Difference between revisions of "Team:Technion HS Israel/Modelling/Parameters"
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+ | <h1><font color="#008080">Parameters</font> </h1> | ||
+ | <p>Good model requires good constants. As a group that has built a constants database, we see it as a duty for us to use constants of a high quality. The following constants were thoroughly researched.</p> | ||
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− | <tr class="tableizer-firstrow"><th>Constant name</th><th>Description</th><th>Value</th><th>units</th><th>Reference</th></tr> | + | <col style="width: 10%;"><col style="width: 20%;"><col style="width: 10%;"><col style="width: 15%;"><col style="width: 45%;"> |
+ | <tr class="tableizer-firstrow"><th>Constant name</th><th>Description</th><th>Value</th><th>units</th><th style="width:40%">Reference</th></tr> | ||
<tr><td>c1</td><td>aa<sub>in</sub>,A<sub>in</sub> → nothing rate, k<sub>cat</sub></td><td>1678.2</td><td>min<sup>-1</sup></td><td>1. Wang LH et al. (2004) Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-Lactonase). J Biol Chem 279:4, 13645-13651.</td></tr> | <tr><td>c1</td><td>aa<sub>in</sub>,A<sub>in</sub> → nothing rate, k<sub>cat</sub></td><td>1678.2</td><td>min<sup>-1</sup></td><td>1. Wang LH et al. (2004) Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-Lactonase). J Biol Chem 279:4, 13645-13651.</td></tr> | ||
− | <tr><td>c2</td><td>A<sub>in</sub> → nothing rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html</td></tr> | + | <tr><td>c2</td><td>A<sub>in</sub> → nothing rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>><a href="http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html">http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html</a></td></tr> |
− | <tr><td>c2'</td><td>AHL cell-external degradation</td><td>4.81E-04</td><td>min<sup>-1</sup></td><td>http://www.springerlink.com/content/v36128k24t558820/</td></tr> | + | <tr><td>c2'</td><td>AHL cell-external degradation</td><td>4.81E-04</td><td>min<sup>-1</sup></td><td><a href="http://www.springerlink.com/content/v36128k24t558820/">http://www.springerlink.com/content/v36128k24t558820/</a></td></tr> |
− | <tr><td>c3</td><td>L<sub>in</sub>,A<sub>in</sub> → [L<sub>in</sub>+A<sub>in</sub>] rate</td><td>8.40E-03</td><td>mol<sup>-1</sup>min<sup>-1</sup></td><td>http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</td></tr> | + | <tr><td>c3</td><td>L<sub>in</sub>,A<sub>in</sub> → [L<sub>in</sub>+A<sub>in</sub>] rate</td><td>8.40E-03</td><td>mol<sup>-1</sup>min<sup>-1</sup></td><td><a href="http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf">http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</a></td></tr> |
− | <tr><td>c4</td><td>LA<sub>in</sub> → L<sub>in</sub>,A<sub>in</sub> rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</td></tr> | + | <tr><td>c4</td><td>LA<sub>in</sub> → L<sub>in</sub>,A<sub>in</sub> rate</td><td>0.6</td><td>min<sup>-1</sup></td><td><a href="http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf">http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</a></td></tr> |
− | <tr><td>c5</td><td>LA<sub>in</sub>,LA<sub>in</sub> → LA2<sub>in</sub> rate</td><td>6.00E-03</td><td>mol<sup>-1</sup>min<sup>-1</sup></td><td>http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</td></tr> | + | <tr><td>c5</td><td>LA<sub>in</sub>,LA<sub>in</sub> → LA2<sub>in</sub> rate</td><td>6.00E-03</td><td>mol<sup>-1</sup>min<sup>-1</sup></td><td><a href="http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf">http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</a></td></tr> |
<tr><td>c6</td><td>LA2<sub>in</sub> → LA<sub>in</sub>,LA<sub>in</sub> rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | <tr><td>c6</td><td>LA2<sub>in</sub> → LA<sub>in</sub>,LA<sub>in</sub> rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | ||
<tr><td>c7</td><td>a0,LA2<sub>in</sub> → a1 rate</td><td>10</td><td>MIN<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | <tr><td>c7</td><td>a0,LA2<sub>in</sub> → a1 rate</td><td>10</td><td>MIN<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | ||
<tr><td>c8</td><td>a1 → a0,LA2 rate</td><td>2</td><td>min<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | <tr><td>c8</td><td>a1 → a0,LA2 rate</td><td>2</td><td>min<sup>-1</sup></td><td>Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013</td></tr> | ||
− | <tr><td>c9</td><td>TRLV → nothing rate</td><td>0.0692</td><td>min<sup>-1</sup></td><td>https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters</td></tr> | + | <tr><td>c9</td><td>TRLV → nothing rate</td><td>0.0692</td><td>min<sup>-1</sup></td><td><a href="https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters">https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters</a></td></tr> |
