Difference between revisions of "Team:NYU Abu Dhabi/Model"
| Line 756: | Line 756: | ||
<br> | <br> | ||
| + | <p>The following parameters were used</p> | ||
| + | <table id="parameters-table" class="table table-hover"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th>Parameter</th> | ||
| + | <th>Variable Name</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td>Forward rate constant for the binding of Recombinase and Primer</td> | ||
| + | <td>\(k1f\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Reverse rate constant for the binding of Recombinase and Primer</td> | ||
| + | <td>\(k1r\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Forward rate constant for the binding of Recombinase, Primer to DNA</td> | ||
| + | <td>\(k2f\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Reverse rate constant for the binding of Recombinase, Primer to DNA</td> | ||
| + | <td>\(k2r\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Forward rate constant for the binding of Recombinase, Primer, DNA to SSB protein</td> | ||
| + | <td>\(k3f\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Reverse rate constant for the binding of Recombinase, Primer, DNA to SSB protein</td> | ||
| + | <td>\(k3r\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Forward rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase</td> | ||
| + | <td>\(k4f\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Reverse rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase</td> | ||
| + | <td>\(k4r\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Forward rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex</td> | ||
| + | <td>\(k5f\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Reverse rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex</td> | ||
| + | <td>\(k5r\)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Rate constant for the replication of DNA with the complex consists of Primer, DNA, SSB Protein, DNA Polymerase</td> | ||
| + | <td>\(kf\)</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | |||
| + | <br> | ||
$$ 1. R + Pr \leftrightharpoons R:Pr $$ | $$ 1. R + Pr \leftrightharpoons R:Pr $$ | ||
Revision as of 21:02, 17 October 2018
Mathematical Modelling
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 |
\(Pr:D:S:P\) |
The following parameters were used
| Parameter | Variable Name |
|---|---|
| Forward rate constant for the binding of Recombinase and Primer | \(k1f\) |
| Reverse rate constant for the binding of Recombinase and Primer | \(k1r\) |
| Forward rate constant for the binding of Recombinase, Primer to DNA | \(k2f\) |
| Reverse rate constant for the binding of Recombinase, Primer to DNA | \(k2r\) |
| Forward rate constant for the binding of Recombinase, Primer, DNA to SSB protein | \(k3f\) |
| Reverse rate constant for the binding of Recombinase, Primer, DNA to SSB protein | \(k3r\) |
| Forward rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase | \(k4f\) |
| Reverse rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase | \(k4r\) |
| Forward rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex | \(k5f\) |
| Reverse rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex | \(k5r\) |
| Rate constant for the replication of DNA with the complex consists of Primer, DNA, SSB Protein, DNA Polymerase | \(kf\) |
$$ 1. R + Pr \leftrightharpoons R:Pr $$ $$ 2. R:Pr + D \leftrightharpoons R:Pr:D $$ $$ 3. R:Pr:D + S \leftrightharpoons R:Pr:D:S $$ $$ 4. R:Pr:D:S + P \leftrightharpoons R:Pr:D:S:P $$ $$ 5. R:Pr:D:S:P \leftrightharpoons R + Pr:D:S:P $$ $$ 6. Pr:D:S:P \to 2D + S + P + Pr + D $$ $$ /frac{d[R]}{dt} = -R/cdot Pr/cdot k_1f + K_1r /cdot R:Pr + k_5f /cdot R:Pr:D:S:P - k_5r /cdot R/cdot Pr:D:S:P $$