Shared Models - RuleBase

Shared Models

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
 
Init file   %agent:CheY(s~u~p) %agent:P(f~0~1,s,x,y) # uses the script for generating the ring/could also build it %init: 1 (P(f~0,s,x!0,y!1), P(f~0,s,x!1,y!2), P(f~0,s,x!2,y!3), P(f~0,s,x!3,y!4), P(f~0,s,x!4,y!5), P(f~0,s,x!5,y!6), P(f~0,s,x!6,y!7), P(f~0,...
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 system. The rates of diffusion rules are modulated by the change in system's energy they produce. In turn, the syst...
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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