Team:Paris Bettencourt/Modeling/tRNA diffusion

• Home
• Presentation
  • Overview
  • Potential applications
  • Collaborations
  • The team
  • Acknowledgements →
    • Host laboratory
    • Sponsors
• Designs
  • Designs overview & concepts
  • Designs list
• Modeling
  • General overview
  • Modeling results for our designs →
    • The basics
    • Our assumptions
    • T7 polymerase diffusion
    • tRNA diffusion
    • ComK/ComS system
    • Parameters
  • Results of our passive diffusion model
  • Toward assisted diffusion
• Data
• Results
  • Achievements
  • Methodologies →
    • Microscopy
    • Micro-fluidic
    • Integration in B.subtilis
    • Kinetics
  • Parts list
  • Notebook
• Human practice & Safety
  • Human practice
  • Safety
  • Brainstorming
  • Bonus track

tRNA Amber genetic design

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.

We have defined two models for this system which both rely on the following assumptions :

• Each mRNA is defined as a 'box'
• All the tRNA molecules are uniformly distributed in the boxes.
• 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 ambers.
• The tRNA_amber placed in a correct box are always used