I am Ruben, a PhD student in the lab of Timon Idema. I am a theoretical physicist by education, but I also like to do computational work in the form of simulations. My project involves understanding and simulating the collective dynamics in biological systems in highly viscous environments. Bacteria and amoebae are examples of such systems, and on a larger scale, a nice example is set by penguins, that huddle together tightly to preserve their body heat. The model that we explore finds its roots in the successful Vicsek Model and granular matter. The Vicsek Model was introduced to describe flocks of birds or schools of fish. The simple model features self-propelling point particles that will align their velocities once they get close to each other. I apply this model for high density systems, similar to granular matter, where particles have a finite size and may jam if no external force is applied. The external force that prevents jamming for biological systems is conveniently provided by the self-propulsion of the particles - a feature that is already present in the Vicsek Model. The combination of these fields (active matter and granular matter) leads to interesting dynamics.
Together with the Martin Depken group we form the theory group in Bionanoscience. We meet every other week in the forum, but in practice we discuss everyday, about big and small problems in research or just completely off-topic. The open atmosphere and lack of hierarchy is one of many things I like about this department. Finally, keep calm and convert tea to theory.
Enough talk, show me the simulation movies.
The movies show the collective dynamics of circular particles. The first 256 frames show the initialisation and thermalisation of the system. The final 256 frames correpond to the last part of the simulation. The colour of the edge indicates the degree of overlap with neighbouring particles. Blue particles have very little overlap, particles turn green, yellow and then red if the overlap increases. The self-propulsion direction is indicated by the radius of the circular particles. A red radius means the particle finds itself in the bulk, a blue radius means the particle exerts an extra force into the colony. Finally, the red triangles indicate the direction that the particle is actually moving in.
You can use the keyboard to navigate in the movies. Note that loading may take some time as the files are of the order of 10 MB.
“Those who know, do. Those that understand, teach.” - Aristotle. And actually it's even more than that. Needing to teach means that you have to think about how to bring the material as clearly and logical as possible. In my opinion, that is what a true understanding means. And that is why I am happy to be involved in the education of students as well. Here you can find the list of courses I assisted in.
I am a theorist, so you can often just find me in my office, hiding behind the computer screen. Feel free to barge in!
We have moved to a brand new location! It is so new, even google doesn't know it yet. This map shows where our building should be. Please refer to the campus map if you have trouble finding us.