Ruud

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.

Research

cell
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 orgaization of the transcribed components, especially small proteins, it seems to me that diffusion on the scale of a E.Coli scale would cause this organization to be a short transient process. Especially short in respect to protein lifetime, this would lead to the conclusion that spatial organization effects are not significant. These conflicting observations attracted me to find what is causing this dissonance of the naive model and experiment. We hope that understanding this effect allows us to more accurately predict the dynamics of synthetic biology designs, currently the procedures of genetic design invlove a lot of trail and error. This is not only time consuming but also writes off genetic cassetes as "not working" while slight spatial adaption might cure the problem, this results in a small libary of accepted "working" gene design components.

Contact


Ruud Stoof

Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group
School of Computing Science
Urban Science Building (USB)
Newcastle University
Newcastle upon Tyne
NE4 5TG