# Team:NYMU-Taipei/ymim1

(Difference between revisions)
 Revision as of 02:31, 27 September 2012 (view source)Jayms (Talk | contribs)← Older edit Revision as of 02:40, 27 September 2012 (view source)Jayms (Talk | contribs) Newer edit → Line 93: Line 93:

In order to  produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to  help us simulate the substrate concentration in a single cell.

In order to  produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to  help us simulate the substrate concentration in a single cell.

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+

Where v=reaction  rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate  concentration, Km= equilibrium  constant of enzyme, Kcat=turnover number.

Where v=reaction  rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate  concentration, Km= equilibrium  constant of enzyme, Kcat=turnover number.

Our pathway  looked like this

Our pathway  looked like this

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+

Reaction 2, 3, 4  were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6,  7 are the new pathways that we engineered.

Reaction 2, 3, 4  were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6,  7 are the new pathways that we engineered.

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For reaction 2,  3, 4, we used the equation
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For reaction 2,  3, 4, we used the equation
- As for the rest, we used  instead.
+ As for the rest, we used  instead.

To determine the  enzyme concentration for our new pathways, we needed another two equations.

To determine the  enzyme concentration for our new pathways, we needed another two equations.

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+

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+

Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation  rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation  rate or Enzyme

Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation  rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation  rate or Enzyme

Combined  the two equations, we got the relationship between enzyme concentration and  time.

Combined  the two equations, we got the relationship between enzyme concentration and  time.

- +

Then we combined  the equation above with Michaelis-Menten’s equation.

Then we combined  the equation above with Michaelis-Menten’s equation.

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+

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## Revision as of 02:40, 27 September 2012

NYMU iGEM

Modeling

Objective

Before designing our experiment, we would like to do a simple simulation to estimate the efficiency and productivity of nitrogen for our modified bacteria.

Description

In order to produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to help us simulate the substrate concentration in a single cell.

Where v=reaction rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate concentration, Km= equilibrium constant of enzyme, Kcat=turnover number.

Our pathway looked like this

Reaction 2, 3, 4 were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6, 7 are the new pathways that we engineered.

For reaction 2, 3, 4, we used the equation
As for the rest, we used  instead.

To determine the enzyme concentration for our new pathways, we needed another two equations.

Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation rate or Enzyme

Combined the two equations, we got the relationship between enzyme concentration and time.

Then we combined the equation above with Michaelis-Menten’s equation.