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Revision as of 15:45, 17 September 2015

Technion 2015 HS Team's Wiki

The Constants Database

namedescriptionvalueunitSourceurlteam
1k1ATranscription Rate of Lac I gene21 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
2k1CTranscription Rate of E7 + Imm gene2.470588 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
3d1ADegradation Rate of Lac I mRNA0.76246 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
4d1CTranscription Rate of E7 + Imm mRNA0.0897 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
5k2ATranslation Rate of Lac I mRNA36 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
6k2CTranslation Rate of E7 + Imm mRNA4.23539 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
7d2A,d2CProtein Degradation Rate0.03465 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
8nCHill coefficeint for E7 + Imm1 This is obtained on the assumption that one Repressor
Protein binds to one Lactose molecule complex		https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
9KCDissociation Constant for E7 + Imm0.8 [1]https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
10aCConstitutive Portion for E7 + Imm0.5 Estimate since a is between 0 and 1
Implication that Lactose may not be
a very strongly Regulated Promoter		https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
11k3ABComplex Formation Rate Between
Lac I Repressor and Lactose		1 Estimate. This is based on the assumption
that the complex formation is only
dependent on the concentrations of
Lac I repressor and Lactose		https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
12kPFPhosphorylation Rate of Ai-21 Estimatehttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
13kPBDephosphorylation Rate of Ai-21 Estimatehttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
14k1CTranscription Rate of LsrR gene4.402517 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
15k1DTranscription Rate of SupD gene46.667 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
16k1ETranscription Rate of t7pTag gene1.5556 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
17k1FTranscription Rate of Lysis gene28 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
18d1CDegradation Rate of LsrR mRNA0.159845 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
19d1DDegradation Rate of SupD mRNA1.694359 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
20d1EDegradation Rate of t7pTag mRNA0.056478 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
21d1FDegradation Rate of Lysis mRNA1.0166 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
22k2CTranslation Rate of LsrR Protein7.54716 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
23k2ETranslation Rate of t7 pTag Protein2.6667 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
24k2FTranslation Rate of Lysis Protein48 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
25d2C,d2E,d2FProtein Degradation Rate0.03465 Made using Earlier assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
26nDHill coefficeint for SupD50 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
27nEHill coefficeint for t7 pTag1 Estimate. It is assuming that
one molecule of iron ion is required
to activate the production of one t7mRNA		https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
28nFHill coefficeint for Lysis1 Estimate. It is assumed that
one molecule of t7 is required
for activation of one Lysis mRNA		https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
29KDDissociation Constant for SupD15 [2]https://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
30KEDissociation Constant for t7 pTag1 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
31KFDissociation Constant for Lysis1 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
32aDConstitutive Portion for SupD0.01 Trial and Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
33aEConstitutive Portion for t7 pTag0.01 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
34aFConstitutive Portion for Lysis0.0001 Trial and Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
35k3BCComplex Formation Rate Between
LsrR Repressor and Ai-2-Phosphorylated		0.01 Trial and Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
36k3DEComplex Formation Rate Between
SupD tRNA and t7 pTag mRNA		0.000000001 Trial and Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
37SAmount of Protein Kinase28.747 From Earlier Assumptionshttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
38kfForward Reaction rate of Complex1.2 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
39krReverse Reaction rate of Complex0.5 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
40rRate of Logistic Growth0.01 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
41A & BVarying Capacity1 & 0.9 Trial And Errorhttps://2008.igem.org/Team:NTU-Singapore/Modelling/ParameterNTU-Singapore
42knPopulation and culture3.85e-3 [1] observed division ratehttps://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
43NmaxPopulation and culture; carrying capacity1e8 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
44VPopulation and culture;1e-11 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
