| Constant name | Description | Value | units | Reference |
|---|
| c1 | aa_in,A_in → nothing rate, k_cat | 1678.2 | 1/min | 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 | A_in → 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 | L_in,A_in → [L_in+A_in] 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 | LA_in → L_in,A_in rate | 0.6 | min^-1 | http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf |
| c5 | LA_in,LA_in → LA2_in 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 | LA2_in → LA_in,LA_in rate | 0.6 | 1/min | Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013 |
| c7 | a0,LA2_in → 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+TRLV_in] → b1 rate | 10 | min^-1 | estimated |
| c11 | b1 → b0,TRLV rate | 2 | min^-1 | estimated |
| c12 | ccdb_in → nothing rate | 4.60E-03 | 1/min | https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2 |
| c12' | rfp_in→ 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 | L_in 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 | L_in → 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 | aa_in producing rate | 5.00E-09 | Mmin^-1 | estimated |
| c17 | aa_in → nothing rate | 0.072 | 1/min | http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf |
| c18 | k_m 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 | A_RBS of TRLV producing | 1 | A.U. | estimated |
| Brbs | B_RBS of ccdb producing | 1 | A.U. | estimated |
| Nmax | | 22400000 | Unitless | |
| A_0 | Concetration of AHL in the Tube | 1E(-2 ~ -9) | M | The concentration range we tested in the lab. |
| N_0 | | 100000 | Unitless | Estimated |
| tot_a | 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 |
| tot_b | 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 |
| V_in | volume of one E.Coli | 2.00E-15 | dm^3 | 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 |
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