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

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.

With my research, I want to answer questions in biology using mathematical tools. I have worked on mechanical models in developmental biology (epithelial-to-mesenchymal transitions), muscle dynamics, molecular dynamics and phage-bacterial interactions.

My mathematical toolset includes mathematical modelling with ordinary, stochastic and partial differential equations. An emphasis lies on constrained systems such as differential inclusions and differential-algebraic equations. My key experties is the implementation of efficient numerical simulations for such models and the development of models in collaboration with biologists.

You can find a description of my current projects in the research section, talk slides here and some more general posts in my blog.

News

Our standalone EMT simulator is online: semtor.github.io.
See also the corresponding preprint Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion for more details.

E-Mail: plunder.steffen.2a@kyoto-u.ac.jp

Links: GitHub/SteffenPL | ResearchGate | ORCID | 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., Schöps, 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.