<tr><td>c10</td><td>[b0+TRLV<sub>in</sub>] → b1 rate</td><td>10</td><td>min<sup>-1</sup></td><td>estimated</td></tr> | <tr><td>c10</td><td>[b0+TRLV<sub>in</sub>] → b1 rate</td><td>10</td><td>min<sup>-1</sup></td><td>estimated</td></tr> | ||
<tr><td>c11</td><td>b1 → b0,TRLV rate</td><td>2</td><td>min<sup>-1</sup></td><td>estimated</td></tr> | <tr><td>c11</td><td>b1 → b0,TRLV rate</td><td>2</td><td>min<sup>-1</sup></td><td>estimated</td></tr> | ||
− | <tr><td>c12</td><td>ccdb<sub>in</sub> → nothing rate</td><td>4.60E-03</td><td>min<sup>-1</sup></td><td>https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2</td></tr> | + | <tr><td>c12</td><td>ccdb<sub>in</sub> → nothing rate</td><td>4.60E-03</td><td>min<sup>-1</sup></td><td><a href="https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2">https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2</a></td></tr> |
<tr><td>c12'</td><td>rfp<sub>in</sub>→ nothing rate</td><td> </td><td> </td><td>Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,Cytometry Part A, Volume 71A Issue 10, 2007</td></tr> | <tr><td>c12'</td><td>rfp<sub>in</sub>→ nothing rate</td><td> </td><td> </td><td>Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,Cytometry Part A, Volume 71A Issue 10, 2007</td></tr> | ||
<tr><td>c13</td><td>X produciong rate</td><td>1</td><td>min<sup>-1</sup></td><td>Depends on the enzyme in question (Remember that our system is generic), and changes the result only up to a constant. Therefore, when we study the behaviour of the system its value has no significance</td></tr> | <tr><td>c13</td><td>X produciong rate</td><td>1</td><td>min<sup>-1</sup></td><td>Depends on the enzyme in question (Remember that our system is generic), and changes the result only up to a constant. Therefore, when we study the behaviour of the system its value has no significance</td></tr> | ||
<tr><td>c14</td><td>L<sub>in</sub> producing rate</td><td>5.00E-09</td><td>Mmin<sup>-1</sup></td><td>Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005</td></tr> | <tr><td>c14</td><td>L<sub>in</sub> producing rate</td><td>5.00E-09</td><td>Mmin<sup>-1</sup></td><td>Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005</td></tr> | ||
− | <tr><td>c15</td><td>L<sub>in</sub> → nothing rate</td><td>0.0231</td><td>min<sup>-1</sup></td><td>http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347</td></tr> | + | <tr><td>c15</td><td>L<sub>in</sub> → nothing rate</td><td>0.0231</td><td>min<sup>-1</sup></td><td><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347">http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347</a></td></tr> |
<tr><td>c16</td><td>aa<sub>in</sub> producing rate</td><td>5.00E-09</td><td>Mmin<sup>-1</sup></td><td>estimated</td></tr> | <tr><td>c16</td><td>aa<sub>in</sub> producing rate</td><td>5.00E-09</td><td>Mmin<sup>-1</sup></td><td>estimated</td></tr> | ||
− | <tr><td>c17</td><td>aa<sub>in</sub> → nothing rate</td><td>0.072</td><td>min<sup>-1</sup></td><td>http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf</td></tr> | + | <tr><td>c17</td><td>aa<sub>in</sub> → nothing rate</td><td>0.072</td><td>min<sup>-1</sup></td><td><a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf">http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf</a></td></tr> |
− | <tr><td>c18</td><td>k<sub>m</sub> of aiia+A->nothing</td><td>3.72E-18</td><td>mol</td><td>https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters</td></tr> | + | <tr><td>c18</td><td>k<sub>m</sub> of aiia+A->nothing</td><td>3.72E-18</td><td>mol</td><td><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters">https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters</a></td></tr> |
− | <tr><td>v1</td><td>TRLV producing without LA2</td><td>3.90E-24</td><td>mol/min</td><td>http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html</td></tr> | + | <tr><td>v1</td><td>TRLV producing without LA2</td><td>3.90E-24</td><td>mol/min</td><td><a href="http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html">http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html</a></td></tr> |
− | <tr><td>v2</td><td>TRLV producing with LA2</td><td>3.90E-21</td><td>mol/min</td><td>http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html</td></tr> | + | <tr><td>v2</td><td>TRLV producing with LA2</td><td>3.90E-21</td><td>mol/min</td><td><a href="http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html">http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html</a></td></tr> |
