|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...