PhD Position in 3D Cell-Based Tissue Simulation Framework (Male/Female)

PhD Position - 3D Cell-Based Tissue Simulation Framework

100%, Basel, fixed-term

ETH Zurich is a world-leading university dedicated to advancing science and technology. The advertised position is based in the Computational Biology (CoBi) group led by Prof. Dagmar Iber, which utilizes advanced imaging and computational tools to develop data-driven, mechanistic models of biological systems. 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, surrounded by leading pharmaceutical and biotech companies.

Project Background

Understanding tissue development through experiments alone is challenging. Cell-based simulations are powerful tools to study how individual cells contribute to tissue structure and dynamics.

The Iber group has developed SimuCell3D, an efficient and scalable 3D tissue simulation framework in C++, that enables the simulation of tissues with up to 100,000 deformable cells—including extracellular matrix and cavities—within a single day (Runser et al., 2024, Nat Comput Sci 4, 299-309; Tweetorial).

SimuCell3D represents a major step forward in simulating tissue mechanics, cell polarization, and morphogenetic processes.

Job Description

We are seeking a highly motivated PhD student to further develop this framework by:

• Implementing numerical solvers for reaction-diffusion systems
• Extending the biophysical capabilities of the existing C++ codebase
• Applying the framework to morphogenetic problems using real imaging data
• Conducting large-scale simulations on ETH's HPC infrastructure
• Performing model calibration, parameter screening, and validation
• Comparing simulation outcomes with experimental data

Profile

We welcome applications from candidates with:

• A strong background in computational science, computational biology, or applied mathematics
• Documented experience in C++ programming and solid software engineering fundamentals
• Familiarity with numerical methods for solving PDEs (e.g., finite difference, finite element methods)
• Experience with HPC systems is a plus, but not required
• Interest in biophysics, developmental biology, or cell signaling (prior expertise is not required)
• A proactive, independent, and structured working style

We also welcome applications from Master's students interested in conducting their Master's thesis on this topic prior to continuing as a PhD student.

Workplace

The workplace will be at the forefront of research within a supportive and collaborative environment.

We Offer

• A fully funded PhD position with an internationally competitive salary and comprehensive benefits, in accordance with ETH Zurich guidelines
• Access to state-of-the-art research infrastructure, including ETH's high-performance computing (HPC) clusters
• A dynamic, interdisciplinary, and supportive research environment at the interface of biology, engineering, and computational science
• Flexibility for partial home office work
• Your job with impact: Become part of ETH Zurich, which not only supports your professional development, but also actively contributes to positive change in society
• We are actively committed to a sustainable and climate-neutral university
• You can expect 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

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.

Curious? So Are We.

We look forward to receiving your online application using the form below. Please include the following documents:

• Letter of Motivation
• CV
• Diplomas & Transcripts
• Contact details of 2 referees

Please note that only applications matching the job profile will be considered.

About ETH Zurich

ETH Zurich is one of the world’s leading universities specializing 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.