45kdilPopulation and culture; dilution ratevaried [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
46kassocIP binding to receptor5e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
47kdissocIP binding to receptor4.55e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
48ks1Synthesis of CRE1, YPD1, SKN7 species6.16e-5 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
49ks2Synthesis of CRE1, YPD1, SKN7 species6.00e-4 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
50ks3Synthesis of CRE1, YPD1, SKN7 species2.46e-4 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
51kdimerSynthesis of CRE1, YPD1, SKN7 species20 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
52kp1Phosphorylation/Dephosphorylation reactions;0.1 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
53kp2Phosphorylation/Dephosphorylation reactions;1243 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
54kp3Phosphorylation/Dephosphorylation reactions;56 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
55kp-3Phosphorylation/Dephosphorylation reactions;4.8 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
56kdp1Phosphorylation/Dephosphorylation reactions;5.33e-2 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
57kdp3Phosphorylation/Dephosphorylation reactions;2.89e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
58kdp3Phosphorylation/Dephosphorylation reactions;4.80e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
59kd1Decay constants;5.33e-2 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
60kd2Decay constants;2.89e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
61kd3Decay constants;4.80e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
62kdipDecay constants;5e-4 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
63kdgfpDecay constants;5.77e-3 [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
64kdtetDecay constants;3.85e-3 Cell division rate (assumed stable)https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
65kdckxDecay constants;<=3.85e-3 Cell division rate, or lower if diffusion is significant.https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
66kbgfp, kbtet, kbckxBasal expression;6e-6 adapted from [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
67ktdimBasal expression;1e3 arbitraryhttps://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
68kgfpInduced expression;6e-3 adapted from [1]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
69ktetInduced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
70kckxInduced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
71Kg, Kt, KcInduced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
72αg, αt αc Induced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
73KiInduced expression;5e-6 Kass = 2e11 M-1 [2], [3]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
74βInduced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
75kipt4Induced expression;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
76ksipIPT4 enzyme kinetics;varied -https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
77CKX enzyme kineticsIPT4 enzyme kinetics;   https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
78KmIPT4 enzyme kinetics;40 ?µM [4]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
79kcatIPT4 enzyme kinetics;0.5-1000 s-1 [5], [6]https://2008.igem.org/Team:University_of_Ottawa/Modeling/ParametersUniversity of Ottawa
80Length of e.coli2μm "University of Alberta Justification: Values come from the University of Alberta?€™s datasheet on MG1655, produced to aid modelling. There is variability in size between strains - for instance, AW405 length varies between 1.5?±0.2μm. But University of Alberta datasheet is specifically for MG1655."https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
81Diameter e. coli 0.8μm University of Albertahttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
82Shape e. coliActually rod-like. A circle with r= 0.714μm will have equivalent surface area to rod-like.Circle r =0.714μm University of Albertahttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
83Mass e. coliGiven 1x10-12g for cell wet weight. Dividing this by gravity (=9.81) gives mass.1.02x10-13g University of Albertahttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
84Swimming Speed e. coli" "50μms-1 University of Alberta
A Method for Measuring Bacterial Chemotaxis Parameters in a Microcapillary Justification: University Alberta's datasheet gives 50μms-1. However, Swimming speed is affected by:
  • Viscosity (as viscosity increases the speed increases to some maximum, then decreases as the viscosity increases further. E.coli (strain:KL227 of length: 1.0μm and diameter: 0.5μm) maximum speed occurs at viscosity 8cp.
  • Temperature
  • Culture medium
  • Vary strain to strain.
  • Experimental methods

Various papers give different speeds for E. coli (most papers provide information on AW405 with a speed of ~20μms-1). The speed itself is nearly uniform during the run. The wet lab may need to measure this experimentally as we are unaware of the conditions that the speed for MG1655 was obtained. Alberta's value is higher than other values, but this probably because MG1655 is a motile strain.

