How liquid is biological signaling? - using random graphs to study protein networks

Tuesday, July 14, 2009

2:15 pm - 3:15 pm

CNLS Conference Room (TA-3, Bldg 1690)

Title How liquid is biological signaling? - using random graphs to study protein networks

Linus J. Schumacher, University of Cambridge

Joint work with Vincent Danos (University of Edinburgh) and Heinz Koeppl (EPFL)

We propose an idealization of protein networks as random graphs to investigate their global statistics and help understand the design constraints for synthetic protein networks. Leaving most mathematical detail and rigor for further reading, we derive a liquidity index that predicts the clustering of agents into a single giant component (as in percolation theory). Using the rule-based language Kappa to describe and simulate such ensembles of idealized proteins, we investigate chemoreceptor clustering in E. coli and discuss the limitations to our theory. Finally we will address extensions to be carried out in future work that will enable us to describe less abstract and more interesting protein networks.