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Team:ETH Zurich/Parameter
From 2013.igem.org
(Difference between revisions)
| Line 38: | Line 38: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td>d<sub> | + | <td>d<sub>AHL,e</sub></td> |
<td>4.8135 x 10<sup>-4</sup> min<sup>-1</sup></td> | <td>4.8135 x 10<sup>-4</sup> min<sup>-1</sup></td> | ||
| - | <td> | + | <td>AHL extracellular decay</td> |
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Horswill2007"/>Horswill <i>et al.</i>, 2007</td> | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/References#Horswill2007"/>Horswill <i>et al.</i>, 2007</td> | ||
</tr> | </tr> | ||
| Line 88: | Line 88: | ||
<td>ρ<sub>R</sub></td> | <td>ρ<sub>R</sub></td> | ||
<td>0.5 μM<sup>-3</sup>min<sup>-1</sup></td> | <td>0.5 μM<sup>-3</sup>min<sup>-1</sup></td> | ||
| - | <td>LuxR/ | + | <td>LuxR/AHL dimerization</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> | ||
| Line 94: | Line 94: | ||
<td>d<sub>R</sub></td> | <td>d<sub>R</sub></td> | ||
<td>0.0231 min<sup>-1</sup></td> | <td>0.0231 min<sup>-1</sup></td> | ||
| - | <td>Dimer LuxR/ | + | <td>Dimer LuxR/AHL degradation 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> | ||
</tr> | </tr> | ||
| Line 100: | Line 100: | ||
<td>K<sub>R</sub></td> | <td>K<sub>R</sub></td> | ||
<td>0.01 μM</td> | <td>0.01 μM</td> | ||
| - | <td>LuxR/ | + | <td>LuxR/AHL activation coefficient</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> | ||
| Line 142: | Line 142: | ||
<td>K<sub>R1</sub></td> | <td>K<sub>R1</sub></td> | ||
<td>4.45 nM</td> | <td>4.45 nM</td> | ||
| - | <td> | + | <td>AHL activation coefficient </td> |
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> | ||
</tr> | </tr> | ||
| Line 172: | Line 172: | ||
<td>K<sub>R2</sub></td> | <td>K<sub>R2</sub></td> | ||
<td>12555 nM</td> | <td>12555 nM</td> | ||
| - | <td> | + | <td>AHL activation coefficient </td> |
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> | ||
</tr> | </tr> | ||
Revision as of 16:24, 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 |
| dAHL,e | 4.8135 x 10-4 min-1 | AHL 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/AHL dimerization | Basu et al., 2005 |
| dR | 0.0231 min-1 | Dimer LuxR/AHL degradation rate | Basu et al., 2005 |
| KR | 0.01 μM | LuxR/AHL 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 | AHL 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 | AHL activation coefficient | estimated from experimental data |
| η2 | 0.8 | Hill coefficient | estimated from experimental data |
| kAES | 0.025 | AES basal expression | estimated |
