PhD Position - C++ Software Engineering 3D Cell- Tissue Simulation Framework

Organisation/Company ETH Zürich Research Field Biological sciences » Biology Computer science » Programming Computer science » Other Mathematics » Applied mathematics Researcher Profile First Stage Researcher (R1) Country Switzerland Final date to receive applications 2 Feb 2026 - 22:59 (UTC) Type of Contract Temporary Job Status Full-time Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure?

No

PhD Position - C++ Software Engineering of a 3D Cell-Based Tissue Simulation Framework

The Computational Biology (CoBi) group, led by Prof. Dagmar Iber, develops data-driven, mechanistic models of biological systems using advanced imaging and computational tools. Our group combines biology, engineering, and computational science to understand how cells organize into complex tissues. Located in Basel, the Department of Biosystems Science and Engineering (D-BSSE) provides a vibrant research environment at the interface of biology, engineering, and medicine, and is surrounded by leading pharmaceutical and biotech companies.

ETH Zurich is a world-leading university dedicated to advancing science and technology.

Project background

We are seeking a highly motivated PhD student to contribute to the further development of SimuCell3D
, a high-performance C++ framework for simulating 3D tissues of thousands deformable cells—including extracellular matrix and cavities—within a single day [Runser et al., 2024, Nat Comput Sci 4, 299–309;
Tweetorial ]. This platform allows investigation of tissue mechanics, cell polarization, and morphogenetic processes at unprecedented scale.

Your role will include:

Extending SimuCell3D with advanced numerical solvers for reaction-diffusion systems

Enhancing the biophysical capabilities of the C++ framework

Applying the framework to morphogenetic questions using real imaging data

Running large-scale simulations on ETH’s HPC infrastructure

Calibrating models, performing parameter screens, and validating predictions against experimental data

Profile

We are looking for candidates with:

Strong computational skills in C++ and software engineering

Strong background in computational science, applied mathematics, or computational biology

Ideally, familiarity with numerical methods for PDEs (e.g., finite difference, finite element)

HPC experience is a plus but not required

Interest in biophysics, developmental biology, or cell signaling (no prior experience required)

Independent, proactive, and structured work style

Master’s students interested in starting with a thesis project on this topic are also encouraged to apply.

We offer

Fully funded PhD with internationally competitive salary and comprehensive benefits, in accordance with ETH Zurich guidelines

Access to ETH’s HPC clusters and state-of-the-art research infrastructure

Supportive, interdisciplinary research environment

Working, teaching and research at ETH Zurich We value diversity and sustainability

In line with our values , ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish.

Sustainability is a core value for us – we are consistently working towards a climate-neutral future .Curious? So are we.

We look forward to receiving your online application with the following documents:

• Letter of Motivation
• CV
• Contact details of 2 referees

Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.

Further information about the group can be found on our website. Questions regarding the position should be directed to Prof Iber by e‑mail: iberd (no applications).

About ETH Zürich

ETH Zurich is one of the world’s leading universities specialising in
science and technology. We are renowned for our excellent education,
cutting‑edge fundamental research and direct transfer of new knowledge
into society. Over 30,000 people from more than 120 countries find our
university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe,
yet forging connections all over the world, we work together to
develop solutions for the global challenges of today and tomorrow.