Center for Computational and Theoretical Biology

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. 


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!



We offer internships, Bachelor and Master theses, und Zulassungsarbeiten (Lehramt) 

Projects that we currently offer are 

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.




2022[ to top ]
  • Schmid, K., Knote, A., Mück, A., Pfeiffer, K., von Mammen, S., & Fischer, S. C. Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus. Frontiers in Bioinformatics. https://doi.org/10.3389/fbinf.2021.774300
2021[ to top ]
  • Kuhn, A., & C, F. S. On-lattice Vicsek model in confined geometries. ArXiv, 2105.08792.
  • Schardt, S., & Fischer, S. C. NANOG/GATA6 Interactions Revisited: A Statistical Mechanics Approach towards Cell Fate Decisions. ArXiv, 2107.04501.
  • Schmid, K., Knote, A., Mück, A., Pfeiffer, K., von Mammen, S., & Fischer, S. C. Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus. BioRxiv, 2021.09.15.460416.
  • Schardt, S., & Fischer, S. Global cell-cell communication enables spatial segregation of cells in organoids of the inner cell mass. ArXiv, 2111.01624.
2020[ to top ]
  • Fischer, S. C., Corujo-Simon, E., Lilao-Garzon, J., Stelzer, E. H. K., & Muñoz-Descalzo, S. The transition from local to global patterns governs the differentiation of mouse blastocysts. PLOS ONE, 15(5), 1-29. https://doi.org/10.1371/journal.pone.0233030
  • Liebisch, T., Drusko, A., Mathew, B., Stelzer, E. H. K., Fischer, S. C., & Matthäus, F. Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach. Scientific Reports, 10(1), 22405-. https://doi.org/10.1038/s41598-020-80141-3
2019[ to top ]
  • Mathew, B., Muñoz-Descalzo, S., Corujo Simon, E., Schröter, C., Stelzer, E. H., & Fischer, S. C. Mouse ICM organoids reveal three-dimensional cell fate clustering. Biophysical Journal, 116, 127-141. https://doi.org/10.1016/j.bpj.2018.11.011
  • Knote, A., Fischer, S. C., Cussat-Blanc, S., Niebling, F., Bernard, D., Cogoni, F., & von Mammen, S. Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures. 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR), 82-89.
  • Fischer, S. C. An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. In H. Husi (Red), Computational Biology. Codon Publications, Brisbane, Australia. https://doi.org/http://dx.doi.org/10.15586/computationalbiology.2019
  • Steuer Costa, W., Van der Auwera, P., Glock, C., Liewald, J. F., Bach, M., Schüler, C., Wabnig, S., Oranth, A., Masurat, F., Bringmann, H., Schoofs, L., Stelzer, E. H., Fischer, S. C., & Gottschalk, A. A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics. Nature Communications, 10(4095), Article 4095.
2018[ to top ]
  • Hofbauer, H. F., Gecht, M., Fischer, S. C., Seybert, A., Frangakis, A. S., Stelzer, E. H. K., Covino, R., Hummer, G., & Ernst, R. The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. J Cell Biol, 217(9), 3109-3126. https://doi.org/10.1083/jcb.201802027
  • Alt, M., Fischer, S., Schenk, S., Zimmermann, S., Ramspeck, K., & Meixner, M. Electroluminescence imaging and automatic cell classification in mass production of silicon solar cells. 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion (WCPEC) (A Joint Conference of 45th IEEE PVSC, 28th PVSEC 34th EU PVSEC), 3298-3304.
  • Smyrek, I., Mathew, B., Fischer, S. C., Lissek, S. M., Becker, S., & Stelzer, E. H. K. E-cadherin, actin, microtubules and {FAK} dominate different spheroid formation phases and important elements of tissue integrity. Biology Open, bio.037051. https://doi.org/10.1242/bio.037051
2017[ to top ]
  • Schmitz, A., Fischer, S. C., Mattheyer, C., Pampaloni, F., & Stelzer, E. H. K. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids. Scientific Reports, 7, 43693. http://dx.doi.org/10.1038/srep43693
2016[ to top ]
  • Dini, S., Binder, B. J., Fischer, S. C., Mattheyer, C., Schmitz, A., Stelzer, E. H. K., Bean, N. G., & Green, J. E. F. Identifying the necrotic zone boundary in tumour spheroids with pair-correlation functions. Journal of The Royal Society Interface, 13, 20160649. https://doi.org/10.1098/rsif.2016.0649
2015[ to top ]
  • Mathew, B., Schmitz, A., Muñoz-Descalzo, S., Ansari, N., Pampaloni, F., Stelzer, E. H. K., & Fischer, S. C. Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. BMC Bioinformatics, 16, 187.
  • Garg, S., Fischer, S. C., Schuman, E. M., & Stelzer, E. H. K. Lateral assembly of N-cadherin drives tissue integrity by stabilizing adherens junctions. Journal of The Royal Society Interface, 12, 20141055. https://doi.org/10.1098/rsif.2014.1055
2014[ to top ]
  • Fischer, S. C., Blanchard, G. B., Duque, J., Adams, R. J., Arias, A. M., Guest, S. D., & Gorfinkiel, N. Contractile and Mechanical Properties of Epithelia with Perturbed Actomyosin Dynamics. PLOS ONE, 9(4), 1-12. https://doi.org/10.1371/journal.pone.0095695
2013[ to top ]
  • Fischer, S., Houston, P., Monk, N. A. M., & Owen, M. R. Is a Persistent Global Bias Necessary for the Establishment of Planar Cell Polarity?. PLOS ONE, 8(4), 1-12. https://doi.org/10.1371/journal.pone.0060064
2011[ to top ]
  • Gorfinkiel, N., Schamberg, S., & Blanchard, G. B. Integrative approaches to morphogenesis: lessons from dorsal closure. Genesis, 49(7), 522-533. https://doi.org/10.1002/dvg.20704
  • Mateus, A. M., Gorfinkiel, N., Schamberg, S., & Martinez Arias, A. Endocytic and recycling endosomes modulate cell shape changes and tissue behaviour during morphogenesis in Drosophila. PLoS One, 6(4), Article 4. https://doi.org/10.1371/journal.pone.0018729
2010[ to top ]
  • Schamberg, S., Houston, P., Monk, N. A. M., & Owen, M. R. Modelling and Analysis of Planar Cell Polarity. Bulletin of Mathematical Biology, 72(3), 645-680. https://doi.org/10.1007/s11538-009-9464-0