Shared Models

Protein clustering on a growing membrane by Ricardo Honorato

Branching and elongation of glucose, + crystallisation (surface, linear) by Sebastian Jaramillo-Riveri

Branching and elongation of glucose (surface, linear) by Sebastian Jaramillo-Riveri

Independent binding (prozone effect) by Vincent Danos
	We consider a model where A, C can bind B independently (B could be a scaffold mediating between A and C). The parameters are relatively sticky resulting in 2/3 of As being bound given an equal number of As and Bs. Likewise for C. We want to study the equilibrium amount of ABC as a functi...

MAPK by Russ Harmer
	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...

Enzyme - Substrate (continued) by Russ Harmer
	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...

Goldbeter - Koshland loop by Russ Harmer
	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...

Enzyme - Substrate by Russ Harmer
	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...

Growing ring and roaming agents with energy-driven binding by Ricardo Honorato
	This is an alternative version of the Kappa model "growing ring with energy-driven moving agents" in which movement and binding are decoupled. As a consequence, we can now measure the number of cluster by observing Sensor agents that are bound on one side but not the other. This...

Ising ring by Vincent Danos
	Below is a model of a ring of 34 protomers, P, with two conformations - depending on the binding of CheY to P, the probabilities of P being in one or the other of these two states will vary; another feature of the model is that Ps tend to align to their neighbours. Agent signatures: ...

Simple allosteric model by Vincent Danos
	This is a simple allosteric model. There are two agents called A and R, R has an internal state 0/1 that represents his conformation. Absent any A, R conformation is uniform. When A binds R, R prefers state 0. Thermodynamic consistency forces a relation between the equilibrium co...

Growing ring with energy-driven moving agents by Ricardo Honorato
	This model grows a one dimensional ring and inserts new agents on it which diffuse along the ring; the idea is that this is a simple model of receptor clustering in a growing membrane. The rates of diffusion rules are modulated by the change in system's energy they produce. In turn, the sy...

Growing ring and roaming agents by Vincent Danos
	This model grows a one dimensional ring and inserts new agents on it which diffuse along the ring; the idea is that this is a simple model of receptor clustering in a growing system.  It is an interesting exercise to refine the diffusion rule to be compatible with a simple Ising potential...

Binding equilibria by Russ Harmer
	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...

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