotoMel to extend existing two-dimensional models of cell migration in complex environments to three dimensions and to validate these against experimental data produced elsewhere in the consortium
• Publication of the results in the scientific literature.

What you bring

• PhD degree in applied mathematics, computational/theoretical physics, theoretical biology, 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 the cell and developmental biology of cancer
• Experience in (numerical) mathematical modeling (e.g., Cellular Potts modeling, vertex-based modeling, particle-based simulations, PDEs);
• Great skills and enthusiasm for scientific programming in C++, Cuda and/or Python.