(Note: I started working at a new department in March 2008. The information on this page is outdated and stems from my previous research projects, I hope to update this page shortly)
My current main interest is in the computational capacities of formalisms that represent biochemical signalling networks. I am employed as a post-doc researcher at the Technische Universiteit Eindhoven, funded by the ESIGNET (Evolving Cell Signalling Networks, in silico) project of the 6th framework of the European Union.
Biochemical signalling networks are amazing systems. They are responsible for the intercellular communication and interpretation of real time environmental signals. A famous example of a signalling network drives the process of chemotaxis in E. coli. An E. coli cell has an array of receptors that can sense concentrations of food particles. Based on the concentrations, the cell can turn its flagella (little motors connected to rotating tails) clockwise or counterclockwise. If the motors run counterclockwise, the flagella string together, which causes the cell to move forward. If the motors turn clockwise, the flagella don't get together, and the cell tumbles in a random direction. Based on input samples that are sensed by the receptors, the cellular signalling circuitry decides in which direction to rotate its motors, in order to move to high concentrations of food, and low concentrations of toxic material.
The signalling in these networks is regulated by kinases and phosphatases, which add/remove a phosphate group from substrate proteins. As such, these proteins become activated, and may be able to perform some action, even (de-)phosphorylate other proteins, and become part of a chain of phosphorylation switches. Indeed, a cycle of phosphorlating and dephosphorylating reactions acts as a sigmoidal switch, activated or inhibited by its phosphorylating and dephosphorylating inputs.
Currently, I am studying a range of models that allow us to model and understand the internal workings of these biochemical circuits. We try to figure out what kind of computations can be expressed with biochemical reaction networks, and design theoretical systems that perform a wide range of complex input-output computations.