<tr><td>u1</td><td>ccdb producing without TRLV</td><td>1.00E-24</td><td>mol/min</td><td>estimated</td></tr> | <tr><td>u1</td><td>ccdb producing without TRLV</td><td>1.00E-24</td><td>mol/min</td><td>estimated</td></tr> | ||
<tr><td>u2</td><td>ccdb producing with TRLV</td><td>1.00E-21</td><td>mol/min</td><td>estimated</td></tr> | <tr><td>u2</td><td>ccdb producing with TRLV</td><td>1.00E-21</td><td>mol/min</td><td>estimated</td></tr> | ||
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<tr><td>A<sub>0</sub></td><td>Concetration of AHL in the Tube</td><td>1E(-2 ~ -9)</td><td>M</td><td>The concentration range we tested in the lab.</td></tr> | <tr><td>A<sub>0</sub></td><td>Concetration of AHL in the Tube</td><td>1E(-2 ~ -9)</td><td>M</td><td>The concentration range we tested in the lab.</td></tr> | ||
<tr><td>N<sub>0</sub></td><td> </td><td>100000</td><td>Unitless</td><td>Estimated</td></tr> | <tr><td>N<sub>0</sub></td><td> </td><td>100000</td><td>Unitless</td><td>Estimated</td></tr> | ||
− | <tr><td>tot<sub>a</sub></td><td>number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell</td><td>600</td><td>Unitless</td><td>Our origion of replication is pMB1 and it is a pUC derived. Copy number comes from: https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids</td></tr> | + | <tr><td>tot<sub>a</sub></td><td>number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell</td><td>600</td><td>Unitless</td><td>Our origion of replication is pMB1 and it is a pUC derived. Copy number comes from: <a href="https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids">https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids</a></td></tr> |
− | <tr><td>tot<sub>b</sub></td><td>number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell</td><td>600</td><td>Unitless</td><td>https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids</td></tr> | + | <tr><td>tot<sub>b</sub></td><td>number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell</td><td>600</td><td>Unitless</td><td><a href="https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids">https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids</a></td></tr> |
<tr><td>total time</td><td> </td><td>18*60</td><td>min</td><td> </td></tr> | <tr><td>total time</td><td> </td><td>18*60</td><td>min</td><td> </td></tr> | ||
− | <tr><td>D</td><td>diffusion constants AHL</td><td>24</td><td>Min<sup>-1</sup></td><td>http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</td></tr> | + | <tr><td>D</td><td>diffusion constants AHL</td><td>24</td><td>Min<sup>-1</sup></td><td><a href="http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf">http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf</a></td></tr> |
− | <tr><td>V<sub>in</sub></td><td>volume of one E.Coli</td><td>2.00E-15</td><td>dm<sup>3</sup></td><td>http://bionumbers.hms.harvard.edu/KeyNumbers.aspx</td></tr> | + | <tr><td>V<sub>in</sub></td><td>volume of one E.Coli</td><td>2.00E-15</td><td>dm<sup>3</sup></td><td><a href="http://bionumbers.hms.harvard.edu/KeyNumbers.aspx">http://bionumbers.hms.harvard.edu/KeyNumbers.aspx</a></td></tr> |
<tr><td>P</td><td>1E-5 ~ 1E -5</td><td>1.00E-05</td><td>Unitless</td><td> </td></tr> | <tr><td>P</td><td>1E-5 ~ 1E -5</td><td>1.00E-05</td><td>Unitless</td><td> </td></tr> | ||
− | <tr><td>T+</td><td>Cell cycle time, with plasmid</td><td>28</td><td>Unitless</td><td>Estimated. This number takes into account the effect of the plasmid on the cycle time. http://textbookofbacteriology.net/growth_3.html</td></tr> | + | <tr><td>T+</td><td>Cell cycle time, with plasmid</td><td>28</td><td>Unitless</td><td>Estimated. This number takes into account the effect of the plasmid on the cycle time. <a href="http://textbookofbacteriology.net/growth_3.html">http://textbookofbacteriology.net/growth_3.html</a></td></tr> |
− | <tr><td>T-</td><td>Cell cycle time, without plasmid</td><td>23</td><td>Unitless</td><td>Estimated. This number takes into account the effect of the antibiotics on the metabolism and thus on the cycle time. http://textbookofbacteriology.net/growth_3.html</td></tr> | + | <tr><td>T-</td><td>Cell cycle time, without plasmid</td><td>23</td><td>Unitless</td><td>Estimated. This number takes into account the effect of the antibiotics on the metabolism and thus on the cycle time. <a href="http://textbookofbacteriology.net/growth_3.html">http://textbookofbacteriology.net/growth_3.html</a></td></tr> |
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Latest revision as of 20:41, 18 September 2015
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Parameters
Good model requires good constants. As a group that has built a constants database, we see it as a duty for us to use constants of a high quality. The following constants were thoroughly researched.
