The Faculty of Science, the Mathematical Institute and the Institute of Biology are looking for a PhD Student in Mathematical Biology

PhD: Modeling the mechanical regulation of plant development and regeneration (1.0 FTE)

Description of the project
The opening is for a research position within the field of mathematical or theoretical biology, computational physics, applied mathematics or computational science. This PhD project is part of the Gravitation programme GreenTE (Green Tissue Engineering), a multidisciplinary consortium of 7 Dutch universities. Together, GreenTE will unravel how plants sense and respond to mechanical stimuli. These fundamental insights will be the basis to develop engineering interventions to improve plant regeneration, seed longevity and defenses against disease. The successful applicant will be an integral member of the GreenTE community, which offers an open, diverse and inspiring environment to engage in multidisciplinary mechanobiology research at the intersection of biology, chemistry and physics, and is expected to participate in GreenTE events, training and collaborations.

Key responsibilities

• Develop and interpret novel two-dimensional multiscale mathematical models of mechanical regulation of plant development and regeneration in close collaboration with members of the GreenTE consortium, in particular the group of experimental plant biologist Prof. dr. Dolf Weijers at Wageningen University.
• Further develop the plant modeling package VirtualLeaf to reflect mechanical manipulation as performed in the experimental lab.
• Incorporate detailed insights into the model of the mechanical properties of cell walls based on experiments and small-scale simulations developed elsewhere in the GreenTE consortium.
• Correct and improve your mathematical models in close collaboration with experimental biologists, particularly PhD students at Wageningen University who will perform mechanical interventions (e.g., stretching, squeezing or poking) of embryo development and root regeneration of the model plant Arabidopsis thaliana.
• At a later stage: extend the models to three dimensions in close collaboration with a postdoc in computational science in our team.

Selection Criteria

• Master’s 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 cell and developmental biology of plants;
• Experience in (numerical) mathematical modeling (e.g., Cellular Potts modeling, particle-based simulations, PDEs, FBA);
• Suitable programming skills in C++ or a related language.

Multiscale Mathematical Biology - The work will be embedded in the Multiscale Mathematical Biology team at the Mathematical Institute and the Institute of Biology Leiden, both at the Faculty of Science at Leiden University. The team carries out mathematical biology research in close interaction with its own experimental work and that of collaborators. The team focuses on cardiovascular development and bacterial ecosystems. More information about the group can be found on mathbioleiden .

LEIDEN UNIVERSITY

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 contribute 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 2,500 staff and almost 6,000 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 Faculty of Science and Working at Leiden University

Terms and conditions

• We offer a full-time appointment of initially one year. After a positive evaluation of the progress of the research, teaching evaluations, personal capabilities and compatibility, the appointment will be extended for another three years.
• The gross salary ranges from € 2.770,- per month in the first year to € 3.539,- gross per month in the fourth year based on a full-time position (pay scale P).
• Additional funding is available to support travel to conferences and workshops abroad.
• Leiden University offers an attractive benefits package including pension build-up, paid parental leave and additional holiday (8%) and end-of-year bonuses (8.3%). Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break. For more information, see our website: Working at Leiden University, Application process and working conditions

All our PhD candidates are embedded in the Leiden University Graduate School of Science.

Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Information
Enquiries about the position can be made to Prof.dr. Roeland Merks, merksrmh@math.leidenuniv.nl

Starting date
1 November 2024, flexible.

Applications
To apply for this vacancy, please ensure that you join to your application the following additional documents:

• A letter of motivation
• An updated CV
• Letters of recommendation or contact details of 1 or 2 former supervisors
• The transcripts of your MSc studies
• Examples of previously written code

Only applications received before 9 September 2024 will be considered.