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A new approach to the modelling of biochemical networks

Obiettivo

Many important cellular processes are controlled by networks of biochemical reactions. The individual components of the network and their interactions are often well known. However, the functioning of these networks remains an important issue for research. Recent research has shown that, due to the very low concentrations of molecules involved, biochemical networks are highly stochastic. Particle-based approaches are needed in order to model the large fluctuations that are involved. Spatial diffusion, localized clustering of molecules and spatial fluctuations are all-important issues that can only be approached by a spatially resolved modelling approach. Current particle-based methods do not resolve the positions of individual particles in space. The proposed project involves the development of a new computer simulation scheme for biochemical networks. This will be particle-based and spatially resolved and so Will naturally address the difficulties of the current methods. The new scheme will represent a considerable advance in computer simulation methodology, since twill allows simulation on timescales up to minutes. To do this, it will use existing analytical solutions of the Schmoluchowski equation for diffusing reactive pairs of particles.
These will be used for time propagation, allowing very large timesteps, limited only by the need for only one collision to occur per particle per timestep. The method will then be applied to several well-characterized examples of biochemical networks. Simple genetic networks, in which DNA is used to make proteins which in turn influence their own production from the DNA, will be modelled in collaboration with experimental workers. Bad erial chemotaxis, which ¡s a mechanism by which bacteria detect and respond to external signals, will also be modelled. The new method will be tested against previous experimental and theoretical results on these systems.

Invito a presentare proposte

FP6-2002-MOBILITY-5
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Coordinatore

STICHTING VOOR FUNDAMENTEEL ONDERZOEK DER MATERIE
Contributo UE
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Indirizzo
Van Vollenhovenlaan 659
UTRECHT
Paesi Bassi

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Costo totale
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