https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
85Aspartate concentration detected by E. coliRelated to Run Tumble Motion.Over ~5 orders of magnitude, 10nM up to 10mM. Can detect changes of as little as ~0.1% Competitive and Cooperative Interactions in Receptor Signalling Complexes Justification: E. coli detect small changes in concentration of 0.1% via temporal comparisons (4s) over a large range ( 10-8 to 10-3 ). Most computer simulations of chemotaxis are based on experimentally determined rates and concentrations. As a result they predict that the minimum detectable concentration of Aspartate is at ~200 nM. Experiments performed by Segall et al. in 1986, exposed tethered E. coli cells to iontophoretically delivered quantities of chemoattractant. These experiments indicated that a change in receptor occupancy of as little as 1/600 could produce an detectable change in swimming behaviour. With a Kd of 1 ?µM, this corresponds to a minimum detectable concentration of about 2 nM Aspartate. Wild type E. coli cells can detect <10nM of Asp and respond to Asp concentrations of upto 1mM,(responding to over ~5 orders of magnitude). M)https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
86Temporal comparison of chemotactic gradientRelated to Run Tumble Motion.4 seconds Temporal comparisons in bacterial chemotaxis
Quantitative analysis of signalling networks
Motility of Escherichia coli cells in clusters formed by chemotactic aggregation Justification: The past second has positive weighting, the previous 3 seconds have negative weighting. E coli compares past and present concentrations by comparing the average occupancy of the receptors over the 4s. Models reflecting this system have been developed by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago c1-4 to the average receptor occupancy during the last second c0-1 . Hence b= c0-1 - c1-4 . If b>0, the cell reduces the tumbling rate to Ttumbling from the ambient value T0 , 1s-1 e.g. b>0 don't tumble. b< 0, tumble at a rate of 1s-1		https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
87Tumbling angleRelated to Run Tumble Motion.Shape parameter 4 Scale parameter 18.32 Location parameter -4.6 Chemotaxis in E. coli anaylsed by three-dimensions
AgentCell: a digital single-cell assay for bacterial chemotaxis
On Torque and tumbling in swimming Escherichia coli Justification: The tumble angle appears not to be dependant on the concentration gradient of chemoattractants/repellents. Nor is there correlation between the length of the run and the change in direction. The program uses a gamma distribution that fits the data collected by Berg and Brown. Several groups though, have observed that the tumble angle is not noramlly distributed but suggest that non-normality was only due to the experimental methods used e.g. in the capillary tube. Tumbling can cause a change in direction when as few as one flagella moves out of the bundle.		https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
88Tumble angle directionRelated to Run Tumble Motion.Bidirectional Justification: Personal communication with Howard Berg. 'The direction is random, more or less, but there is a slight forward bias. It varies from tumble to tumble. The turn-angle distribution peaks at 68?° rather than 90?°. Tumbles turn out to be more complex than believed in 1972. Motors switch independently, and a tumble can occur if one or just a few motors change their directions of rotation. Tumbles are short, as judged by the tracking microscope, because they involve filament physics rather than motor physics: a transformation in polymorphic form, following motor reversal, from normal to semi-coiled. See Darnton, N.C., Turner, L., Rojevsky, S. and Berg, H.C. On torque and tumbling in swimming Escherichia coli, J. Bacteriol. 189, 1756-1764 (2007).'https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
89Tumbling timeRelated to Run Tumble Motion.0.14?±0.19s "Chemotaxis in E. Coli anaylsed by three-dimensional tracking Justification: Exponential distribution fitted (stated to be exponential by Berg and Brown) using only the mean tumble length (not STDEV)."https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
90Relationship between tumbling angle and timeRelated to Run Tumble Motion.   https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
91Speed while TumblingRelated to Run Tumble Motion.0μm.s-1 Chemotaxis in E. Coli anaylsed by three-dimensional tracking Justification: Berg and Brown noted that AW405 slowed/stopped while tumbling.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
92Drift during runRelated to Run Tumble Motion.23?±23?° "Chemotaxis in E. Coli anaylsed by three-dimensional tracking
Persistence of direction increases the drift velocity of run and tumble chemotaxis
Bray computer modelling Justification: Drift was observed. It is what would be expected from rotational diffusion. (at 2.7cp at 32?C drift was 23?±23?°). Rotational Brownian motion cause the cell to veer off course, so that in between tumbles the probability density function f of the swimming direction e evolves according to the Fokker-Planck equation. Drift velocity in steep gradient of attractant ~7 ?µm.s-1(Berg & Turner, 1990. Note our model did not include the effects of drift"		https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
93ThrustRelated to Run Tumble Motion.Down an Asp gradient 0.41pN, Up an Asp gradient 0.4387pN Chemotaxis in E. Coli anaylsed by three-dimensional tracking
On Torque and Tumbling in Swimming E. coli
