2026-08-13 –, Room 1
MicroSwimmers.jl is a package for simulating the dynamics of flagellated microswimmers in low-Reynolds-number fluid environments where geometry and actuation determine global behaviour. Built on the boundary-element regularised Stokeslet method, it provides a composable framework for constructing time-dependent swimmer morphologies and exploring parameter-driven transitions in trajectories and flow fields, integrated with the Julia scientific computing ecosystem.
Flagella (also known as cilia) are cellular appendages that beat with self-organised, large amplitude waves. Active, elastic and evolutionarily ancient structures, flagella perform a remarkable diversity of functions in modern-day organisms. They can be found driving fluid flow in our brains, respiratory tract, and reproductive systems, as well as allowing single-celled microorganisms to swim, navigate, feed, hunt and avoid predators. The multi-scale and multi-physics approaches needed to study these complex systems provide numerous computational challenges.
MicroSwimmers.jl is designed to explore the functions of ciliated cells by combining rapid solutions to fluid dynamical problems using the boundary element-regularised stokeslet method with a composable framework for the design and variation of microswimmer morphologies and kinematics. The software connects with the existing Julia ecosystem (e.g. DifferentialEquations.jl for calculating trajectories and Makie.jl for a suite of visualisation tools). Work is ongoing to improve auto-differentiation compatibility to explore optimal behaviour patterns across fluid environments and geometries.
The Julia implementation will enable biological and clinical research without knowledge of numerical methods or computational geometry, with the goal of rapid simulation and parameter variation on a laptop. I will demonstrate the accessible interface for adding new flagellar beating models and body geometries, and show a few examples of the pipeline from design to results visualisation, including a filter-feeding organism that generates a vortex ring inside a cavity, driving fluid flow over a ciliary band where nutrients are captured.
The biophysics of diverse ciliated single-celled organisms is largely unexplored, and both the mechanistic origins of how cells control their flagella to exhibit diverse multi-stable patterns (in the absence of neural control) and the ecological significance of such patterns are highly debated. A better understanding has implications for health, the environment and bio-inspired technologies.
I'm a postdoctoral researcher at the University of Exeter interested in dynamical models with biological applications. I use analytical and numerical techniques applied to systems away from equilbrium, and am interested in methods to fit experimental data to nonlinear differential equation models.
For my PhD I studied the internal nonlinear mechanics of eukaryotic cilia and flagella. The big open question is how individual molecular motor proteins act collectively to generate propagating waves that enable microorganisms to swim or pump fluid. Now I am interested in how seemingly 'intelligent' behaviour of single-celled organisms can be controlled through e.g. bioelectricity or genetic networks and how to model such situations mathematically and computationally.