Date/Time
Date(s) – 24/01/2018
3:30 pm – 4:30 pm
Location
W152
Categories
Switches in Biological and Physical Computation
Abstract
Switches are ubiquitous in both physical and biological circuits and play a pivotal role in their exquisite behaviour. We will discuss chemical “switches” in two separate scenarios.
1) In the context of chemical reaction networks, we study the combinatorics of certain special switches called “autocatalysts” with a view towards the persistence conjecture. We introduce the notions of “self-replicable” (or autocatalytic) and “drainable” siphons. We show that: every minimal critical siphon is either drainable or self-replicable and non-autocatalytic weakly-reversible networks are persistent. Consequently, we obtain an elementary proof of the persistence of non-catalytic weakly-reversible networks.
2) In synthetic biology, we study the behaviour of switches in the context of catalysts that convert proteins to their active form. In particular, we consider retroactivity(the back effect on the upstream catalyst when connected to the downstream substrate), and attempt to minimise it using insulating push-pull motifs. We find that it is possible to reduce retroactivity at low fuel cost by coupling weakly to the push-pull motif. However, this approach is not robust to leak reactions, and compromises the ability to respond to rapidly varying signals.