Difference between revisions of "Team:NTNU Trondheim/Modeling"

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             </mrow>
 
             </mrow>
 
             </mrow>
 
             </mrow>
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             <mi>C</mi>
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             <msub>
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            <mrow>
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            <mi>C</mi>
 
             <mn>1</mn>
 
             <mn>1</mn>
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            <mo stretchy="false">−</mo>
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            </msub>
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             <mn>2</mn>
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             <msub>
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            </mrow>
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              <mi>-2C</mi>
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            <mi>C</mi>
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              <mn>1</mn>
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            <mn>2</mn>
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            </msub>
 
           </mrow>
 
           </mrow>
 
           </mtd>
 
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       </math>
 
       </math>
  
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<math xmlns="http://www.w3.org/1998/Math/MathML" display="inline">            <mi mathvariant="italic">PGad</mi>
 
 
   
 
   
 
<p>where <math xmlns="http://www.w3.org/1998/Math/MathML" display="inline">              <msub>
 
<p>where <math xmlns="http://www.w3.org/1998/Math/MathML" display="inline">              <msub>
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               <mi mathvariant="italic">mCherry</mi>
 
               <mi mathvariant="italic">mCherry</mi>
 
               <mi>m</mi>
 
               <mi>m</mi>
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             </msub></math> is mature mCherry. The rate constants are described below
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             </msub></math> is mature mCherry. The rate constants are described below in <b>Table 1</b>.
  
  

Revision as of 00:43, 19 September 2015

Modeling

The pathway triggering the expression of mCherry upon reception of Glucose is shown in Figure 1

Figure 1. Biological molecules involved in the P. Putida signaling pathway for expressing mCherry.

Using the generalized mass action equations and the pathway shown in the figure above, we can write the kinetics of the systems in the following form:

d KGN i dt = k c ( GLC e − KGN i ) − k 1 KGN i 2 PtxS 2 + k 1 C 1 d C 1 dt = k 1 KGN i PtxS − k 1 C 1 k 2 PGad d C 2 dt = k 2 C 1 PGad − k 2 C 2 − k tr C 2 d KGN 2 dt = k Gad − 2 C 1 -2C 1 d mCherry i dt = k tr C 2 − k m mCherry i − k d mCherry i d mCherry m dt = k m G i − k d mCherry m

where KGN i is the internal ketogluconate concentration, GLC e is the external glucose concentration, PtxS is the population of free PtxS, C 1 is the KGN-PtXs dimer, C 2 is the complex that involves the dimer bound to the promoter sequence, PGad is the Gad promoter concentration, mCherry i is the immature mCherry, and mCherry m is mature mCherry. The rate constants are described below in Table 1.

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