Swimming efficiency of bacterium E. coli. Justification: Average thrust =0.41pN. In the Berg and Brown paper it states that the speed of the bacteria up an aspartate chemotactic gradient increases by 7%. Therefore in our model we shall use the following; thrust DOWN the Asp gradient =0.41pN, up the Asp gradient = 0.4387pN. Data was obtained from 32 AW405s, a strain which has provided the majority of our previous parameters but is not as motile as MG1655. The value was obtained at 23?C in viscosity 0.93 and 3.07 cP for motility buffer and motility buffer with 0.18% methylcellulose, respectively. The standard deviation is not used as the speed is fixed at 50?µm.s-1 . 0.57pN is the average thrust generated in strain HCB30 (a non tumbling strain). The thrust value was obtained when the imposed flow (U) U=0 at 23?C. O.41pN was calculated using the resistance force theory treating the flagellar bundle as a single filament. The body was assumed to be prolate elipsoid using values roughly similar to ours, 2μm for length and 0.86μm for diameter.		https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
94Isotropic run lengthsRelated to Run Tumble Motion.0.86?±1.18s Chemotaxis in E. Coli anaylsed by three-dimensional tracking Justification: Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.4 Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distributionhttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
95Run length UP Aspartate gradientRelated to Run Tumble Motion.1.07?±1.80s Chemotaxis in E. Coli anaylsed by three-dimensional tracking
UCSF wiki Justification: Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown). The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution.		https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
96Run length DOWN Aspartate gradientRelated to Run Tumble Motion.0.8?±1.38s Chemotaxis in E. Coli anaylsed by three-dimensional tracking Justification: Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distributionhttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
97ViscosityRelated to Run Tumble Motion.Viscosity of water is 1.002cP at 20?°C The rotary motor of bacterial flagella., On Torque and Tumbling in swimming Escherichia coli Justification: At present the medium being used by the lab is still be discussed. Currently though the medium most resembles water and therefore the water's viscosity value can be used. This allows us to assume that the medium is Newtonian (dilute aqueous medium that doesn?€™t contain long unbranched molecules such as methylcellulose or polyvinylpyrrolidone. Note that methlycellulose does not alter the run and tumble statistics, only bundle and motor rotation rates are affected by the addition of methylcellulose). If agar were to be used then the medium would be Non-Newtonian. Even though it would be Non- Newtonian John Hogan in passing said that we could assume it is Newtonian.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
98CpMax Maximal CpxR protein concentrationUnknown (varied in the program)  https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
99kCp Maximal transcription rate of pCpxR promoter0.075min-1
ESTIMATED 		 Surface Sensing and Adhesion of Escherichia Coli controlled by the cpx-signalling pathway.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
100thetaCpx Threshold for pCpxR promoter Hill Function1 x 10-9 M
ESTIMATED		 iGEM 2008 KULeuven https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
101mCpx Co-operativity of pCpxR promoter Hill function1  https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
102dIm Degradation rate of GFP mRNA3.6 x 10-1 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
103kIp Rate of LuxI protein translation9.6 x 10-1 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
104dIp Degradation rate of LuxI protein1.67 x 10-2 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
105dGm Degradation rate of GFP protein1.65 x 10-3 min-1  Efficient GFP mutations profoundly affect mRNA transcription and translation rates https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
106kGp Rate of GFP protein translation2.4 x 10-1 min-1  Quantitative measurement of green fluorescent protein expressionhttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
107dGp Degradation rate of GFP protein2.14 x 10-4 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
108Aprod AHL production rate per LuxI enzyme3.6 min-1  [Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
109dA Degradation rate of AHL molecule1 x 10-2 min-1  A synthetic multicellular system for programmed pattern formation https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
110DA Diffusion coefficient of AHL0.23s-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
111kTp Maximal Transcription rate of ptetR promoter0.08min-1  iGEM 2007Imperial College Londonhttps://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
112dRm Degradation rate of LuxR mRNA3.6 x 10-1 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
113kRp Rate of Lux protein translation9.6 x 10-1 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
114dRp Degration rate of LuxR protein2.31 x 10-2 min-1  Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
115kLuxR Maximal transcription rate of LuxR promoter0.11 min-1  iGEM 2008 KULeuven https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
116thetaLuxR Threshold for LuxR pR promoter Hill function1.5 x 10-9 M iGEM 2008 KULeuven https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
