Theory development for problems of modeling, system identification, system reduction, and control of large biochemical reaction systems. Examples are the metabolic network of Trypanosoma brucei and a genetic network of Escherichia coli.
- Dirk De Vos (as of 1 February 2009)
- Hanna Hardin
- Jana Nveemcova
- Jan van Schuppen
- System reduction of metabolic reaction networks
Period: From 1 April 2005 till 15 May 2009.
Hanna M. Hardin, Jan H. van Schuppen, and Hans V. Westerhoff (VU.FALW)
The problem is to reduce a biochemical reaction system in the form of a differential equation with inputs and outputs to a system of lower complexity. The biochemical reaction system of glycolysis in yeast has been used as an example.
Financial support: NWO.CLS1.
- Biomathematics in mass spectroscopy based proteomics for identification and modeling of protein networks
Period: 1 November 2006 till 1 April 2010.
Dirk De Vos and Jan H. van Schuppen
Modeling and system identification of protein networks.
The example of the GATA1 network in red blood cell development is a primarily example.
Financial support: NBIC.
Cooperation: Frank Grosveld and Sjaak Philipsen (Erasmus University - Medical Center).
- Realization and control of rational systems
Period: 1 November 2005 till 1 November 2009.
Jana Nemcova and Jan H. van Schuppen
When does an input-output map have a realization as a rational system? When has such a realization a minimal dimension? What is the relation between minimal realizations? What are necesary and sufficient conditions for structural identifability?
An example used is the peptide chain network.
Financial support: NWO.EW.
Cooperation: Dr. M. Petreczky (TUE/CWI).
- System reduction of genetic networks
Period: 1 February 2007 till 1 February 2010.
Jan van Schuppen
How to reduce large biochemical reaction systems describing a genetic network by one of smaller complexity? Ammonium assimilation in Esscherichia coli has been investigated for system reduction. Abstraction of systems to automata is also investigated.
Financial support: European Commission (Project EC-MOAN).
Cooperation: INRIA Grenoble (Hidde de Jong, Delphine Ropers), and Mazaryk University Brno (Lubos Brim, David Safranek), and Vrije Universiteit (Fred Boogerd, Frank Bruggeman, Hans V. Westerhoff).