Steffen Plunder

Mathematician · Computational Biologist · Developer

Post-doctoral researcher at ASHBi, Kyoto University. I develop mathematical models and high-performance simulations that bridge theory and experiment, in developmental biology, particle dynamics, and beyond.
Math + coding + applications = ❤️

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Projects

Research and software for computational biology and applied mathematics

Research

Nematic orientation maps in epiblast formation

Topological defect transitions and cell alignment in mouse epiblast, my role was to bridge experiments and theory with quantitative image analysis.

PythonTopological defectsDevelopmental Biology

Code →

NatMatNatPhys

Epithelial-to-mesenchymal transitions

Mechanical modelling of different EMT scenarios and their effect on cell delamination and migration.

JuliaPythonCell migration

Code →

NatCommsNatComms

First-order position-based dynamics

Convergence analysis and efficient numerical scheme for inequality constrained ODEs from computer graphics.

JuliaParticle simulationsNumerical analysis

Code → Web teaser →

arxiv

Modelling digit formation in organoids

Agent-based model for symmetry breaking and digit-like elongation in limb organoids.

PythonGPU ProgrammingPDE

bioRxiv

All research →

Software

SpatialHashTables.jl

Julia package for spatial hashing, enabling fast neighbor queries in particle simulations.

JuliaGPU ProgrammingPerformance

Code →

BoundedDegreeGraphs.jl

Memory-efficient graph data structure with bounded vertex degree for agent-based simulations.

JuliaGPU ProgrammingPerformance

Code →

PortMidi.jl

Julia wrapper for the PortMidi library, enabling MIDI input/output for live coding music performances.

JuliaC++Music

Code →

All software →

Selected Publications

Selected works in computational biology and applied mathematics

2026

Boundary geometry controls a topological defect transition that determines lumen nucleation in embryonic development

P. C. Guruciaga, T. Ichikawa, S. Plunder, T. Hiiragi, A. Erzberger

Nature Materials [accepted]

arxiv →

2026

Boundary-guided cell alignment drives mouse epiblast maturation.

T. Ichikawa, P. C. Guruciaga, S. Hu, S. Plunder, M. Makino, M. Hamaji, A. Stokkermans, S. Yoshida, A. Erzberger, T. Hiiragi

Nature Physics [accepted]

bioRxiv →

2024

Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion.

S. Plunder, C. Danesin, B. Glise, M. A. Ferreira, S. Merino-Aceituno, E. Theveneau

Nature Communications

DOI:10.1038/s41467-024-51372-z →

2025

The directionality of collective cell delamination is governed by tissue architecture and cell adhesion in a Drosophila carcinoma model.

M. Mira Osuna, S. Plunder, E. Theveneau, Roland Le Borgne

iScience

DOI: 10.1016/j.isci.2025.113663 →

Complete list →

Overview

An interactive map of research, software, publications, talks, and blog posts

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