Team:Paris Bettencourt/Modeling

From 2011.igem.org

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=== tRNA amber system ===
=== tRNA amber system ===
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[[Team:Paris_Bettencourt/tRNA_diffusion|The amber suppressor tRNA diffusion.]] The idea of the system is to pass tRNA amber molecules through the nanotubes. At every moment of time in the receiver cell there is a certain amount of transcripted mRNA-T7 among the others mRNA. The behavior of tRNA amber that arrived to a receiver cell is random, so to describe its interaction with mRNA-T7 and its further translation we can reason in terms of probability.
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[[Team:Paris_Bettencourt/tRNA_diffusion|The amber suppressor tRNA diffusion.]] The idea of the system is to pass tRNA amber molecules through the nanotubes. At every moment of time in the receiver cell there is a certain amount of transcribed mRNA-T7 among the others mRNA. The behavior of tRNA amber that arrived in a receiver cell is random, so in order to describe its interaction with mRNA-T7 and its further translation we can reason in terms of probability.
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We can consider two types of events : a tRNA amber molecule gets close to a mRNA molecule and once it is close, it fits its anti-codon to some codon of the mRNA. The way of reasoning is chosen because there is an easy analogy to this problem : the problem of boxes and balls. There are two types of boxes, a of the first type and b of the second(that corresponds to the set of mRNA-T7 and mRNA-non-T7), and there are t balls(tRNA amber). All the balls are randomly distributed in the boxes. If there is two or more balls in some box of the first type(two or more tRNA amber per mRNA-T7) then a T7 molecule will be produced with a chance P_0.
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We can reason in two steps : first a tRNA amber molecule gets close to a mRNA molecule. Then, it binds it's anti-codon with a codon of the mRNA. This reasoning is similar to the problem of boxes and balls. There are two types of boxes: 'a' of the first type and 'b' of the second (which corresponds to the set of mRNA-T7 and mRNA-non-T7), and there are 't' balls(tRNA amber). All the balls are randomly distributed in the boxes. If there are two or more balls in some box of the first type (two or more tRNA amber per mRNA-T7) then a T7 molecule will be produced with a chance P_0.
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* All the molecules in the cell are uniformly distributed.
* All the molecules in the cell are uniformly distributed.
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* The number of tRNA amber diffused through the nanotubes is much more smaller than the one of the mRNA. So the chance that three or more tRNA amber will "find" one mRNA-T7 is negligible comparing to the one of two tRNA amber. In our model we will consider that at one moment of time each mRNA interacts with 0, 1 or 2 tRNA amber.
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* The number of tRNA amber diffused through the nanotubes is much more smaller than the one of the mRNA. Thus the chance that three or more tRNA amber will "find" one mRNA-T7 is negligible comparing to the one of two tRNA amber (finding a mRNA-T7). In our model we will consider that at one moment of time each mRNA interacts with 0, 1 or 2 tRNA amber.
== Master/Slave ==
== Master/Slave ==

Revision as of 16:16, 25 July 2011

Team IGEM Paris 2011




Contents

Modeling

Direct observation

Characterization

Relevant parameters for modeling
Allosteric equations for modeling

T7 system

First T7 model without delay between receptor and amplifier
T7 model with delay between receptor and amplifier


tRNA amber system

The amber suppressor tRNA diffusion. The idea of the system is to pass tRNA amber molecules through the nanotubes. At every moment of time in the receiver cell there is a certain amount of transcribed mRNA-T7 among the others mRNA. The behavior of tRNA amber that arrived in a receiver cell is random, so in order to describe its interaction with mRNA-T7 and its further translation we can reason in terms of probability.


We can reason in two steps : first a tRNA amber molecule gets close to a mRNA molecule. Then, it binds it's anti-codon with a codon of the mRNA. This reasoning is similar to the problem of boxes and balls. There are two types of boxes: 'a' of the first type and 'b' of the second (which corresponds to the set of mRNA-T7 and mRNA-non-T7), and there are 't' balls(tRNA amber). All the balls are randomly distributed in the boxes. If there are two or more balls in some box of the first type (two or more tRNA amber per mRNA-T7) then a T7 molecule will be produced with a chance P_0.


This system can be modelled after making some important assumptions :

  • All the molecules in the cell are uniformly distributed.
  • The number of tRNA amber diffused through the nanotubes is much more smaller than the one of the mRNA. Thus the chance that three or more tRNA amber will "find" one mRNA-T7 is negligible comparing to the one of two tRNA amber (finding a mRNA-T7). In our model we will consider that at one moment of time each mRNA interacts with 0, 1 or 2 tRNA amber.

Master/Slave

Bi-directional communication









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