Constant name | Description | Value | units | Reference |
---|---|---|---|---|
c1 | aain,Ain → nothing rate, kcat | 1678.2 | min-1 | 1. Wang LH et al. (2004) Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-Lactonase). J Biol Chem 279:4, 13645-13651. |
c2 | Ain → nothing rate | 0.6 | min-1 | >http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html |
c2' | AHL cell-external degradation | 4.81E-04 | min-1 | http://www.springerlink.com/content/v36128k24t558820/ |
c3 | Lin,Ain → [Lin+Ain] rate | 8.40E-03 | mol-1min-1 | http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf |
c4 | LAin → Lin,Ain rate | 0.6 | min-1 | http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf |
c5 | LAin,LAin → LA2in rate | 6.00E-03 | mol-1min-1 | http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf |
c6 | LA2in → LAin,LAin rate | 0.6 | min-1 | Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013 |
c7 | a0,LA2in → a1 rate | 10 | MIN-1 | Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013 |
c8 | a1 → a0,LA2 rate | 2 | min-1 | Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013 |
c9 | TRLV → nothing rate | 0.0692 | min-1 | https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters |
c10 | [b0+TRLVin] → b1 rate | 10 | min-1 | estimated |
c11 | b1 → b0,TRLV rate | 2 | min-1 | estimated |
c12 | ccdbin → nothing rate | 4.60E-03 | min-1 | https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2 |
c12' | rfpin→ nothing rate | Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,Cytometry Part A, Volume 71A Issue 10, 2007 | ||
c13 | X produciong rate | 1 | min-1 | Depends on the enzyme in question (Remember that our system is generic), and changes the result only up to a constant. Therefore, when we study the behaviour of the system its value has no significance |
c14 | Lin producing rate | 5.00E-09 | Mmin-1 | Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005 |
c15 | Lin → nothing rate | 0.0231 | min-1 | http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347 |
c16 | aain producing rate | 5.00E-09 | Mmin-1 | estimated |
c17 | aain → nothing rate | 0.072 | min-1 | http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf |
c18 | km of aiia+A->nothing | 3.72E-18 | mol | https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters |
v1 | TRLV producing without LA2 | 3.90E-24 | mol/min | http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html |
v2 | TRLV producing with LA2 | 3.90E-21 | mol/min | http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html |
u1 | ccdb producing without TRLV | 1.00E-24 | mol/min | estimated |
u2 | ccdb producing with TRLV | 1.00E-21 | mol/min | estimated |
u1' | rfp producing without TRLV | 1.00E-24 | mol/min | estimated |
u2' | rfp producing with TRLV | 1.00E-21 | mol/min | estimated |
Arbs | ARBS of TRLV producing | 1 | A.U. | estimated |
Brbs | BRBS of ccdb producing | 1 | A.U. | estimated |
Nmax | 22400000 | Unitless | ||
A0 | Concetration of AHL in the Tube | 1E(-2 ~ -9) | M | The concentration range we tested in the lab. |
N0 | 100000 | Unitless | Estimated | |
tota | number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell | 600 | Unitless | Our origion of replication is pMB1 and it is a pUC derived. Copy number comes from: https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids |
totb | number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell | 600 | Unitless | https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids |
total time | 18*60 | min | ||
D | diffusion constants AHL | 24 | Min-1 | http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf |
Vin | volume of one E.Coli | 2.00E-15 | dm3 | http://bionumbers.hms.harvard.edu/KeyNumbers.aspx |
P | 1E-5 ~ 1E -5 | 1.00E-05 | Unitless | |
T+ | Cell cycle time, with plasmid | 28 | Unitless | Estimated. This number takes into account the effect of the plasmid on the cycle time. http://textbookofbacteriology.net/growth_3.html |
T- | Cell cycle time, without plasmid | 23 | Unitless | Estimated. This number takes into account the effect of the antibiotics on the metabolism and thus on the cycle time. http://textbookofbacteriology.net/growth_3.html |