I'm a program-specific researcher (post doc) at ASHBi, KUIAS, Kyoto University.

My expertise is to apply math and computer science to real biology.

I studied mathematics at TU Kaiserslautern with stays at TU Delft and The University of Auckland, obtained my PhD at University of Vienna in Sara Merino-Aceituno's group and did a post doc in Seirin-Lee's lab.

You can find a description of my current projects in the research section, talk and activities here and more info in my CV.

News and Blog

  • May 2025: Two new preprints!
  • September 2024: New Nature Communications publications on EMT and gastrulation are out!
  • March 2024: Our standalone EMT simulator[1] is online semtor.github.io! 🎉

My blog posts:

📧 plunder.steffen.2a@kyoto-u.ac.jp

🔗 GitHub/SteffenPL | Google Scholar | ORCID | researchmap.jp | ResearchGate | LinkedIn | Twitter/X

Preprints

  1. T. Ichikawa, P. C. Guruciaga, S. Hu, S. Plunder, M. Makino, M. Hamaji, A. Stokkermans, S. Yoshida, A. Erzberger, T. Hiiragi, Boundary-guided cell alignment drives mouse epiblast maturation. (2025) bioRxiv.

  2. M. Mira Osuna, S. Plunder, E. Theveneau, Roland Le Borgne, The directionality of collective cell delamination is governed by tissue architecture and cell adhesion in a Drosophila carcinoma model. (2024) bioRxiv.

  3. P. C. Guruciaga, T. Ichikawa, S. Plunder, T. Hiiragi, A. Erzberger, Boundary geometry controls a topological defect transition that determines lumen nucleation in embryonic development (2024) arxiv.

  4. S. Plunder, S. Merino-Aceituno, Convergence proof for first-order position-based dynamics: An efficient scheme for inequality constrained ODEs. (2023) arxiv.

Publications (peer-reviewed)

  1. S. Merino-Aceituno, S. Plunder, C. Wytrzens, H. Yoldaş, Macroscopic effects of an anisotropic Gaussian-type repulsive potential: nematic alignment and spatial effects. Mathematical Models and Methods in Applied Sciences (2025) DOI:10.1142/S0218202525500356, arxiv.

  2. H. Jäger, É. Grosjean, S. Plunder, C. Redenbach, A. Keilmann, B. Simeon, C. Surulescu, Cell seeding dynamics in a porous scaffold material designed for meniscus tissue regeneration. Proceedings in Applied Mathematics & Mechanics (2024) DOI: 10.1002/pamm.202400133.

  3. E. Despin-Guitard, V. S. Rosa, S. Plunder, N. Mathiah, K. Van Schoor, E. Nehme, S. Merino-Aceituno, J. Egea, M. N. Shahbazi, E. Theveneau & I. Migeotte, Non-apical mitoses contribute to cell delamination during mouse gastrulation. Nature Communications (2024) DOI:10.1038/s41467-024-51638-6.

  4. S. Plunder, C. Danesin, B. Glise, M. A. Ferreira, S. Merino-Aceituno, E. Theveneau, Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion. Nature Communications (2024) DOI:10.1038/s41467-024-51372-z.

  5. S. Plunder, M. Burkard, T, Helling, U. M. Lauer, L. E. Hoelzle, L. Marongiu, Determination of optimal phage load and administration time for antibacterial treatment. Current Protocols (2024) DOI:10.1002/cpz1.954.

  6. S. Plunder, B. Simeon, The mean-field limit for particle systems with uniform full-rank constraints. Kinetic and Related Models (2023) DOI:10.3934/krm.2023012, arxiv.

  7. S. Plunder, M. Burkard, U. Lauer, S. Venturelli, L. Marongiu, Determination of phage load and administration time in simulated occurrences of antibacterial treatments. Frontiers of Medicine (2022) DOI: 10.3389/fmed.2022.1040457.

  8. S. Plunder, B. Simeon, Coupled Systems of Linear Differential-Algebraic and Kinetic Equations with Application to the Mathematical Modelling of Muscle Tissue. In: Reis, T., Grundel, S., Schöps, S. (eds) Progress in Differential-Algebraic Equations II. Differential-Algebraic Equations Forum. Springer (2020) DOI: 10.1007/978-3-030-53905-4_12, arxiv.

Software packages

I am currently making various tools for agent-based modelling available as Julia packages.

  • SpatialHashTables.jl: A Julia package for spatial hashing of particles (in 2D and 3D). This allows fast collision detection even is unbounded domains.
  • BoundedDegreeGraphs.jl: A Julia package for graphs with bounded degree, with focus on allocation free operations commonly used in agent-based modelling.

  1. EMT stands for epithelial-to-mesenchymal transitions, a process responsible for good things like neural crest formation and wound healing, but also bad thinks like cancer and fibrosis. ↩︎