Team:DTU-Denmark/Modeling

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We have modeled several aspects of the project to answer some key questions about our project:
We have modeled several aspects of the project to answer some key questions about our project:
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* [[Team:DTU-Denmark/Kinetic Model|Kinetic Model]] -- How long will it take to convert ammonia into nitrous oxide?
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==Kinetic Model==
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<b>How long will it take to convert ammonia into nitrous oxide?</b>
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In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engeneered E. coli cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed E. coli cells will be able to do this within less than 10 minutes.  
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In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engineered ''E. coli'' cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed ''E. coli'' cells will be able to do this within less than 15 minutes.  
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* [[Team:DTU-Denmark/Reactor Model|Reactor Model]] -- How large a reactor will we need?
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[[Team:DTU-Denmark/Kinetic Model|Go to Kinetic Model]]
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We want to get a first estimate of how large a reactor filled with our transformed E. coli cells must be to treat ammonia polluted wastewater. Since Mutant 2 requires anaerobic conditions, we plan to build two reactors in series. With our model, we find that the second should be around 10 times the size of the first. This is under the assumption that all transformed proteins will be expressed at the same level, so expressing proteins at different levels is something we should look into if we want to avoid a large difference in reactor sizes.
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== Reactor Model==
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<b>How large a reactor will we need?</b>
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* [[Team:DTU-Denmark/Codon Optimization|Codon Optimization]] -- Will we need to codon optimize the ''Nitrosomonas europaea'' and ''Pseudomonas aeruginosa'' genes we are expressing in ''E. coli''?
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We want to get a first estimate of how large a reactor filled with our transformed ''E. coli'' cells must be to treat ammonia polluted wastewater. Since Mutant 2 requires anaerobic conditions, we plan to build two reactors in series. With our model, we find that the second should be around 10 times the size of the first. This is under the assumption that all transformed proteins will be expressed at the same level, so expressing proteins at different levels is something we should look into if we want to avoid a large difference in reactor sizes.
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* [[Team:DTU-Denmark/HelloWorld#Modeling|Model of Periplasmic Contents for Hello World Pilot Project]] -- What fluorescence cross section will the cell have when we express GFP in the periplasm and RFP in the cytoplasm?
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* [[Team:DTU-Denmark/Protein Models|Protein Models]] -- What are the structures of the proteins we are expressing in ''E. coli''?
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[[Team:DTU-Denmark/Reactor Model|Go to Reactor Model]]
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 +
==Codon Optimization==
 +
 
 +
<b>Will we need to codon optimize the ''N. europaea'' and ''P. aeruginosa'' genes we are expressing in ''E. coli''?</b>
 +
 
 +
Using the tRNA adaptation index (tAI), we find that the tRNA pools for these organisms are similar enough that we do not need to codon optimize. 
 +
 
 +
[[Team:DTU-Denmark/Codon Optimization|Go to Codon Optimization]]
 +
 
 +
==Model of Periplasmic Contents for Hello World Pilot Project==
 +
 
 +
<b>What fluorescence cross section will the cell have when we express GFP in the periplasm and RFP in the cytoplasm?</b>
 +
 
 +
We provide a dynamic javascript model that allows parameters of the cellular model to be modified and the results shown in real time. 
 +
 
 +
[[Team:DTU-Denmark/HelloWorld#Modeling|Go to Model of Periplasmic Contents for Hello World Pilot Project]]
 +
 
 +
==Protein Models==
 +
<b>What are the structures of the proteins we are expressing in ''E. coli''?</b>
 +
 
 +
See the details in our [[Team:DTU-Denmark/Protein Models|PyMol protein models]]!
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{{:Team:DTU-Denmark/Templates/EndPage}}
{{:Team:DTU-Denmark/Templates/EndPage}}

Latest revision as of 19:22, 4 October 2013

Modeling

We have modeled several aspects of the project to answer some key questions about our project:

Contents

Kinetic Model

How long will it take to convert ammonia into nitrous oxide?

In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engineered E. coli cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed E. coli cells will be able to do this within less than 15 minutes.

Go to Kinetic Model

Reactor Model

How large a reactor will we need?

We want to get a first estimate of how large a reactor filled with our transformed E. coli cells must be to treat ammonia polluted wastewater. Since Mutant 2 requires anaerobic conditions, we plan to build two reactors in series. With our model, we find that the second should be around 10 times the size of the first. This is under the assumption that all transformed proteins will be expressed at the same level, so expressing proteins at different levels is something we should look into if we want to avoid a large difference in reactor sizes.

Go to Reactor Model

Codon Optimization

Will we need to codon optimize the N. europaea and P. aeruginosa genes we are expressing in E. coli?

Using the tRNA adaptation index (tAI), we find that the tRNA pools for these organisms are similar enough that we do not need to codon optimize.

Go to Codon Optimization

Model of Periplasmic Contents for Hello World Pilot Project

What fluorescence cross section will the cell have when we express GFP in the periplasm and RFP in the cytoplasm?

We provide a dynamic javascript model that allows parameters of the cellular model to be modified and the results shown in real time.

Go to Model of Periplasmic Contents for Hello World Pilot Project

Protein Models

What are the structures of the proteins we are expressing in E. coli?

See the details in our PyMol protein models!

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