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Minnesota/9 June 2009
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Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.<br> | Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.<br> | ||
The model created was similar to that described previously except with the addition of a second tet operon (tetO2):<br><br> | The model created was similar to that described previously except with the addition of a second tet operon (tetO2):<br><br> | ||
| + | {| class="wikitable" style="text-align:center" border = "1" | ||
| + | |- | ||
| + | ! Rxn # | ||
| + | ! Reaction | ||
| + | ! Forward Kinetic Constant | ||
| + | ! Reverse Kinetic Constant | ||
| + | |- | ||
| + | |1/2||RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP||1E+07|| 1 | ||
| + | |- | ||
| + | |3||RNA:lacP -> RNAp:lacP* || .01 || | ||
| + | |- | ||
| + | |4||RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp||30|| | ||
| + | |- | ||
| + | |5||RNAp:DNAgfp -> RNAp + gfp_mRNA||30|| | ||
| + | |- | ||
| + | |6||gfp_mRNA + rib -> rib:gfp_mRNA||100000|| | ||
| + | |- | ||
| + | |7||rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA||33|| | ||
| + | |- | ||
| + | |8||rib:gfp_mRNA_1 -> rib + gfp||33|| | ||
| + | |- | ||
| + | |9||gfp_mRNA -> Ø||1.16E-03|| | ||
| + | |- | ||
| + | |10||gfp -> Ø||3.21E-05|| | ||
| + | |- | ||
| + | |11\12||tetR2 + aTc ↔ tetR2:aTc||1E+08||1E-03 | ||
| + | |- | ||
| + | |13\14||tetR2:aTc + aTc ↔ tetR2:aTc2||1E+08||1E-03 | ||
| + | |- | ||
| + | |15\16||tetR2 + tetO1 ↔ tetR2:tetO1||1E+08||1E-03 | ||
| + | |- | ||
| + | |17\18||tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1 | ||
| + | |- | ||
| + | |19\20||tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+05 | ||
| + | |- | ||
| + | |21\22||tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03 | ||
| + | |- | ||
| + | |23\24||tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2||1E+08||1E-03 | ||
| + | |- | ||
| + | |25\26||tetR2 + tetO2 ↔ tetR2:tetO2||1E+08||1E-03 | ||
| + | |- | ||
| + | |27\28||tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc||1E+08||1 | ||
| + | |- | ||
| + | |29\30||tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc2||1E+08||1E+05 | ||
| + | |- | ||
| + | |31\32||tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc||1E+08||1E-03 | ||
| + | |- | ||
| + | |33\34||tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc2||1E+08||1E-03 | ||
| + | |- | ||
| + | |35||tetR2 -> Ø||2.89E-04|| | ||
| + | |- | ||
| + | |36||tetR2:aTc -> aTc||2.89E-04|| | ||
| + | |- | ||
| + | |37||tetR2:aTc2 -> 2 aTc||2.89E-04|| | ||
| + | |- | ||
| + | |38\39||tetR2 + nsDNA ↔ tetR2:nsDNA||1000||3.2409 | ||
| + | |- | ||
| + | |40\41||tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA||1000||3.2409 | ||
| + | |- | ||
| + | |42||tetR2:aTc:nsDNA -> aTc + nsDNA||1.93E-04|| | ||
| + | |- | ||
| + | |43||tetR2:nsDNA -> nsDNA||1.93E-04|| | ||
| + | |- | ||
| + | |44||Ø -> tetR2||1E-11|| | ||
| + | |- | ||
| + | |45||Ø -> aTc||3.3E-04|| | ||
| + | |} | ||
| + | <br>Since we needed to have the aTc concentration constant both of the models created eliminated the aTc in all the equations and physically set each kinetic constant according to the desired aTc concentration. | ||
Latest revision as of 16:26, 2 August 2009
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Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.
The model created was similar to that described previously except with the addition of a second tet operon (tetO2):
| Rxn # | Reaction | Forward Kinetic Constant | Reverse Kinetic Constant |
|---|---|---|---|
| 1/2 | RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP | 1E+07 | 1 |
| 3 | RNA:lacP -> RNAp:lacP* | .01 | |
| 4 | RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp | 30 | |
| 5 | RNAp:DNAgfp -> RNAp + gfp_mRNA | 30 | |
| 6 | gfp_mRNA + rib -> rib:gfp_mRNA | 100000 | |
| 7 | rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA | 33 | |
| 8 | rib:gfp_mRNA_1 -> rib + gfp | 33 | |
| 9 | gfp_mRNA -> Ø | 1.16E-03 | |
| 10 | gfp -> Ø | 3.21E-05 | |
| 11\12 | tetR2 + aTc ↔ tetR2:aTc | 1E+08 | 1E-03 |
| 13\14 | tetR2:aTc + aTc ↔ tetR2:aTc2 | 1E+08 | 1E-03 |
| 15\16 | tetR2 + tetO1 ↔ tetR2:tetO1 | 1E+08 | 1E-03 |
| 17\18 | tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc | 1E+08 | 1 |
| 19\20 | tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2 | 1E+08 | 1E+05 |
| 21\22 | tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc | 1E+08 | 1E-03 |
| 23\24 | tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2 | 1E+08 | 1E-03 |
| 25\26 | tetR2 + tetO2 ↔ tetR2:tetO2 | 1E+08 | 1E-03 |
| 27\28 | tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc | 1E+08 | 1 |
| 29\30 | tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc2 | 1E+08 | 1E+05 |
| 31\32 | tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc | 1E+08 | 1E-03 |
| 33\34 | tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc2 | 1E+08 | 1E-03 |
| 35 | tetR2 -> Ø | 2.89E-04 | |
| 36 | tetR2:aTc -> aTc | 2.89E-04 | |
| 37 | tetR2:aTc2 -> 2 aTc | 2.89E-04 | |
| 38\39 | tetR2 + nsDNA ↔ tetR2:nsDNA | 1000 | 3.2409 |
| 40\41 | tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA | 1000 | 3.2409 |
| 42 | tetR2:aTc:nsDNA -> aTc + nsDNA | 1.93E-04 | |
| 43 | tetR2:nsDNA -> nsDNA | 1.93E-04 | |
| 44 | Ø -> tetR2 | 1E-11 | |
| 45 | Ø -> aTc | 3.3E-04 |
Since we needed to have the aTc concentration constant both of the models created eliminated the aTc in all the equations and physically set each kinetic constant according to the desired aTc concentration.
