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

Application Deadline

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.

Job description

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

• Flexible home office arrangements

• Numerous benefits , such as public transport season tickets and car sharing, a wide range of sports offered by the ASVZ , childcare and attractive pension benefits

Working, teaching and research at ETH Zurich We value diversity and sustainabilityIn 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
• Diplomas & Transcripts
• 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@ethz.ch (no applications).

About ETH ZürichETH 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.

Website

https://academicpositions.com/ad/eth-zurich/2025/phd-position-c-software-engine…

Research Field

Biological sciences

Years of Research Experience

1 - 4

Research Field

Computer science

Years of Research Experience

1 - 4

Research Field

Computer science

Years of Research Experience

1 - 4

Research Field

Mathematics

Years of Research Experience

1 - 4

Website for additional job details

https://academicpositions.com

Number of offers available

1

Company/Institute

ETH Zürich

Country

Switzerland

City

Zurich

Postal Code

8006

Street

Rämistrasse 101

Geofield

City

Zurich

Website

https://ethz.ch/en.html

Postal Code

8006