"
Team:Groningen/Modelling
From 2009.igem.org
(Difference between revisions)
(Team:Groningen/Modelling moved to Team:Groningen/Modelling/Arsenic: Most of the page is specifically about arsenic.) |
(General modelling stuff.) |
||
| Line 1: | Line 1: | ||
| - | + | '''Bold text'''{{Team:Groningen/Header}} | |
| + | [[Category:Team:Groningen/Disciplines/Analysis_and_Design|Modelling]] | ||
| + | [[Category:Team:Groningen/Roles/Modeller|Modelling]] | ||
| + | |||
| + | Our initial ideas on how and what to model can be found at [[Team:Groningen/Brainstorm/Modelling|Brainstorm/Modelling]]. | ||
| + | |||
| + | Usage of graphs in wiki: [https://2009.igem.org/Template:Graph Graphs] | ||
| + | |||
| + | ==Models== | ||
| + | Apart from some computations on [[Team:Groningen/Project/Vesicle|gas vesicles]] we have the following models involving import, export and accumulation of heavy metals: | ||
| + | |||
| + | * [[Team:Groningen/Modelling/Arsenic|Arsenic]] | ||
| + | * {{todo}} [[Team:Groningen/Modelling/Arsenic|Copper]] | ||
| + | * {{todo}} [[Team:Groningen/Modelling/Arsenic|Zinc]] (integrate with copper?) | ||
| + | |||
| + | == 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. {{todo|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 10<sup>8</sup>-10<sup>9</sup> (see appendix A of [[Team:Groningen/Literature#Alon2007|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)). ??? | ||
Revision as of 07:51, 28 July 2009
Bold text
[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]
| Modelling
|
|---|
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 models involving import, export and accumulation of heavy metals:
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)). ???
