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Team:Peking/Modeling/Luminesensor/Simulation
From 2012.igem.org
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<td style="text-align:center;">r<sub>b</sub> = 1 - [D<sub>L</sub>]/[D<sub>T</sub>]</td> | <td style="text-align:center;">r<sub>b</sub> = 1 - [D<sub>L</sub>]/[D<sub>T</sub>]</td> | ||
| - | <td style="font-size:14px;width:250px;padding: | + | <td style="font-size:14px;width:250px;padding:5px;">This indicates the repressing degree.</td> |
<td style="font-size:12px;width:200px;line-height:12px;">D<sub>T</sub> indicates the total specific binding sites, while the D<sub>L</sub> indicates the free ones among D<sub>T</sub>.</td> | <td style="font-size:12px;width:200px;line-height:12px;">D<sub>T</sub> indicates the total specific binding sites, while the D<sub>L</sub> indicates the free ones among D<sub>T</sub>.</td> | ||
</tr><tr> | </tr><tr> | ||
<td style="text-align:center;">r<sub>d</sub> = 2[L<sub>A</sub><sup>2</sup>X]/[L<sub>T</sub>]</td> | <td style="text-align:center;">r<sub>d</sub> = 2[L<sub>A</sub><sup>2</sup>X]/[L<sub>T</sub>]</td> | ||
| - | <td style="font-size:14px;width:250px;padding: | + | <td style="font-size:14px;width:250px;padding:5px;">This indicates the dimerizing degree.</td> |
<td style="font-size:12px;width:200px;line-height:12px;">L<sub>T</sub> indicates the total <i>Luminesensor</i> molecules, and L<sub>A</sub><sup>2</sup>X indicates all dimered <i>Luminesensor</i> molecules, <i>i.e.</i> L<sub>A</sub><sup>2</sup> + L<sub>A</sub><sup>2</sup>D<sub>L</sub>.</td> | <td style="font-size:12px;width:200px;line-height:12px;">L<sub>T</sub> indicates the total <i>Luminesensor</i> molecules, and L<sub>A</sub><sup>2</sup>X indicates all dimered <i>Luminesensor</i> molecules, <i>i.e.</i> L<sub>A</sub><sup>2</sup> + L<sub>A</sub><sup>2</sup>D<sub>L</sub>.</td> | ||
</tr><tr> | </tr><tr> | ||
<td style="text-align:center;">r<sub>a</sub> = <br /> ( [L<sub>A</sub>X] + 2[L<sub>A</sub><sup>2</sup>X] ) /[L<sub>T</sub>]</td> | <td style="text-align:center;">r<sub>a</sub> = <br /> ( [L<sub>A</sub>X] + 2[L<sub>A</sub><sup>2</sup>X] ) /[L<sub>T</sub>]</td> | ||
| - | <td style="font-size:14px;width:250px;padding: | + | <td style="font-size:14px;width:250px;padding:5px;">This indicates the activating degree.</td> |
<td style="font-size:12px;width:200px;line-height:12px;">L<sub>A</sub>X indicates all monomer <i>Luminesensor</i> molecules, <i>i.e.</i> L<sub>A</sub> + L<sub>A</sub>D<sub>L</sub>.</td> | <td style="font-size:12px;width:200px;line-height:12px;">L<sub>A</sub>X indicates all monomer <i>Luminesensor</i> molecules, <i>i.e.</i> L<sub>A</sub> + L<sub>A</sub>D<sub>L</sub>.</td> | ||
</tr></table> | </tr></table> | ||
| - | + | <p> | |
| - | + | The simulation result is shown below: | |
| + | </p> | ||
| + | <div class="floatC"> | ||
| + | <img src="/wiki/images/5/5e/Peking2012_ode(h).png" alt="Simulation Result" /> | ||
| + | <div> | ||
| + | <p class="description"> | ||
| + | Fig 2. ODE Simulation Result of the prototype Luminesensor. | ||
| + | </p> | ||
| + | </div> | ||
| + | </div> | ||
| + | <p> | ||
| + | From the figure above, we discovered that the activation and decay of <i>Luminesensor</i> are the pioneers of progress, and the activating rate is the most completely switched variable as lighting varies. The promoter sequences in the DNA are repressed even though the <i>Luminesensor</i> has not all dimered. | ||
| + | </p> | ||
</div> | </div> | ||
| + | </html>{{Template:Peking2012_Color_Epilogue}} | ||
Revision as of 02:00, 23 September 2012
ODE model
According to the previous network and ODE model, we listed all the differential equations (detail here) and simulated this system with MATLAB. We specifically watched three expressions to understand the mechanism for Luminesensor.
| Expression | Description | Remark |
| rb = 1 - [DL]/[DT] | This indicates the repressing degree. | DT indicates the total specific binding sites, while the DL indicates the free ones among DT. |
| rd = 2[LA2X]/[LT] | This indicates the dimerizing degree. | LT indicates the total Luminesensor molecules, and LA2X indicates all dimered Luminesensor molecules, i.e. LA2 + LA2DL. |
| ra = ( [LAX] + 2[LA2X] ) /[LT] |
This indicates the activating degree. | LAX indicates all monomer Luminesensor molecules, i.e. LA + LADL. |
The simulation result is shown below:
.png)
Fig 2. ODE Simulation Result of the prototype Luminesensor.
From the figure above, we discovered that the activation and decay of Luminesensor are the pioneers of progress, and the activating rate is the most completely switched variable as lighting varies. The promoter sequences in the DNA are repressed even though the Luminesensor has not all dimered.
