Vincent Danos

Shared Models (4)

Simple allosteric model
	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 and roaming agents
	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...

Ising ring
	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: ...

Independent binding (prozone effect)
	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...