Russ Harmer

Shared Models (5)

Enzyme - Substrate
	We have two kinds of agents, an enzyme E and its substrate S, each with a single site, s, equipped with a binary state, 0 or 1, for inactive or active. The simplest possible binding rule allows the association of active enzyme with its substrate: 'r1' E(s~1), S(s) -> E...

Goldbeter - Koshland loop
	This model extends the simple enzyme-substrate model. Read the classic paper by Goldbeter and Koshland for a detailed analysis. We still have a single substrate agent S but now have two different enzyme agents, K and P, one catalyzing the state change of the substrate from 0 to 1...

Binding equilibria
	We suppose two agents called A and B, each with one site called s. Consider the rule A(s), B(s) <-> A(s!0), B(s!0) @ kon, koff that, read from left-to-right, performs the binding of A to B and, read from right-to-left, undoes that binding. The rate constant for unbinding is k...

Enzyme - Substrate (continued)
	In the first part of this exercise, we used three rules equipped with mass action kinetics. The overall effect of these rules can itself be written as a rule E(s~1), S(s~0) -> E(s~1), S(s~1) but how would we express the desired rate of this rule? In general, this cannot...

MAPK
	This exercise investigates some of the properties of a generic MAPK-style signalling cascade. The 'input' signal is the agent S and there are three kinases - MAP3K, MAP2K and MAPK - each with its own personal phosphatase. Investigate how varying the strength of the input S aff...