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Mr Patrick de Vries
Research Student
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Publications
PhD Project Summary
I started here at the 29th of September 2008.
My PhD project is focused on the behaviour of E.coli bacteria.
The cells develop fimbriae in order to attach itself to a host body. This stimulates the host to release sialic acid, which in low concentrations can serve as a nutrient for the E.coli bacteria. When over-stimulated, the host body may release a higher amount of sialic acid as well as some other defence mechanism, which may kill the entire colony.
The DNA and environment is identical for all cells, but not all cells will develop these fimbriae, however, all cells will benefit.
So, even though dealing with a homogeneous colony of bacteria in an environment, the behaviour of the cells is not homogeneous.
Analysing this phenomena using only biological methods does not give a clear picture of the actual processes, as there are many smaller and larger mechanisms involved that lead to the cells expressing these fimbriae. Therefore we are building an Agent Based Model that simulates the most important of these processes and mechanisms to clear up the mystery as to why E.coli bacteria have such an elaborate system with a host of redundancies. The agent based model will be compared to experimental data and models based on deterministics rather than stochastics.
Research Interests
I am a member of the following research groups:
About me
I received my MSc in Environmental Chemistry from the University of Amsterdam in 1999 on the modelling of the biodegradation of a dioxin by a bacterium found in lake Ketelmeer in the Netherlands. The bacterium had been exposed to 1,2,3,4-tetrachloro-dibenzo-p-dioxin and became capable of breaking this dioxin down, one chloro-atom at a time.
After my masters I've worked as a researcher for the University of Groningen on a project in Combustion Engineering in co-operation with the Royal Gasunie.