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 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

Preprints

  1. 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.

  2. 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, 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.

  2. 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.

  3. 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.