Team:Groningen/Modelling

From 2009.igem.org

Our initial ideas on how and what to model can be found at Brainstorm/Modelling.

Usage of graphs in wiki: Graphs

Models

Apart from some computations on gas vesicles we have the following model involving import, export and accumulation of arsenic (showing the "reactions" in the model):

Kinetic Laws

TODO Add references.

TODO Find out how to determine experimentally which is applicable (and if you know, what the parameters are).

Mass Action

Molecules randomly interact, the reaction rate is simply the product of the concentrations of the reactants (multiplied by a constant).

Michaelis-Menten

Applicable to situations where there is a maximum reaction rate (due to needing a catalyst/transporter/binding site of which there is only a limited amount for example) under the assumption that there is much more of the "main" reactant than of the catalyst/transporter. Has two constants, the maximum reaction rate and the concentration at which the reaction rate is half the maximum reaction rate.

Michaelis-Menten reversible

TODO

Hill

Generalization of Michaelis-Menten. More detail.

For rate parameters it is best to have both the forward and reverse reaction rates, if you don't then a dissociation constant can be used (which is the ratio of the reverse and forward rates), in combination with a "standard" rate of 10⁸-10⁹ (see appendix A of Alon2007), in the case of two reactants at least.

See http://www.biomodels.net/ for a database of models.

Protein production

Concepts:

translation rate

Number of amino acids per second that are translated (per mRNA). Expressed in amino acids per second per mRNA?

ribosome occupancy

Fraction of mRNA bound to ribosomes.

mRNA abundance

Amount of mRNA (molecules per cell or concentration).

translational activity / protein production rate ?

Translation rate per mRNA times mRNA abundance (units?: 1/(mol*sec) * mol/L = 1/(sec*L)). ???