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Team:Aberdeen Scotland/parameters
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<td><b>Reference</b></td> | <td><b>Reference</b></td> | ||
</tr> | </tr> | ||
| + | <tr> | ||
| + | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>mRNA</sub></td> | ||
| + | <td>Degradation of mRNA</td> | ||
| + | <td>0.003</td> | ||
| + | <td>1</td> | ||
| + | </tr> | ||
| + | |||
<tr> | <tr> | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>X</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>X</sub></td> | ||
<td>Degradation of X</td> | <td>Degradation of X</td> | ||
| - | <td> | + | <td>0.00000802</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
| Line 22: | Line 29: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Y</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Y</sub></td> | ||
<td>Degradation of Y</td> | <td>Degradation of Y</td> | ||
| - | <td> | + | <td>0.00000802</td> |
<td>4</td> | <td>4</td> | ||
</tr> | </tr> | ||
| Line 29: | Line 36: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>λ-CI</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>λ-CI</sub></td> | ||
<td>Degradation of lambda CI</td> | <td>Degradation of lambda CI</td> | ||
| - | <td> | + | <td>0.002888</td> |
<td>6</td> | <td>6</td> | ||
</tr> | </tr> | ||
| Line 37: | Line 44: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>LacI</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>LacI</sub></td> | ||
<td>Degradation of LacI</td> | <td>Degradation of LacI</td> | ||
| - | <td> | + | <td>0.001155</td> |
<td>8</td> | <td>8</td> | ||
</tr> | </tr> | ||
| Line 44: | Line 51: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>TetR</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>TetR</sub></td> | ||
<td>Degradation of TetR</td> | <td>Degradation of TetR</td> | ||
| - | <td> | + | <td>0.00288811</td> |
<td>10</td> | <td>10</td> | ||
</tr> | </tr> | ||
| Line 51: | Line 58: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Holin</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Holin</sub></td> | ||
<td>Degradation of Holin</td> | <td>Degradation of Holin</td> | ||
| - | <td> | + | <td>0.0002</td> |
| - | <td> | + | <td>guessed; half-life of an hour</td> |
</tr> | </tr> | ||
| Line 58: | Line 65: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Endolysin</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Endolysin</sub></td> | ||
<td>Degradation of Endolysin</td> | <td>Degradation of Endolysin</td> | ||
| - | <td> | + | <td>0.0002</td> |
| - | <td> | + | <td>guessed; half-life of an hour</td> |
</tr> | </tr> | ||
| Line 65: | Line 72: | ||
<td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Antiholin</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>Antiholin</sub></td> | ||
<td>Degradation of Antiholin</td> | <td>Degradation of Antiholin</td> | ||
| - | <td> | + | <td>0.0002</td> |
| - | <td> | + | <td>guessed; half-life of an hour</td> |
| + | </tr> | ||
| + | |||
| + | |||
| + | <tr> | ||
| + | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>LuxI</sub></td> | ||
| + | <td>Degradation of LuxI</td> | ||
| + | <td>0.002888</td> | ||
| + | <td>tagged; half-life of 4 min</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>LuxR</sub></td> | ||
| + | <td>Degradation of LuxR</td> | ||
| + | <td>0.0002</td> | ||
| + | <td>0</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td><img src="https://static.igem.org/mediawiki/2009/7/79/Alpha.gif"><sub>HSL</sub></td> | ||
| + | <td>Degradation of HSL</td> | ||
| + | <td>0.00016667</td> | ||
| + | <td>0; value for AHL</td> | ||
</tr> | </tr> | ||
| Line 72: | Line 101: | ||
<td><img src="https://static.igem.org/mediawiki/2009/d/d9/Gamma.gif"><sub>Protein</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/d/d9/Gamma.gif"><sub>Protein</sub></td> | ||
