Difference between revisions of "Team:NYU Abu Dhabi/Model"

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<br><br>
 
<br><br>
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<p>The following species were used</p>
+
    <h2>The following species were used</h2>
 
     <table id="species-table" class="table table-hover">
 
     <table id="species-table" class="table table-hover">
 
         <thead>
 
         <thead>
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             <tr>
 
             <tr>
 
                 <td>Recombinase</td>
 
                 <td>Recombinase</td>
−
                 <td>R</td>
+
                 <td>\(R\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>Primer</td>
 
                 <td>Primer</td>
−
                 <td>Pr</td>
+
                 <td>\(Pr\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>DNA</td>
 
                 <td>DNA</td>
−
                 <td>D</td>
+
                 <td>\(D\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>DNA Polymerase</td>
 
                 <td>DNA Polymerase</td>
−
                 <td>P</td>
+
                 <td>\(P\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>Single Strand Binding Protein (SSB)</td>
 
                 <td>Single Strand Binding Protein (SSB)</td>
−
                 <td>S</td>
+
                 <td>\(S\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>A specific binding of recombinase to a primer to form a closed complex</td>
 
                 <td>A specific binding of recombinase to a primer to form a closed complex</td>
−
                 <td>R:Pr</td>
+
                 <td>\(R:Pr\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>A specific binding of recombinase and primer to the DNA to form a closed complex</td>
 
                 <td>A specific binding of recombinase and primer to the DNA to form a closed complex</td>
−
                 <td>R:Pr:D</td>
+
                 <td>\(R:Pr:D\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>A specific binding of recombinase, primer, SSB protein to the DNA to form a closed complex</td>
 
                 <td>A specific binding of recombinase, primer, SSB protein to the DNA to form a closed complex</td>
−
                 <td>R:Pr:D:S</td>
+
                 <td>\(R:Pr:D:S\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>A specific binding of recombinase, primer, SSB protein, DNA Polymerase to the DNA to form a closed complex</td>
 
                 <td>A specific binding of recombinase, primer, SSB protein, DNA Polymerase to the DNA to form a closed complex</td>
−
                 <td>R:Pr:D:S:P</td>
+
                 <td>\(R:Pr:D:S:P\)</td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
                 <td>A specific binding of primer, SSB protein, DNA Polymerase to the DNA to form a closed complex</td>
 
                 <td>A specific binding of primer, SSB protein, DNA Polymerase to the DNA to form a closed complex</td>
−
                 <td>Pr:D:S:P</td>
+
                 <td>\(Pr:D:S:P\)</td>
−
            </tr>
+
−
 
+
−
 
+
−
            <tr>
+
−
                <td>Intermediate TetR dimer that has one specific site cleaved</td>
+
−
                <td>\(cTetR:TetR\)</td>
+
−
            </tr>
+
−
            <tr>
+
−
                <td>Intermediate TetR dimer that has one TetR cleaved binded to Cruzipain</td>
+
−
                <td>\(cTetR:TetR:Cruzipain\)</td>
+
−
            </tr>
+
−
            <tr>
+
−
                <td>Intermediate TetR dimer that has both specific sites cleaved</td>
+
−
                <td>\(cTetR_{2}\)</td>
+
−
            </tr>
+
−
            <tr>
+
−
                <td>Intermediate TetR that has its specific site cleaved</td>
+
−
                <td>\(cTetR\)</td>
+
−
            </tr>
+
−
            <tr>
+
−
                <td>TetR dimer binded to Cruzipain</td>
+
−
                <td>\(TetR_2:Cruzipain\)</td>
+
−
            </tr>
+
−
            <tr>
+
−
                <td>TetR binded to Cruzipain</td>
+
−
                <td>\(TetR:Cruzipain\)</td>
+
 
             </tr>
 
             </tr>
 
         </tbody>
 
         </tbody>

Revision as of 20:35, 17 October 2018

Mathematical Modeling


The following species were used

Species Name Symbol Used
Recombinase \(R\)
Primer \(Pr\)
DNA \(D\)
DNA Polymerase \(P\)
Single Strand Binding Protein (SSB) \(S\)
A specific binding of recombinase to a primer to form a closed complex \(R:Pr\)
A specific binding of recombinase and primer to the DNA to form a closed complex \(R:Pr:D\)
A specific binding of recombinase, primer, SSB protein to the DNA to form a closed complex \(R:Pr:D:S\)
A specific binding of recombinase, primer, SSB protein, DNA Polymerase to the DNA to form a closed complex \(R:Pr:D:S:P\)
A specific binding of primer, SSB protein, DNA Polymerase to the DNA to form a closed complex \(Pr:D:S:P\)
$$ 1. R + Pr \leftrightharpoons R:Pr $$ $$ 2. R:Pr + D \leftrightharpoons R:Pr:D $$ $$ 3. R:Pr:D + S \leftrightharpoons R:Pr:D:S $$ $$ 4. R:Pr:D:S + P \leftrightharpoons R:Pr:D:S:P $$ $$ 5. R:Pr:D:S:P \leftrightharpoons R + Pr:D:S:P $$ $$ 6. Pr:D:S:P \to 2D + S + P + Pr + D $$ $$ /frac{d[R]}{dt} = -R/cdot Pr/cdot k_1f + K_1r /cdot R:Pr + k_5f /cdot R:Pr:D:S:P - k_5r /cdot R/cdot Pr:D:S:P $$
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