Team:Colombia Uniandes/Modeling

From 2013.igem.org

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(Nickel removal system)
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<li><b> T:</b> The tretamer is formed when four repressor subunits bind together, it binds to the DNA in order to block the production of the porine and when there is nickel inside the cell each of the repressor subunits coordinates a nickel atom unbinding the repressor from DNA and enabling transcription downstream.
<li><b> T:</b> The tretamer is formed when four repressor subunits bind together, it binds to the DNA in order to block the production of the porine and when there is nickel inside the cell each of the repressor subunits coordinates a nickel atom unbinding the repressor from DNA and enabling transcription downstream.
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[[File:Tetramer.png|center|500x280px]]
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[[File:Tetramer.png|center|500x250px]]
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<li><b> P: </b> The Porine is produced at a low basal when the tretameric repressor is binded to the promoter. Once the repressor binds to the nickel it is released and allows the production of the porine.
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[[File:Porin.png|center|350x250px]]
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Revision as of 22:53, 17 July 2013

Diferential ecuations

We use the mathematical model to check if the design works, before starting to work at the lab. To develop this model the first step is the do the deterministic model, which is based in differential equations. This type of model describe the mean behaviour for each of the substances in the synthetic circuit over time. However, it does not take into account the probabilities involved in each of the events described, the population interactions and the noise of the system.

The deterministic model is based in the law of mass conservation and expresses the inputs and outputs of the system with expressions that use the law of mass action and known models like HIll's or Michaelis Menten.

Below are shown and explained the differential equations that allowed us to work in both projects:


Glucocorticoid sensor

Below it is shown how differential equations for the Glucocorticoid Sensor based in the circuit shown in the project description . However, before describing the modeled system ,it is necessary to know all the symbols that will be use in the documents and the simulation. The following table contains all the substances involved in the processes and the constants required for the simulation.

Symbols used in the document and simulation


Nickel removal system

As in the Glucocorticoid Sensor project the differential equations were based on the circuit shown in the project description . Before explaining the equations ,it is necessary to know all the symbols that will be use in the documents and the simulation. The following table contains all the substances involved in the processes and the constants required for the simulation.

Symbols used in the document and simulation