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Team:ETH Zurich/Parameter
From 2013.igem.org
(Difference between revisions)
| Line 14: | Line 14: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td>D<sub> | + | <td>D<sub>AHL</sub></td> |
<td>4.9 x 10<sup>-6</sup> cm<sup>2</sup>/s</td> | <td>4.9 x 10<sup>-6</sup> cm<sup>2</sup>/s</td> | ||
| - | <td> | + | <td>AHL diffusion constant</td> |
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Stewart2003"/> Stewart P.S., 2003</td> | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Stewart2003"/> Stewart P.S., 2003</td> | ||
</tr> | </tr> | ||
| Line 26: | Line 26: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td>α<sub> | + | <td>α<sub>AHL</sub></td> |
<td>0.01 min<sup>-1</sup></td> | <td>0.01 min<sup>-1</sup></td> | ||
| - | <td> | + | <td>AHL synthesis rate</td> |
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td> | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td>d<sub> | + | <td>d<sub>AHL</sub></td> |
<td>0.01 min<sup>-1</sup></td> | <td>0.01 min<sup>-1</sup></td> | ||
| - | <td> | + | <td>AHL degradation rate (intracellular)</td> |
<td><a href="https://2013.igem.org/Team:ETH_Zurich/References#Basu2005"/>Basu <i>et al.</i>, 2005</td> | <td><a href="https://2013.igem.org/Team:ETH_Zurich/References#Basu2005"/>Basu <i>et al.</i>, 2005</td> | ||
</tr> | </tr> | ||
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<tr> | <tr> | ||
| - | <td>η<sub> | + | <td>η<sub>AHL</sub></td> |
<td>2</td> | <td>2</td> | ||
<td>Diffusion rate across the cell membrane</td> | <td>Diffusion rate across the cell membrane</td> | ||
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<td>α<sub>LuxR</sub></td> | <td>α<sub>LuxR</sub></td> | ||
| - | <td>0. | + | <td>0.005 μ M/min</td> |
<td>LuxR synthesis rate</td> | <td>LuxR synthesis rate</td> | ||
<td><a href="https://2013.igem.org/Team:ETH_Zurich/References#Basu2005">Basu <i>et al.</i>, 2005 </td> | <td><a href="https://2013.igem.org/Team:ETH_Zurich/References#Basu2005">Basu <i>et al.</i>, 2005 </td> | ||
| Line 81: | Line 81: | ||
<tr> | <tr> | ||
<td>d<sub>LuxR</sub></td> | <td>d<sub>LuxR</sub></td> | ||
| - | <td>0. | + | <td>0.01 min<sup>-1</sup></td> |
<td>LuxR degradation rate</td> | <td>LuxR degradation rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/References | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/References">Manefield <i>et al.</i>, 2001</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
Revision as of 16:23, 26 October 2013
Parameters
Overview of the parameters used in the models.
| Parameter | Value | Description | Reference |
|---|---|---|---|
| DAHL | 4.9 x 10-6 cm2/s | AHL diffusion constant | Stewart P.S., 2003 |
| Cagar | 0.9 | Reduced diffusion coefficient | Fatin-Rouge et al., 2004 |
| αAHL | 0.01 min-1 | AHL synthesis rate | Garcia-Ojalvo et. al., 2004 |
| dAHL | 0.01 min-1 | AHL degradation rate (intracellular) | Basu et al., 2005 |
| dOHHL,e | 4.8135 x 10-4 min-1 | OHHL extracellular decay | Horswill et al., 2007 |
| ηAHL | 2 | Diffusion rate across the cell membrane | Garcia-Ojalvo et. al., 2004 |
| ηext | 1 | Average diffusion rate for all cells | Garcia-Ojalvo et. al., 2004 |
| αLuxI | 1 μM/min | LuxI synthesis rate | Basu et al., 2005 |
| dLuxI | 0.0167 min-1 | LuxI degradation rate | MIT iGEM 2010 |
| k | 0.888 h-1 | Cell growth rate | estimated from experimental data |
| αLuxR | 0.005 μ M/min | LuxR synthesis rate | Basu et al., 2005 |
| dLuxR | 0.01 min-1 | LuxR degradation rate | Manefield et al., 2001 |
| ρR | 0.5 μM-3min-1 | LuxR/OHHL dimerization | Basu et al., 2005 |
| dR | 0.0231 min-1 | Dimer LuxR/OHHL degradation rate | Basu et al., 2005 |
| KR | 0.01 μM | LuxR/OHHL activation coefficient | Basu et al., 2005 |
| η | 1 | Hill coefficient | Basu et al., 2005 |
| αGFP | 2 μM min-1 | GFP synthesis rate | Basu et al., 2005 |
| kGFP | 0.025 | GFP basal expression | estimated |
| dGFP | 4.4432 x 10-4 min-1 | GFP degradation rate | Corish and Tyler-Smith, 1999 |
| αGusA | 1 μM min-1 | GusA synthesis rate | estimated |
| dGusA | 9.6270-5 s-1 | GusA degradation (half-life 55oC 2 hr) | Jefferson, 1995 |
| KR1 | 4.45 nM | LuxR/OHHL activation coefficient | estimated from experimental data |
| η1 | 1.7 | Hill coefficient | estimated from experimental data |
| kGusA | 0.025 | GusA basal expression | estimated |
| αAES | 1 μM min-1 | AES synthesis rate | estimated |
| dAES | 9.6270-5 s-1 | AES degradation (half-life 55oC 2 hr) | Jefferson, 1995 |
| KR2 | 12555 nM | LuxR/OHHL activation coefficient | estimated from experimental data |
| η2 | 0.8 | Hill coefficient | estimated from experimental data |
| kAES | 0.025 | AES basal expression | estimated |