117mLuxR Co-operativity of LuxpR promoter Hill function1.6 iGEM 2008 KULeuven https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
118rhoC LuxR/AHL dimerisation0.5 micro M-3 min-1 A synthetic multicellular system for programmed pattern formation https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
119dC Degradation rate of mCherry mRNA0.0231 min-1  A synthetic multicellular system for programmed pattern formation https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
120dMm Degradation rate of LuxR/AHL complex1.65 x 10-3 min-1  Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
121kMp Rate of mCherry protein translation2.4 x 10-1 min-1  Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
122dMp Degradation rate of mCherry protein2.14 x 10-4 min-1  Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.https://2008.igem.org/Team:BCCS-Bristol/Modeling-ParametersBCCS-Bristol
123Rate of production of HSL from LuxI0.451/s[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
124HSLRate of diffusion of HSL in/out of the cell0.41/s[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
125IPTGRate of diffusion of IPTG in/out of the cell0.0141/s[3]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
126pproductionNumber of plasmids10 medium copy plasmid number; decided within the teamhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
127platchNumber of plasmids10 medium copy plasmid number; decided within the teamhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
128plysisNumber of plasmids10 medium copy plasmid number; decided within the teamhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
129panti-lysisNumber of plasmids10 medium copy plasmid number; decided within the teamhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
130pQSNumber of plasmids10 medium copy plasmid number; decided within the teamhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
131max_productionMaximal production rate of lux box promoter0.44pops[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
132min_productionMinimal production rate of lux box promoter0.013popsestimatedhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
133latchMaximal production rate of latch promoter0.28popsSee Belowhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
134lysisMaximal production rate of lysis promoter0.0426popsSee Belowhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
135anti-lysisMaximal production rate of anti-lysis promoter0.0066popsSee Belowhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
136QSMaximal production rate of QS promoter0.018popsSee Belowhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
137KLacIDissociation constant for LacI to LacO700mSee Explanationhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
138KLacI-IPTGDissociation constant for IPTG to LacI1200mSee Explanationhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
139KTetRDissociation constant for TetR to TetO7000mSee Explanationhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
140KcIDissociation constant for cI to operon7000mSee Explanationhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
141KPDissociation constant for P to lux box700mSee Explanationhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
142nLacIHill coefficient2 [10]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
143ncIHill coefficient2 [11]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
144nTetRHill coefficient3 [1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
145nPHill coefficient2 [1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
146mRNADegradation of mRNA0.002881/s[2]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
147XDegradation of X0.000008021/s[5]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
148YDegradation of Y0.000008021/s[5]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
149λ-CIDegradation of lambda CI0.0028881/s[5]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
150LacIDegradation of LacI0.0011551/s[8]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
151TetRDegradation of TetR0.002888111/stagged; half-life of 4 minhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
152HolinDegradation of Holin0.00021/sestmated; half-life of an hourhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
153EndolysinDegradation of Endolysin0.00021/sestimated; half-life of an hourhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
154AntiholinDegradation of Antiholin0.00021/sestimated; half-life of an hourhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
155LuxIDegradation of LuxI0.0028881/stagged; half-life of 4 minhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
156LuxRDegradation of LuxR0.00021/s[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
157HSLDegradation of HSL0.000166671[8]; value for AHLhttps://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
158ProteinTranslation rate of Protein0.11/s[2]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
159PRate of formation of the HSL-LuxI complex0.00011/ms[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
160-PRate of dissociation of the HSL-LuxI complex0.0031/s[1]https://2009.igem.org/Team:Aberdeen_Scotland/parametersAberdeen Scotland
161k_1Max Transcription rate of tRNA46.67nM/minAssumption, sensitivity:0.19https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
162k_2Synthesis rate of Aa-tRNA0.08min^-1Sensitivity: 0.09https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
163k_3Max Transcription rate of T7RNAP1.5625nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
