PhD position in modeling the mechanical regulation of plant development and regeneration (1.0 FTE)

Teaser Text

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

What you will do

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. Your task will be to  further develop two-dimensional and three-dimensional models of plant development, incorporating mechanical feedback loops to regulate cellular decision making and polarization. The goal will be to unravel how plant shape and size is regulated by feedback loops between the tissue and organ levels and cellular and molecular levels. The project will further develop a two-dimensional open source package for modeling plant tissues, called Virtual Leaf, which coupled a Hamiltonian description of cell wall strains and stresses and turgor pressures with sets of ordinary differential equations describing the biochemical networks regulating cellular decision making. Models will be initiated with simulated data and 2D and 3D imaging data of plant tissues (the thale cress Arabidopsis and the aquatic fern Ceratopteris). 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 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 (https://www.mathbioleiden.nl/software.html#virtualleaf).
• 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 based on Virtual Leaf3D currently under development by a postdoctoral researcher in our team
• Publication of the results in the scientific literature and writing a PhD thesis.
• Co-teaching of relevant courses and student supervision.

Where you will work

What you bring

• Master’s degree in applied numerical 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 collaboration with 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., vertex-based or Cellular Potts modeling, particle-based simulations, PDEs, FBA);
• Suitable programming skills in C++ or a related language

What we offer

Our goal is to work together to create a transparent and inclusive work environment in which everyone feelswelcome 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. 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 contractfalls under the CLA of Dutch Universities;
• A salary between € 3204 - € 4051 gross per month, based on a full-time appointment (38 hours) (PhDstudent);
• 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 afull-time working week of 38 hours; you can also save for extra leave, for example by working 40 hours aweek, 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 employmen tindividual choices model, you can exchange leave days and/or salary for benefits such as anadvantageous 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 Application process and working conditions - Working at Leiden University - Leiden University 

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?