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PhD Position: 3D cell-based tissue simulation framework 100%, Basel, fixed-termprint Drucken
We develop data-driven, predictive models of biological signaling networks with a view to gain a comprehensive understanding of the dynamics and evolution of cellular signaling.
Project backgroundThe experimental characterization of developing tissues is often difficult. Cell-based simulations have long been used to study the contribution of single cells to the overall architecture and dynamic behavior of tissues. However, computational studies have long been limited by the level of detail that can be represented. The Iber group has recently developed a highly efficient 3D cell-based simulation framework that allows for the fast and efficient simulation of large tissues at an unprecedented resolution 1. Tissues can be grown from a single cell to a tissue with 100'000 cells within a week. The tissue simulation framework also represents cavities and extracellular matrix, and cells can freely deform and detach such that complex developmental processes can also be represented and simulated.
1 Runser, S., Vetter, R. and Iber, D. (2023). 3D Simulation of Tissue Mechanics with Cell Polarization. bioRxiv; Tweetorial.
Job descriptionWe are looking for a PhD student with a strong background in computational science, computational biology or applied mathematics to extend a recently developed C++- based cell-based tissue simulation framework to represent further biophysical features, and to include a numerical solver for reaction- diffusion equations. You will integrate available image processing and meshing algorithms to create an integrated framework that simulates imaged tissues at cellular resolution. The framework will be applied to morphogenetic problems in developmental biology using imaging data. The simulations will be performed by the student on the cluster computing infrastructure of ETH. Your tasks will also include model calibration, extensive validation and testing, parameter screening and optimization, simulation post-processing, quantitative comparison between numerical results and imaged tissues, and data visualization.
Your profileThe project would suit students with a strong background in numerical modeling and C++ programming. Prior knowledge of the finite difference method (FDM), finite element method (FEM), or similar is desirable. Experience with cluster computing is welcome, but not required. A general interest in biophysics, developmental biology and biochemical signaling would be a plus. You must be able to work with a high level of independence and dedication. We particularly welcome applications from Master students interested in carrying out their Master thesis on the topic before starting a PhD.
Your workplace Your workplace We offerchevronright Working, teaching and research at ETH Zurich
We value diversityIn 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 with the following documents:
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: [email protected] (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.
Curious? So are we.We look forward to receiving your online application with the following documents:
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: [email protected] (no applications).
Apply online now
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.
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