164k_4Max Translation rate of T7RNAP2.68*0.05min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
165k_5Max Transcription rate of trigger CI5.6nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
166k_6Transcription rate of bistable CI5.6nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
167k_6'Transcription rate of bistable CI1nM/minSensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
168k_7Transcription rate of T3RNAP1.75nM/minAssumption, sensitivity:1.34https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
169k_7'Transcription rate of T3RNAP1nM/minSensitivity: Sensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
170k_8Translation rate of trigger CI9.6*0.045min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
171k_8'Translation rate of bistable CI9.6*0.3min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
172k_9Max Transcription rate of CI4345.92nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
173k_10Transcription rate of CI43410.14*0.5min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
174k_11Max Translation rate of T3RNAP3*0.15min^-1Assumption, sensitivity:1.34https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
175k_12Max Transcription rate of GFP from Sal5.25nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
176k_12'Max Trasncription rate of GFP from T3RNAP5.25nM/minAssumption, sensitivity:1.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
177k_13Translation rate of GFP9*0.6min^-1Assumption, sensitivity:1.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
178k_srate of AND Gate 10.3nM^-1Sensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
179k_s'rate of AND Gate 20.3nM^-1Sensitivity: 0.18https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
180K_1dissociation constant of AraC,tRNA14nMSensitivity: 0.03https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
181K_3dissociation constant of Sal,T7RNAP0.5nMSensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
182K_5dissociation constant of T7RNAP,trigger CI3nMRefhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
183K_6dissociation constant of CI,bistable CI40nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
184K_6'dissociation constant of CI434,bistable CI50nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
185K_7dissociation constant of CI,T3RNAP40nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
186K_7'dissociation constant of CI434,T3RNAP50nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
187K_9dissociation constant of CI,CI43440nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
188K_12dissociation constant of Sal,GFP0.5nMSensitivity: Sensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
189K_12'dissociation constant of T3RNAP,GFP55nMRef: The FEBS journal 2006,273:17https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
190n_1Hill co-effiency of AraC,tRNA2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
191n_3Hill co-effiency of Sal,T7RNAP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
192n_5Hill co-effiency of T7RNAP,CI2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
193n_6Hill co-effiency of CI,bistable CI4 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
194n_6'Hill co-effiency of CI434,bistable CI2 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
195n_7Hill co-effiency of CI,T3RNAP4 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
196n_7'Hill co-effiency of CI434,T3RNAP2 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
197n_9Hill co-effiency of CI,CI4344 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
198n_12Hill co-effiency of Sal,GFP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
199n_12'Hill co-effiency of T3RNAP,GFP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
200γ_1Degradation rate of tRNA1/30+1/60min^-1Since half life of tRNA is very long,
we decided to use 60 mins instead		https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
201γ_2Degradation rate of Aa-tRNA1/30+1/40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
202γ_2'Real Degradation rate of Aa-tRNAינו-40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
203γ_3Degradation rate of T7RNAP mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
204γ_4Degradation rate of T7RNAP1/30+1/40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
205γ_5Degradation rate of trigger CI mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
206γ_6Degradation rate of bistable CI mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
207γ_7Degradation rate of T3RNAP mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
208γ_8Degradation rate of CI1/30+1/44min^-1Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
209γ_9Degradation rate of CI434 mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
210γ_10Degradation rate of CI4341/30+1/11min^-1Ref: iGEM 2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
211γ_11Degradation rate of T3RNAP1/30+1/30min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
212γ_12Degradation rate of GFP mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
213γ_13Degradation rate of GFP1/30+1/60min^-1Since half life of GFP is very long,
we use 60 mins instead		https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
214k_1Max Transcription rate of tRNA46.67nM/minAssumption, sensitivity:1.41https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
215k_2Synthesis rate of Aa-tRNA0.08min^-1Sensitivity: 0.81https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
