PSU Mark
Eberly College of Science Mathematics Department

Meeting Details

For more information about this meeting, contact Tim Reluga, Andrew Belmonte, Mari Royer.

Title:Network-free Simulation Method for Rule-Based Models of Biochemical Systems
Seminar:The Pritchard Lab Seminar
Speaker:James Faeder, Dept of Computational Biology, University of Pittsburgh
Abstract:
Signalling with cells generally involves protein-protein interactions, which can produce myriad protein complexes. Such protein-protein interactions can be represented compactly and precisely using graphical reaction rules, which can be processed automatically to obtain a chemical reaction network. However, reaction networks implied by typical sets of rules are often too large for conventional simulation procedures to handle. To address this challenge, we have developed a kinetic Monte Carlo method that can take advantage of a rule-based model specification. Rules are used directly to advance a simulation, thus avoiding the computationally expensive step of generating the underlying chemical reaction network implied by the rules. Unlike previously proposed methods that adaptively generate species and reactions in response to network activity, the method is not overwhelmed when the likelihood of encountering new species each time a reaction fires becomes high. The method is illustrated by using it to characterize the interaction of a trivalent ligand with a bivalent cell-surface receptor. The results of the simulations suggest formation of extremely large receptor aggregates under typical experimental conditions.

Room Reservation Information

Room Number:MB216
Date:03 / 16 / 2009
Time:02:30pm - 03:30pm