http://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&feed=atom&action=historyTeam:Bologna/Modeling - Revision history2024-03-29T10:35:44ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=168741&oldid=prevMarilisa at 03:46, 22 October 20092009-10-22T03:46:30Z<p></p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==T-REX device==</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In the below figure there's the T-REX device behaviour simulated with the mathematical model. In particular the figure number 10 outlines how the affinity between CIS and TRANS influences the production of GFP.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:cistrans.jpg|center|750px|thumb|Figure 10: T-REX Device]] </ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td></tr>
</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=168298&oldid=prevMarilisa at 03:37, 22 October 20092009-10-22T03:37:05Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td></tr>
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</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=168279&oldid=prevMarilisa: /* T-REX system */2009-10-22T03:36:38Z<p><span class="autocomment">T-REX system</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=T-REX system=</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><font size="4"></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Results of the <del class="diffchange diffchange-inline">other </del>model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Results of the model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td></tr>
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</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=167358&oldid=prevMarco.cavina at 03:08, 22 October 20092009-10-22T03:08:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= Mathematical Model =</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= Mathematical Model =</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><br></del><font size="4"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><font size="4"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Transcription and translation processes are considered similar to a second order kinetics like an enzymatic reaction: RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates. The binding between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the polymerase-promoter complex and protein for the ribosome-RBS complex. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Transcription and translation processes are considered similar to a second order kinetics like an enzymatic reaction: RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates. The binding between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the polymerase-promoter complex and protein for the ribosome-RBS complex. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Reactions=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Reactions=</div></td></tr>
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</table>Marco.cavinahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=167116&oldid=prevMarco.cavina at 03:02, 22 October 20092009-10-22T03:02:22Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>=Reactions<del class="diffchange diffchange-inline">=</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Reactions=</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. 2, Fig. 3 and Fig. 4 </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. 2, Fig. 3 and Fig. 4 </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tabella.jpg|center|500px|thumb|Table 1. Legend]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tabella.jpg|center|500px|thumb|Table 1. Legend]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>=Differential Equations<del class="diffchange diffchange-inline">=</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Differential Equations=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font size="4"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font size="4"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>=T-REX system<del class="diffchange diffchange-inline">=</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=T-REX system=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font size="4"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font size="4"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </div></td></tr>
</table>Marco.cavinahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=167077&oldid=prevMarco.cavina at 03:01, 22 October 20092009-10-22T03:01:14Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reactions==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><font size="4"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. 2, Fig. 3 and Fig. 4 </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. 2, Fig. 3 and Fig. 4 </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Symbol definitions are listed in Table 1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Symbol definitions are listed in Table 1</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tabella.jpg|center|500px|thumb|Table 1. Legend]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tabella.jpg|center|500px|thumb|Table 1. Legend]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"></font></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Differential Equations==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Differential Equations==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><font size="4"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure 5. Differential Equations]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure 5. Differential Equations]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:constantsvalue.jpg|center|800px|thumb|Table 2. Model parameters; Value of parameter was taken from the literature or obtained from experimantal data]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:constantsvalue.jpg|center|800px|thumb|Table 2. Model parameters; Value of parameter was taken from the literature or obtained from experimantal data]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To simulate the model we implemented the equation in Simulink (Figure 3 and Figure 4). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To simulate the model we implemented the equation in Simulink (Figure 3 and Figure 4). </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure 9: Simulink Model]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure 9: Simulink Model]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></font></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==T-REX system==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==T-REX system==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><font size="4"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the other model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Results of the other model simulations are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></font></ins></div></td></tr>
