Fully Funded PhD Position in Mathematical Biology; Regulation of Plant Development and Regeneration at Leiden University, Netherlands

Vacancy Overview

• Vacancy Number: 16814
• Position: PhD Candidate (Theoretical or Mathematical Biology)
• Institution: Leiden University, Faculty of Science (Mathematical Institute & Institute of Biology Leiden)
• Consortium: GreenTE (Green Tissue Engineering)
• Contract: 1.0 FTE (38 hours/week), 1 year initial extending to 4 years total upon positive review
• Salary Range: €3,204 to €4,051 gross per month (under CLA of Dutch Universities)
• Location: Leiden, Netherlands
• Application Deadline: September 15, 2026
• Target Start Date: Fall or Winter 2026 (flexible)

The Faculty of Science at Leiden University, jointly via the Mathematical Institute and the Institute of Biology, is recruiting a full-time PhD candidate in theoretical biology, computational physics, or applied mathematics.

This research project forms an essential computational pillar within GreenTE (Green Tissue Engineering), a national Gravitation programme uniting seven Dutch universities. The consortium investigates how plant tissues sense, process, and react to physical forces. By decoding these biomechanical mechanisms, GreenTE aims to establish foundational principles for improving tissue regeneration, seed viability, and disease resistance in agricultural settings.

Research Focus and Computational Framework

Plant morphogenesis depends on continuous mechanical feedback loops operating across molecular, cellular, and organ-level scales. As a PhD candidate in this position, your primary focus will be designing, running, and refining two-dimensional and three-dimensional computational models to isolate how mechanical stresses guide cell polarization and fate choices.

Key Research Objectives:

• VirtualLeaf Enhancement: Extend the open-source C++ computational simulation framework VirtualLeaf, which integrates Hamiltonian physics for cell wall strain/stress and turgor pressure with systems of ordinary differential equations (ODEs) modeling internal biochemical networks.
• Experimental Data Integration: Initialize and validate simulation models using quantitative 2D/3D microscopy imaging data from Arabidopsis thaliana (thale cress) and Ceratopteris (aquatic fern).
• Consortium Collaboration: Work directly with experimental plant biologists—notably the laboratory of Prof. dr. Dolf Weijers at Wageningen University—to simulate real-world biomechanical manipulations such as cell stretching, compression, and mechanical poking during embryonic growth and root regeneration.
• 3D Framework Scaling: Transition existing 2D models into complete three-dimensional representations by leveraging VirtualLeaf3D, currently under development by team postdoctoral researchers.

Academic Environment

The candidate will be embedded directly in the interdisciplinary Multiscale Mathematical Biology (MMB) group, jointly situated within the Mathematical Institute and the Institute of Biology Leiden. The MMB group operates as part of qBioLeiden, an initiative unifying quantitative biological inquiry across Leiden University.

Research is conducted at the Leiden Bio Science Park, one of Europe’s leading scientific innovation clusters. Candidates will also be enrolled in the Leiden University Graduate School of Science, which offers systematic doctoral coursework and professional development monitoring.

Candidate Qualifications

Applicants are evaluated based on their strong quantitative background paired with a genuine curiosity for plant developmental systems.

Required Qualifications:

• Master’s degree in applied numerical mathematics, computational/theoretical physics, theoretical biology, computer science, or a closely aligned discipline.
• Proven background in numerical mathematical modeling methodologies (e.g., vertex-based modeling, Cellular Potts models, particle-based methods, partial differential equations, or flux balance analysis).
• High proficiency in C++ or a related object-oriented programming language.
• High oral and written communication skills in English, alongside the ability to communicate across mathematical and biological domains.

Salary, Benefits, and Employment Terms

The position is offered under the Collective Labour Agreement (CLA) of Dutch Universities.

Benefit Component	Details
Gross Monthly Salary	€3,204 (Year 1) rising to €4,051 (Year 4) for 38 FTE hours/week
Annual Allowances	8% Holiday allowance + 8.3% End-of-year bonus
Contract Duration	1 year initial contract, extended to 4 years total upon successful evaluation
Paid Leave Allowance	Minimum 29 days per year (option to accrue up to 96 extra hours by working 40h/week)
Pension & Transport	ABP Pension scheme; full coverage for public transport commuting expenses
Flexible Working Support	Provided laptop, home-working allowance, and individual choices model (sports/bicycle options)

Application Instructions

If you want to apply straight away, click the application button. To ensure full consideration, submit all required documentation by September 15, 2026. Apply now

Required Application Documents:

1. A detailed motivation letter detailing your research interests.
2. Complete academic CV.
3. MSc study transcripts (academic records).
4. A copy or draft version of your Master’s thesis.
5. Contact information for 1 or 2 academic references.
6. Representative code samples demonstrating programming experience.
7. Apply now

Direct informal inquiries regarding project scope to Prof. dr. Roeland Merks via merksrmh@math.leidenuniv.nl

Frequently Asked Questions

What is the core focus of the GreenTE PhD project?

The project focuses on building multiscale computational models to study mechanical force regulation in plant cells and tissues, utilizing and extending the VirtualLeaf software package to understand plant growth, regeneration, and structural development.

Can international students apply for this PhD position?

Yes. Leiden University hosts an international scientific community. The position requires strong oral and written English proficiency, but knowledge of the Dutch language is not a prerequisite.

What programming experience is needed for this role?

Applicants should possess solid object-oriented programming skills, specifically in C++ or closely related languages, along with experience using mathematical or numerical modeling techniques (such as PDEs, vertex models, or particle simulations).

How long is the doctoral contract?

The appointment starts with an initial 1-year contract. Upon a positive progress evaluation assessing research viability and mutual compatibility, the contract is extended for an additional 3 years (4 years total).