PhD Position - C++ Software Engineering of a 3D Cell-Based Tissue Simulation Framework
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PhD Position - C++ Software Engineering of a 3D Cell-Based Tissue Simulation Framework
100%, Basel, fixed-term
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:
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Extending SimuCell3D with advanced numerical solvers for reaction-diffusion systems
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Enhancing the biophysical capabilities of the C++ framework
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Applying the framework to morphogenetic questions using real imaging data
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Running large-scale simulations on ETH’s HPC infrastructure
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Calibrating models, performing parameter screens, and validating predictions against experimental data
Profile
We are looking for candidates with:
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Strong computational skills in C++ and software engineering
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Strong background in computational science, applied mathematics, or computational biology
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Ideally, familiarity with numerical methods for PDEs (e.g., finite difference, finite element)
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HPC experience is a plus but not required
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Interest in biophysics, developmental biology, or cell signaling (no prior experience required)
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Independent, proactive, and structured work style
Master’s students interested in starting with a thesis project on this topic are also encouraged to apply.
Workplace
Workplace
We offer
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Fully funded PhD with internationally competitive salary and comprehensive benefits, in accordance with ETH Zurich guidelines
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Access to ETH’s HPC clusters and state-of-the-art research infrastructure
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Supportive, interdisciplinary research environment
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Flexible home office arrangements
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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
We value diversity and sustainability
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).