About Me

Hi, I am Ruud and I am a Phd student in the ICOS group. I have a background as a (bio)physicist; a master and bachelor degree in Physics at the Universities of Amsterdam (Vrije Univesiteit and Universiteit van Amsterdam). My main interest is the physics of life. The way nature/natural selection has "made" solutions to cope with all kinds of different problems fascinates me.



In my current research, I look at how the spatial location of genetic information plays a role in single-cell system dynamics. It is seen that increasing the distance of two parts of a simple pathway can drastically affect its dynamics. When I think of spatial organisation of the transcribed components, especially small proteins, it seems to me that diffusion on the scale of an E.Coli would cause this organisation to be a short transient process. This would lead to the conclusion that spatial organisation effects are not significant over a protein lifetime. These conflicting observations attracted me to find what is causing this dissonance of this initial model and experiment. We hope that understanding this effect allows us to predict the dynamics of synthetic biology designs more accurately, and save some of the labour intensive and time consuming trial and error. This is not only time consuming but also writes off genetic cassettes as "not working" while slight spatial adaption might provide a cure, this results in a small library of accepted "working" gene design components.



Our team

Ruud Stoof

Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group
School of Computing Science
Urban Science Building (USB)
Newcastle University
Newcastle upon Tyne