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

ETH Zürich • Basel • vor 2Tg

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

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