Working group: "Computational Biology"
2010, the 09th of March
Jérôme Feret
Title: Internal coarse-graining of molecular systems
Abstract:
Modelers of molecular signaling networks must cope with the combinatorial
explosion of protein states generated by post-translational modifications
and complex formation. Rule-based models provide a powerful alternative to
approaches that require an explicit enumeration of all possible molecular
species of a system. Such models consist of formal rules stipulating the
(partial) contexts for specific protein-protein interactions to occur. These
contexts specify molecular patterns that are usually less detailed than
molecular species. Yet, the execution of rule-based dynamics requires
stochastic simulation, which can be very costly. It thus appears desirable
to convert a rule-based model into a reduced system of differential
equations by exploiting the lower resolution at which rules specify
interactions.