I'm a program-specific researcher (post doc) at ASHBi, KUIAS, Kyoto University in Seirin-Lee's lab.

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, and obtained my PhD at University of Vienna in Sara Merino-Aceituno's group.

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

March 2024: Our standalone EMT simulator[1] is online semtor.github.io! πŸŽ‰

Newest blog entries: πŸ¦™ How to chat with LLama3; πŸ“‘ Spellchecking in LaTeX with Grammarly; 🎨 MyPaintEdSlides; 🍎 Interactive modelling with p5.js;

πŸ“§ plunder.steffen.2a@kyoto-u.ac.jp

πŸ”— GitHub/SteffenPL | Google Scholar | ORCID | ResearchGate | LinkedIn | Twitter/X

Preprints

  1. E. Despin-Guitard, S. Plunder, N. Mathiah, E. Theveneau, I. Migeotte Occurrence of non-apical mitoses at the primitive streak, induced by relaxation of actomyosin and acceleration of the cell cycle, contributes to cell delamination during mouse gastrulation. (2024) bioRxiv.

  2. 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. (2023) bioRxiv.

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

  2. 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.

  3. 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.

  4. 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., SchΓΆps, S. (eds) Progress in Differential-Algebraic Equations II. Differential-Algebraic Equations Forum. Springer, Cham. (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. β†©οΈŽ