<td>Translation rate of Protein</td> | <td>Translation rate of Protein</td> | ||
| - | <td>1</td> | + | <td>0.1</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
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<td><img src="https://static.igem.org/mediawiki/2009/9/90/Mu.gif"></td> | <td><img src="https://static.igem.org/mediawiki/2009/9/90/Mu.gif"></td> | ||
<td>Rate of production of HSL from LuxI</td> | <td>Rate of production of HSL from LuxI</td> | ||
| - | <td> | + | <td>0.45</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
| Line 86: | Line 115: | ||
<td><img src="https://static.igem.org/mediawiki/2009/0/09/Theta.gif"><sub>HSL</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/0/09/Theta.gif"><sub>HSL</sub></td> | ||
<td>Rate of diffusion of HSL in/out of the cell</td> | <td>Rate of diffusion of HSL in/out of the cell</td> | ||
| - | <td> | + | <td>0.4</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
| Line 93: | Line 122: | ||
<td><img src="https://static.igem.org/mediawiki/2009/0/09/Theta.gif"><sub>IPTG</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/0/09/Theta.gif"><sub>IPTG</sub></td> | ||
<td>Rate of diffusion of IPTG in/out of the cell</td> | <td>Rate of diffusion of IPTG in/out of the cell</td> | ||
| - | <td> | + | <td>0.014</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
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<td><img src="https://static.igem.org/mediawiki/2009/9/99/K.gif"><sub>P</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/9/99/K.gif"><sub>P</sub></td> | ||
<td>Rate of formation of the HSL-LuxI complex</td> | <td>Rate of formation of the HSL-LuxI complex</td> | ||
| - | <td> | + | <td>0.00010</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
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<td><img src="https://static.igem.org/mediawiki/2009/9/99/K.gif"><sub>-P</sub></td> | <td><img src="https://static.igem.org/mediawiki/2009/9/99/K.gif"><sub>-P</sub></td> | ||
<td>Rate of dissociation of the HSL-LuxI complex</td> | <td>Rate of dissociation of the HSL-LuxI complex</td> | ||
| - | <td> | + | <td>0.003</td> |
<td>2</td> | <td>2</td> | ||
</tr> | </tr> | ||
Revision as of 12:46, 13 August 2009
University of Aberdeen - Pico Plumber
iGEM 2009
Internal Dynamics Parameters
When modeling any process, it is essential to use parameters which reflect reality, otherwise the model will not give accurate predictions. Thus we spend a considerable time researching, analysing and estimating parameters so that our model will reflect real life behaviour as accuratly as possible.
| Parameter | Description | Value | Reference |
 mRNA |
Degradation of mRNA | 0.003 | 1 |
| X |
Degradation of X | 0.00000802 | 2 |
| Y |
Degradation of Y | 0.00000802 | 4 |
| λ-CI |
Degradation of lambda CI | 0.002888 | 6 |
| LacI |
Degradation of LacI | 0.001155 | 8 |
| TetR |
Degradation of TetR | 0.00288811 | 10 |
| Holin |
Degradation of Holin | 0.0002 | guessed; half-life of an hour |
| Endolysin |
Degradation of Endolysin | 0.0002 | guessed; half-life of an hour |
| Antiholin |
Degradation of Antiholin | 0.0002 | guessed; half-life of an hour |
| LuxI |
Degradation of LuxI | 0.002888 | tagged; half-life of 4 min |
| LuxR |
Degradation of LuxR | 0.0002 | 0 |
| HSL |
Degradation of HSL | 0.00016667 | 0; value for AHL |
 Protein |
Translation rate of Protein | 0.1 | 2 |
 |
Rate of production of HSL from LuxI | 0.45 | 2 |
 HSL |
Rate of diffusion of HSL in/out of the cell | 0.4 | 2 |
| IPTG |
Rate of diffusion of IPTG in/out of the cell | 0.014 | 2 |
 P |
Rate of formation of the HSL-LuxI complex | 0.00010 | 2 |
| -P |
Rate of dissociation of the HSL-LuxI complex | 0.003 | 2 |
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