About Me

Hi, I am Ruud and I am a Phd student in the ICOS group. I have a background as a (bio)physicist; I have a master and bachelor degree in Physics at the Universities of Amsterdam (my Primary research and education was at the Vrije Univesiteit with a combined Masters degree from the Universiteit van Amsterdam). My main interest is the physics of life, because I am fascinated by how nature/natural selection has made interesting "ways" to cope with all kinds of different problems.


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 . I would like to know the physical mechanism leading to this different behaviour. I believe that this effect allows more complex systems with limited building materials. From the perspectife of aplication, synthetic bioligy considering this effect in designing genetic circuits might lead to drastically less limitation by the limited biulding blocks currently used. From an evolutionairy perspective I hypothesize about how natural selection could have selected on this increasing effect in organisms to allow more complex system with a better adaptivity.
To start this progess I created a model of the repressilator with spatial effect which clearly implicate effect on the oscilations.

In this video,the top portion is the concentration of LacI, the middle part is the concentration of TetR and on the bottom we see the concentration of CL.


Ruud Stoof

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