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Team:TorontoMaRSDiscovery/Modeling
From 2009.igem.org
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| - | + | ||
| + | =Objective= | ||
| + | |||
| + | =Model= | ||
| + | |||
| + | Click [[Image:here]] for excel file | ||
| + | |||
| + | <html> | ||
| + | <table> | ||
| + | <tr> | ||
| + | <td><b><u>Reaction</u></b></td> | ||
| + | <td><b><u>Rate Constant</u></b></td> | ||
| + | </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | |||
| + | |||
| + | <tr> <td><b> Constitutive Expression </b></td> <td> </td> </tr> | ||
| + | <tr> <td> --> lacl4 </td> <td> 1E-10 </td> </tr> | ||
| + | <tr> <td> --> tetR2 </td> <td> 1E-10 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Multimerization </b></td> <td> </td> </tr> | ||
| + | <tr> <td> 2 lacI --> lacI2 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> lacI2 --> 2 lacI </td> <td> 10 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> 2 lacI2 --> lacI4 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> lacI4 --> 2 lacI2 </td> <td> 10 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> 2 tetR --> tetR2 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> tetR2 --> 2 tetR </td> <td> 10 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> 2 Enc --> Enc2 </td> <td> 100 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Encapsulation </b></td> <td> </td> </tr> | ||
| + | <tr> <td> Enc2 + eCFPt --> Enc2:eCFPt </td> <td> 100 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Transcription</b> </td> <td> </td> </tr> | ||
| + | <tr> <td> RNAp + BBa_R0010 + LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site </td> <td> 10000000 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0010:LacI_binding_site --> RNAp + BBa_R0010 + LacI_binding_site </td> <td> 0.057 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0010:LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site* </td> <td> 0.1 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0010:LacI_binding_site* --> RNAp:DNA_eCFPt + BBa_R0010 + LacI_binding_site </td> <td> 30 </td> </tr> | ||
| + | <tr> <td> RNAp:DNA_eCFPt --> RNAp + mRNA_eCFPt </td> <td> 0.035 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> RNAp + BBa_R0040 + TetR_1 + TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2 </td> <td> 10000000 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp + BBa_R0040 + TetR_1 + TetR_2 </td> <td> 0.057 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2* </td> <td> 0.1 </td> </tr> | ||
| + | <tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2* --> RNAp:DNA_Enc + BBa_R0040 + TetR_1 + TetR_2 </td> <td> 30 </td> </tr> | ||
| + | <tr> <td> RNAp:DNA_Enc --> RNAp + mRNA_Enc </td> <td> 0.0375 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Translation </b></td> <td> </td> </tr> | ||
| + | <tr> <td> rib + mRNA_eCFPt --> rib:mRNA_eCFPt </td> <td> 100000 </td> </tr> | ||
| + | <tr> <td> rib:mRNA_eCFPt --> rib:mRNA_eCFPt_1 + mRNA_eCFPt </td> <td> 33 </td> </tr> | ||
| + | <tr> <td> rib:mRNA_eCFPt_1 --> rib + eCFPt </td> <td> 0.1154 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> rib + mRNA_Enc --> rib:mRNA_Enc </td> <td> 100000 </td> </tr> | ||
| + | <tr> <td> rib:mRNA_Enc --> rib:mRNA_Enc_1 + mRNA_Enc </td> <td> 33 </td> </tr> | ||
| + | <tr> <td> rib:mRNA_Enc_1 --> rib + Enc </td> <td> 0.1234 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Protein-DNA </b></td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4 + nsDNA --> lacI4:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> lacI4:nsDNA --> lacI4 + nsDNA </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4 + LacI_binding_site --> lacI4:LacI_binding_site </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> lacI4:LacI_binding_site --> lacI4 + LacI_binding_site </td> <td> 0.005 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2 + nsDNA --> tetR2:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> tetR2:nsDNA --> tetR2 + nsDNA </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2 + TetR_1 --> tetR2:TetR_1 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> tetR2:TetR_1 --> tetR2 + TetR_1 </td> <td> 0.005 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2 + TetR_2 --> tetR2:TetR_2 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> tetR2:TetR_2 --> tetR2 + TetR_2 </td> <td> 0.005 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Protein - Effector - DNA </b></td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4 + IPTG --> lacI4:IPTG </td> <td> 50000000 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG --> lacI4 + IPTG </td> <td> 0.1 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG + LacI_binding_site --> lacI4:IPTG:LacI_binding_site </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG:LacI_binding_site --> lacI4:IPTG + LacI_binding_site </td> <td> 0.7 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4:LacI_binding_site + IPTG --> lacI4:IPTG:LacI_binding_site </td> <td> 1000000 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG:LacI_binding_site --> lacI4:LacI_binding_site + IPTG </td> <td> 0.4 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG + nsDNA --> lacI4:IPTG:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG:nsDNA --> lacI4:IPTG + nsDNA </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4:nsDNA + IPTG --> lacI4:IPTG:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG:nsDNA --> lacI4:nsDNA + IPTG </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2 + aTc --> tetR2:aTc </td> <td> 50000000 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc --> tetR2 + aTc </td> <td> 0.1 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:aTc + TetR_1 --> tetR2:aTc:TetR_1 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:TetR_1 --> tetR2:aTc + TetR_1 </td> <td> 0.7 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:TetR_1 + aTc --> tetR2:aTc:TetR_1 </td> <td> 1000000 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:TetR_1 --> tetR2:TetR_1 + aTc </td> <td> 0.4 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:aTc + TetR_2 --> tetR2:aTc:TetR_2 </td> <td> 1.00E+09 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:TetR_2 --> tetR2:aTc + TetR_2 </td> <td> 0.7 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:TetR_2 + aTc --> tetR2:aTc:TetR_2 </td> <td> 1000000 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:TetR_2 --> tetR2:TetR_2 + aTc </td> <td> 0.4 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:aTc + nsDNA --> tetR2:aTc:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:nsDNA --> tetR2:aTc + nsDNA </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> tetR2:nsDNA + aTc --> tetR2:aTc:nsDNA </td> <td> 1000 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:nsDNA --> tetR2:nsDNA + aTc </td> <td> 1.6225 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Degredation</b> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4 --> </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> tetR2 --> </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> mRNA_eCFPt --> </td> <td> 0.0015 </td> </tr> | ||
| + | <tr> <td> mRNA_Enc --> </td> <td> 0.0015 </td> </tr> | ||
| + | <tr> <td> eCFPt --> </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> Enc2 --> </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> Enc2:eCFPt --> </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td> </td> <td> </td> </tr> | ||
| + | <tr> <td><b> Dilution</b> </td> <td> </td> </tr> | ||
| + | <tr> <td> lacI4:nsDNA --> nsDNA </td> <td> 0.000193 </td> </tr> | ||
| + | <tr> <td> tetR2:nsDNA --> nsDNA </td> <td> 0.000193 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG --> IPTG </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc --> aTc </td> <td> 0.000289 </td> </tr> | ||
| + | <tr> <td> lacI4:IPTG:nsDNA --> IPTG + nsDNA </td> <td> 0.000193 </td> </tr> | ||
| + | <tr> <td> tetR2:aTc:nsDNA --> aTc + nsDNA </td> <td> 0.000193 </td> </tr> | ||
| + | |||
| + | </table> | ||
| + | <br><br> | ||
| + | </html> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | =Simulations= | ||
| + | |||
