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Team:ETH Zurich/Parameter
From 2013.igem.org
(Difference between revisions)
| Line 71: | Line 71: | ||
<td>0.888 h<sup>-1</sup></td> | <td>0.888 h<sup>-1</sup></td> | ||
<td>Cell growth rate</td> | <td>Cell growth rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Modeling/Reaction_Diffusion_OOHL#growthRate">estimated</td> | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Modeling/Reaction_Diffusion_OOHL#growthRate">estimated from experimental data</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 119: | Line 119: | ||
<td> 0.025 </td> | <td> 0.025 </td> | ||
<td>GFP basal expression</td> | <td>GFP basal expression</td> | ||
| - | <td> | + | <td>estimated</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 131: | Line 131: | ||
<td>1 μM min<sup>-1</sup></td> | <td>1 μM min<sup>-1</sup></td> | ||
<td>GusA synthesis rate</td> | <td>GusA synthesis rate</td> | ||
| - | <td> | + | <td>estimated</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 143: | Line 143: | ||
<td>4.45 nM</td> | <td>4.45 nM</td> | ||
<td>LuxR/OHHL activation coefficient </td> | <td>LuxR/OHHL activation coefficient </td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated</a></td> | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 149: | Line 149: | ||
<td>1.7</td> | <td>1.7</td> | ||
<td>Hill coefficient</td> | <td>Hill coefficient</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated</a></td> | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 155: | Line 155: | ||
<td> 0.025 </td> | <td> 0.025 </td> | ||
<td>GusA basal expression</td> | <td>GusA basal expression</td> | ||
| - | <td> | + | <td>estimated</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 161: | Line 161: | ||
<td>1 μM min<sup>-1</sup></td> | <td>1 μM min<sup>-1</sup></td> | ||
<td>AES synthesis rate</td> | <td>AES synthesis rate</td> | ||
| - | <td> | + | <td>estimated</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 173: | Line 173: | ||
<td>12555 nM</td> | <td>12555 nM</td> | ||
<td>LuxR/OHHL activation coefficient </td> | <td>LuxR/OHHL activation coefficient </td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated</a></td> | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 179: | Line 179: | ||
<td>0.8</td> | <td>0.8</td> | ||
<td>Hill coefficient</td> | <td>Hill coefficient</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated</a></td> | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 185: | Line 185: | ||
<td> 0.025 </td> | <td> 0.025 </td> | ||
<td>AES basal expression</td> | <td>AES basal expression</td> | ||
| - | <td> | + | <td>estimated</td> |
</tr> | </tr> | ||
Revision as of 17:32, 22 October 2013
Parameters
Overview of the parameters used in the models.
| Parameter | Value | Description | Reference |
|---|---|---|---|
| DOHHL | 4.9 x 10-6 cm2/s | OHHL diffusion constant | Stewart P.S., 2003 |
| Cagar | 0.9 | Reduced diffusion coefficient | Fatin-Rouge et al., 2004 |
| αOHHL | 0.01 min-1 | OHHL synthesis rate | Garcia-Ojalvo et. al., 2004 |
| dOHHL | 0.01 min-1 | OHHL degradation rate (intracellular) | Basu et al., 2005 |
| dOHHL,e | 4.8135 x 10-4 min-1 | OHHL extracellular decay | Horswill et al., 2007 |
| ηOHHL | 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 | 0.001 μ M/min | LuxR synthesis rate | Basu et al., 2005 |
| dLuxR | 0.002 min-1 | LuxR degradation rate | Basu et al., 2005 |
| 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 |