</table>Marco.cavinahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=166456&oldid=prevMarilisa at 02:48, 22 October 20092009-10-22T02:48:28Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reactions==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. <del class="diffchange diffchange-inline">1</del>, Fig. <del class="diffchange diffchange-inline">2 </del>and Fig. <del class="diffchange diffchange-inline">2 </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>All the biochemical reactions occurring in the testing circuit are listed in Fig. <ins class="diffchange diffchange-inline">2</ins>, Fig. <ins class="diffchange diffchange-inline">3 </ins>and Fig. <ins class="diffchange diffchange-inline">4 </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Reazioniagg.jpg|center|940px|thumb|Figure <del class="diffchange diffchange-inline">1</del>: GFP transcription and GFP translation (left); LacI transcription, LacI translation and LacI dimerization (right) ]]<br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Reazioniagg.jpg|center|940px|thumb|Figure <ins class="diffchange diffchange-inline">2</ins>: GFP transcription and GFP translation (left); LacI transcription, LacI translation and LacI dimerization (right) ]]<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[Image:Pag3.jpg|450px|thumb|Figure <del class="diffchange diffchange-inline">2</del>: Other Chemical Reactions]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[Image:Pag3.jpg|450px|thumb|Figure <ins class="diffchange diffchange-inline">3</ins>: Other Chemical Reactions]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[Image:Trans-reactions2.jpg|450px|thumb|Figure <del class="diffchange diffchange-inline">3</del>. Trans-Reactions]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[Image:Trans-reactions2.jpg|450px|thumb|Figure <ins class="diffchange diffchange-inline">4</ins>. Trans-Reactions]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Symbol definitions are listed in Table 1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Symbol definitions are listed in Table 1</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Differential Equations==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Differential Equations==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The differential equations describing the above biochemical reaction are obtained appling the law of mass action. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure <del class="diffchange diffchange-inline">3</del>. Differential Equations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure <ins class="diffchange diffchange-inline">5</ins>. Differential Equations]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Transequations2.jpg|center||540px|thumb| Figure <del class="diffchange diffchange-inline">4</del>. Differential Equations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Transequations2.jpg|center||540px|thumb| Figure <ins class="diffchange diffchange-inline">6</ins>. Differential Equations]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[Image:Constants3.jpg|center|550px|thumb|Figure <del class="diffchange diffchange-inline">5</del>: Equilibrium Constants]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[Image:Constants3.jpg|center|550px|thumb|Figure <ins class="diffchange diffchange-inline">7</ins>: Equilibrium Constants]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[Image:Algebricalconstrain2.jpg|center|650px|thumb|Figure <del class="diffchange diffchange-inline">6</del>: Algebraic Constrains]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[Image:Algebricalconstrain2.jpg|center|650px|thumb|Figure <ins class="diffchange diffchange-inline">8</ins>: Algebraic Constrains]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To simulate the model we implemented the equation in Simulink (Figure 3 and Figure 4). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To simulate the model we implemented the equation in Simulink (Figure 3 and Figure 4). </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure <del class="diffchange diffchange-inline">8</del>: Simulink Model]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure <ins class="diffchange diffchange-inline">9</ins>: Simulink Model]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Results of model <del class="diffchange diffchange-inline">simulation </del>are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==T-REX system==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In the graph above is shown the T-REX system behaviour predicted by the mathematical model. In particular figure 10 shows how the affinity influence the production of GFP. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Results of <ins class="diffchange diffchange-inline">the other </ins>model <ins class="diffchange diffchange-inline">simulations </ins>are shown in the wet lab parts [https://2009.igem.org/Team:Bologna/Characterization characterization].</div></td></tr>
</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=165436&oldid=prevMarilisa at 02:27, 22 October 20092009-10-22T02:27:07Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure 3. Differential Equations]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Differentialequations3.jpg|940px|thumb| Figure 3. Differential Equations]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Transequations2.jpg|center||540px|thumb| Figure 4. Differential Equations]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Transequations2.jpg|center||540px|thumb| Figure 4. Differential Equations]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">[[Image:constantsvalue.jpg|center|800px|thumb|Table 2. Model parameters; Value of parameter was taken from the literature or obtained from experimantal data]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|align="center"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Constants3.jpg|center|550px|thumb|Figure 5: Equilibrium Constants]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Constants3.jpg|center|550px|thumb|Figure 5: Equilibrium Constants]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Algebricalconstrain2.jpg|center|650px|thumb|Figure 6: Algebraic Constrains]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Algebricalconstrain2.jpg|center|650px|thumb|Figure 6: Algebraic Constrains]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:constantsvalue.jpg|center|800px|thumb|Table 2. Model parameters; Value of parameter was taken from the literature or obtained from experimantal data]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Simulations=</div></td></tr>
</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=165153&oldid=prevMarilisa at 02:20, 22 October 20092009-10-22T02:20:46Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure 8: Simulink Model]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ModelSandro.png|center|750px|thumb|Figure 8: Simulink Model]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Results of model simulation are shown in the wet lab parts characterization.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Results of model simulation are shown in the wet lab parts <ins class="diffchange diffchange-inline">[https://2009.igem.org/Team:Bologna/Characterization </ins>characterization<ins class="diffchange diffchange-inline">]</ins>.</div></td></tr>
</table>Marilisahttp://2009.igem.org/wiki/index.php?title=Team:Bologna/Modeling&diff=165055&oldid=prevMarilisa: /* Mathematical Model */2009-10-22T02:18:27Z<p><span class="autocomment">Mathematical Model</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= Mathematical Model =</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= Mathematical Model =</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><font size="4"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><font size="4"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Transcription and translation processes are considered similar to a second <del class="diffchange diffchange-inline">oder </del>kinetics like an enzymatic reaction: RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates. The binding between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the polymerase-promoter complex and protein for the ribosome-RBS complex. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Transcription and translation processes are considered similar to a second <ins class="diffchange diffchange-inline">order </ins>kinetics like an enzymatic reaction: RNA polymerase and ribosome perform enzymes' role, while gene promoter and RBS sequence act as substrates. The binding between enzyme and substrate leads to the formation of a complex, yielding to the final product: mRNA for the polymerase-promoter complex and protein for the ribosome-RBS complex. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></font></div></td></tr>
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</table>Marilisa