Team:Bologna/Modeling

From 2009.igem.org

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<font face="Dom Casual" font size="3" color="#000000"><i><b>"The theory is when you know everything and nothing works. Practice is when everything works and nobody knows why. We have put together the theory and practice: there is nothing that works ... and nobody knows why."</b>
<font face="Dom Casual" font size="3" color="#000000"><i><b>"The theory is when you know everything and nothing works. Practice is when everything works and nobody knows why. We have put together the theory and practice: there is nothing that works ... and nobody knows why."</b>
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= Introduction =
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In order to test and characterize our T-REX device, we developed the following genetic circuit (Fig. 1):
In order to test and characterize our T-REX device, we developed the following genetic circuit (Fig. 1):
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[[Image:circuit2OK.jpg|center|900px|thumb|<center>Figure 1 - Genetic Circuit to test CIS and TRANS' mRNA affinity</center>]]
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[[Image:circuit2OK.jpg|center|900px|thumb|<center>Figure 1 - Genetic Circuit to test CIS and TRANS' mRNA functionality</center>]]
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= Mathematical Model =
= Mathematical Model =
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In this context, RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates.
In this context, RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates.
<br> The interaction between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the RNA polymerase - promoter complex and ribosome - RBS sequence complex.
<br> The interaction between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the RNA polymerase - promoter complex and ribosome - RBS sequence complex.
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==Reactions==
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=Reactions=
Here below are shown all the reactions occurring the circuit (Fig. 1 and Fig. 2).
Here below are shown all the reactions occurring the circuit (Fig. 1 and Fig. 2).
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[[Image:Modello1.png|center|940px||thumb|Figure 1: GFP transcription and GFP translation (left); LacI transcription, LacI translation and LacI dimerization (right) ]]<br>
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[[Image:Modello1.png|center|940px||thumb|Figure 1: GFP transcription and translation (left); LacI transcription, translation and dimerization (right) ]]<br>
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|[[Image:Pag3.jpg|450px|thumb|Figure 2: Other Chemical Reactions]]
|[[Image:Pag3.jpg|450px|thumb|Figure 2: Other Chemical Reactions]]
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=Differential Equations=
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==Differential Equations==
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Differential equations, that describes the project, are obtained appling the law of mass action at the reactions above.  
Differential equations, that describes the project, are obtained appling the law of mass action at the reactions above.  
[[Image:Differentialequations3.jpg|940px||thumb| Figure 4. Differential Equations]]
[[Image:Differentialequations3.jpg|940px||thumb| Figure 4. Differential Equations]]
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[[Image:Constants3.jpg|center|500px||thumb|Figure 6: Equilibrium Constants]]
[[Image:Constants3.jpg|center|500px||thumb|Figure 6: Equilibrium Constants]]
[[Image:Algebricalconstrain2.jpg|center|650px||thumb|Figure 7: Algebraic Constrains]]
[[Image:Algebricalconstrain2.jpg|center|650px||thumb|Figure 7: Algebraic Constrains]]
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=Simulations=

Revision as of 00:25, 22 October 2009

ProvaBol2.png
HOME TEAM PROJECT SOFTWARE MODELING WET LAB PARTS HUMAN PRACTICE JUDGING CRITERIA


"The theory is when you know everything and nothing works. Practice is when everything works and nobody knows why. We have put together the theory and practice: there is nothing that works ... and nobody knows why."

A. Einstein


Contents

Introduction

In order to test and characterize our T-REX device, we developed the following genetic circuit (Fig. 1):

Figure 1 - Genetic Circuit to test CIS and TRANS' mRNA functionality



Mathematical Model


The mathematical model is based on the law of mass action, and the processes involved in gene expression, that is transcription and translation, are considered similar to enzymathic reactions.
In this context, RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates.
The interaction between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the RNA polymerase - promoter complex and ribosome - RBS sequence complex.

Reactions

Here below are shown all the reactions occurring the circuit (Fig. 1 and Fig. 2).

Figure 1: GFP transcription and translation (left); LacI transcription, translation and dimerization (right)

Figure 2: Other Chemical Reactions
Figure 3: Trans-Reactions

Differential Equations

Differential equations, that describes the project, are obtained appling the law of mass action at the reactions above.

Figure 4. Differential Equations
Figure 5. Differential Equations
Figure 6: Equilibrium Constants
Figure 7: Algebraic Constrains

Simulations

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