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Revision as of 20:01, 18 September 2015
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Home
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Project
More about our project
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Documents
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Modelling
We take our math seriously
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Software
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Team
We are a bunch of nerdy nerds
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Practices
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 |