| + | =Future Work= | ||
Revision as of 07:36, 24 September 2009
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| Home | The Team | The Project | Parts Submitted to the Registry | Modeling | Notebook |
|---|
Contents |
Objective
Model
Click File:Here for excel file
| Reaction | Rate Constant |
| Constitutive Expression | |
| --> lacl4 | 1E-10 |
| --> tetR2 | 1E-10 |
| Multimerization | |
| 2 lacI --> lacI2 | 1.00E+09 |
| lacI2 --> 2 lacI | 10 |
| 2 lacI2 --> lacI4 | 1.00E+09 |
| lacI4 --> 2 lacI2 | 10 |
| 2 tetR --> tetR2 | 1.00E+09 |
| tetR2 --> 2 tetR | 10 |
| 2 Enc --> Enc2 | 100 |
| Encapsulation | |
| Enc2 + eCFPt --> Enc2:eCFPt | 100 |
| Transcription | |
| RNAp + BBa_R0010 + LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site | 10000000 |
| RNAp:BBa_R0010:LacI_binding_site --> RNAp + BBa_R0010 + LacI_binding_site | 0.057 |
| RNAp:BBa_R0010:LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site* | 0.1 |
| RNAp:BBa_R0010:LacI_binding_site* --> RNAp:DNA_eCFPt + BBa_R0010 + LacI_binding_site | 30 |
| RNAp:DNA_eCFPt --> RNAp + mRNA_eCFPt | 0.035 |
| RNAp + BBa_R0040 + TetR_1 + TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2 | 10000000 |
| RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp + BBa_R0040 + TetR_1 + TetR_2 | 0.057 |
| RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2* | 0.1 |
| RNAp:BBa_R0040:TetR_1:TetR_2* --> RNAp:DNA_Enc + BBa_R0040 + TetR_1 + TetR_2 | 30 |
| RNAp:DNA_Enc --> RNAp + mRNA_Enc | 0.0375 |
| Translation | |
| rib + mRNA_eCFPt --> rib:mRNA_eCFPt | 100000 |
| rib:mRNA_eCFPt --> rib:mRNA_eCFPt_1 + mRNA_eCFPt | 33 |
| rib:mRNA_eCFPt_1 --> rib + eCFPt | 0.1154 |
| rib + mRNA_Enc --> rib:mRNA_Enc | 100000 |
| rib:mRNA_Enc --> rib:mRNA_Enc_1 + mRNA_Enc | 33 |
| rib:mRNA_Enc_1 --> rib + Enc | 0.1234 |
| Protein-DNA | |
| lacI4 + nsDNA --> lacI4:nsDNA | 1000 |
| lacI4:nsDNA --> lacI4 + nsDNA | 1.6225 |
| lacI4 + LacI_binding_site --> lacI4:LacI_binding_site | 1.00E+09 |
| lacI4:LacI_binding_site --> lacI4 + LacI_binding_site | 0.005 |
| tetR2 + nsDNA --> tetR2:nsDNA | 1000 |
| tetR2:nsDNA --> tetR2 + nsDNA | 1.6225 |
| tetR2 + TetR_1 --> tetR2:TetR_1 | 1.00E+09 |
| tetR2:TetR_1 --> tetR2 + TetR_1 | 0.005 |
| tetR2 + TetR_2 --> tetR2:TetR_2 | 1.00E+09 |
| tetR2:TetR_2 --> tetR2 + TetR_2 | 0.005 |
| Protein - Effector - DNA | |
| lacI4 + IPTG --> lacI4:IPTG | 50000000 |
| lacI4:IPTG --> lacI4 + IPTG | 0.1 |
| lacI4:IPTG + LacI_binding_site --> lacI4:IPTG:LacI_binding_site | 1.00E+09 |
| lacI4:IPTG:LacI_binding_site --> lacI4:IPTG + LacI_binding_site | 0.7 |
| lacI4:LacI_binding_site + IPTG --> lacI4:IPTG:LacI_binding_site | 1000000 |
| lacI4:IPTG:LacI_binding_site --> lacI4:LacI_binding_site + IPTG | 0.4 |
| lacI4:IPTG + nsDNA --> lacI4:IPTG:nsDNA | 1000 |
| lacI4:IPTG:nsDNA --> lacI4:IPTG + nsDNA | 1.6225 |
| lacI4:nsDNA + IPTG --> lacI4:IPTG:nsDNA | 1000 |
| lacI4:IPTG:nsDNA --> lacI4:nsDNA + IPTG | 1.6225 |
| tetR2 + aTc --> tetR2:aTc | 50000000 |
| tetR2:aTc --> tetR2 + aTc | 0.1 |
| tetR2:aTc + TetR_1 --> tetR2:aTc:TetR_1 | 1.00E+09 |
| tetR2:aTc:TetR_1 --> tetR2:aTc + TetR_1 | 0.7 |
| tetR2:TetR_1 + aTc --> tetR2:aTc:TetR_1 | 1000000 |
| tetR2:aTc:TetR_1 --> tetR2:TetR_1 + aTc | 0.4 |
| tetR2:aTc + TetR_2 --> tetR2:aTc:TetR_2 | 1.00E+09 |
| tetR2:aTc:TetR_2 --> tetR2:aTc + TetR_2 | 0.7 |
| tetR2:TetR_2 + aTc --> tetR2:aTc:TetR_2 | 1000000 |
| tetR2:aTc:TetR_2 --> tetR2:TetR_2 + aTc | 0.4 |
| tetR2:aTc + nsDNA --> tetR2:aTc:nsDNA | 1000 |
| tetR2:aTc:nsDNA --> tetR2:aTc + nsDNA | 1.6225 |
| tetR2:nsDNA + aTc --> tetR2:aTc:nsDNA | 1000 |
| tetR2:aTc:nsDNA --> tetR2:nsDNA + aTc | 1.6225 |
| Degredation | |
| lacI4 --> | 0.000289 |
| tetR2 --> | 0.000289 |
| mRNA_eCFPt --> | 0.0015 |
| mRNA_Enc --> | 0.0015 |
| eCFPt --> | 0.000289 |
| Enc2 --> | 0.000289 |
| Enc2:eCFPt --> | 0.000289 |
| Dilution | |
| lacI4:nsDNA --> nsDNA | 0.000193 |
| tetR2:nsDNA --> nsDNA | 0.000193 |
| lacI4:IPTG --> IPTG | 0.000289 |
| tetR2:aTc --> aTc | 0.000289 |
| lacI4:IPTG:nsDNA --> IPTG + nsDNA | 0.000193 |
| tetR2:aTc:nsDNA --> aTc + nsDNA | 0.000193 |
