Supramolecular and Cellular Simulations
We work on data-driven modelling and simulations of processes at the subcellular, multicellular and multitissue scale. For the data analyses, we develop and apply tools that range from classical statistics to machine learning approaches. To test hypotheses about interactions of structure and function at the different scales, we use mathematical modelling and simulations. In particular, we use on- and off-lattice agent-based modelling in two and three spatial dimensions as well as three-dimensional morphological modelling with Blender.
We are part of the DFG priority program SPP 2332 "Physics of Parasitism” and associated to the SFB / TRR 225 “Biofabrication”.
Beta-Tester for julia programming course

We are looking people that are interested in learning the programming language julia.
If you want to have a go, feel free to download our course and work on one or more parts of it. We would appreciate it a lot if you would let us know any feedback that you might have. Thank you!
Download:
We offer internships, Bachelor and Master theses, und Zulassungsarbeiten (Lehramt)
Projects that we currently offer are
- Agent-based modelling of microtubule dynamics
- Quantitative characterisation of three-dimensional capillary networks in organoids
In general, we are looking for highly motivated candidates, who are team-oriented, willing to learn and work independently and precisely:
- Keen interest in one of our projects, quantitative data analysis and/or mathematical modelling, and programming (prior knowledge in any of these is not required)
- Enthusiasm for communication with experts from other disciplines
We offer a friendly working environment, excellent computing infrastructure and supportive supervision.
If you are interested, please contact Sabine Fischer for further details.
Publications
- [ 2023 ]
- [ 2022 ]
- [ 2021 ]
- [ 2020 ]
- [ 2019 ]
- [ 2018 ]
- [ 2017 ]
- [ 2016 ]
- [ 2015 ]
- [ 2014 ]
- [ 2013 ]
- [ 2011 ]
- [ 2010 ]
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The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours. in bioRxiv (2023). 2023.05.04.539359.
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Recognition and reconstruction of cell differentiation patterns with deep learning in arXiv (2022). 2212.10058.
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Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus in Frontiers in Bioinformatics (2022).
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Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing in arXiv (2022). 2211.07241.
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On-lattice Vicsek model in confined geometries in arXiv (2021). 2105.08792.
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NANOG/GATA6 Interactions Revisited: A Statistical Mechanics Approach towards Cell Fate Decisions in arXiv (2021). 2107.04501.
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Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus in bioRxiv (2021). 2021.09.15.460416.
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Global cell-cell communication enables spatial segregation of cells in organoids of the inner cell mass in arXiv (2021). 2111.01624.
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The transition from local to global patterns governs the differentiation of mouse blastocysts in PLOS ONE (2020). 15(5) 1–29.
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Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach in Scientific Reports (2020). 10(1) 22405-.
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Mouse ICM organoids reveal three-dimensional cell fate clustering in Biophysical Journal (2019). 116 127–141.
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Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures in 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR) (2019). 82–89.
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An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians in Computational Biology, H. Husi (red.) (2019).
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A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics in Nature Communications (2019). 10(4095)
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The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1 in J Cell Biol (2018). 217(9) 3109–3126.
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Electroluminescence imaging and automatic cell classification in mass production of silicon solar cells in 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion (WCPEC) (A Joint Conference of 45th IEEE PVSC, 28th PVSEC 34th EU PVSEC) (2018). 3298–3304.
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E-cadherin, actin, microtubules and {FAK} dominate different spheroid formation phases and important elements of tissue integrity in Biology Open (2018). bio.037051.
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Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids in Scientific Reports (2017). 7 43693.
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Identifying the necrotic zone boundary in tumour spheroids with pair-correlation functions in Journal of The Royal Society Interface (2016). 13 20160649.
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Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition in BMC Bioinformatics (2015). 16 187.
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Lateral assembly of N-cadherin drives tissue integrity by stabilizing adherens junctions in Journal of The Royal Society Interface (2015). 12 20141055.
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Contractile and Mechanical Properties of Epithelia with Perturbed Actomyosin Dynamics in PLOS ONE (2014). 9(4) 1–12.
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Is a Persistent Global Bias Necessary for the Establishment of Planar Cell Polarity? in PLOS ONE (2013). 8(4) 1–12.
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Integrative approaches to morphogenesis: lessons from dorsal closure in Genesis (2011). 49(7) 522–533.
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Endocytic and recycling endosomes modulate cell shape changes and tissue behaviour during morphogenesis in Drosophila in PLoS One (2011). 6(4)
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Modelling and Analysis of Planar Cell Polarity in Bulletin of Mathematical Biology (2010). 72(3) 645–680.