216k_3Max Transcription rate of T7RNAP1.5625nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
217k_4Max Translation rate of T7RNAP2.68*0.05min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
218k_5Max Transcription rate of trigger CI5.6nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
219k_6Transcription rate of bistable CI5.6nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
220k_6'Transcription rate of bistable CI1nM/minSensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
221k_7Transcription rate of P216.8nM/minAssumption, sensitivity:1.23https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
222k_7'Transcription rate of P21nM/minSensitivity: Sensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
223k_8Translation rate of trigger CI9.6*0.05min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
224k_8'Translation rate of bistable CI9.6*0.5min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
225k_9Max Transcription rate of CI4345.92nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
226k_10Transcription rate of CI43410.14*1min^-1Assumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
227k_11Max Translation rate of P228.8*0.0045min^-1Assumption, sensitivity:1.23https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
228k_12Max Transcription rate of GFP from Sal5.25nM/minAssumption, sensitivity:0.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
229k_12'Max Trasncription rate of GFP from P25.25nM/minAssumption, sensitivity:1.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
230k_13Translation rate of GFP9*0.6min^-1Assumption, sensitivity:1.00https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
231k_srate of AND Gate 10.3nM^-1Sensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
232k_s'rate of AND Gate 20.01nM^-1Sensitivity: 1.29https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
233K_1dissociation constant of AraC,tRNA14nMSensitivity: 0.2https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
234K_3dissociation constant of Sal,T7RNAP0.5nMSensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
235K_5dissociation constant of T7RNAP,trigger CI3nMRefhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
236K_6dissociation constant of CI,bistable CI40nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
237K_6'dissociation constant of CI434,bistable CI50nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
238K_7dissociation constant of CI,P240nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
239K_7'dissociation constant of CI434,P250nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
240K_9dissociation constant of CI,CI43440nMRef: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
241K_12dissociation constant of Sal,GFP0.5nMSensitivity: 0https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
242K_12'dissociation constant of P2,GFP35nMSensitivity: 1.29https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
243n_1Hill co-effiency of AraC,tRNA2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
244n_3Hill co-effiency of Sal,T7RNAP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
245n_5Hill co-effiency of T7RNAP,CI2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
246n_6Hill co-effiency of CI,bistable CI4 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
247n_6'Hill co-effiency of CI434,bistable CI2 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
248n_7Hill co-effiency of CI,P24 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
249n_7'Hill co-effiency of CI434,P22 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
250n_9Hill co-effiency of CI,CI4344 Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
251n_12Hill co-effiency of Sal,GFP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
252n_12'Hill co-effiency of P2,GFP2  https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
253γ_1Degradation rate of tRNA1/30+1/60min^-1Since half life of tRNA is very long,
we decided to use 60 mins instead		https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
254γ_2Degradation rate of Aa-tRNA1/30+1/40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
255γ_2'Real Degradation rate of Aa-tRNAינו-40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
256γ_3Degradation rate of T7RNAP mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
257γ_4Degradation rate of T7RNAP1/30+1/40min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
258γ_5Degradation rate of trigger CI mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
259γ_6Degradation rate of bistable CI mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
260γ_7Degradation rate of P2 mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
261γ_8Degradation rate of CI1/30+1/44min^-1Ref: iGEM2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
262γ_9Degradation rate of CI434 mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
263γ_10Degradation rate of CI4341/30+1/11min^-1Ref: iGEM 2007 PKU Teamhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
264γ_11Degradation rate of P21/30+1/30min^-1 https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
265γ_12Degradation rate of GFP mRNA1/30+1/4.4min^-1Assumptionhttps://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
266γ_13Degradation rate of GFP1/30+1/60min^-1Since half life of GFP is very long,
we use 60 mins instead		https://2009.igem.org/Team:PKU_Beijing/Modeling/ParametersPKU Beijing
267cpLacmaximum transcription rate (M/min)5E-10 [1]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
268cpTetmaximum transcription rate (M/min)0.00000015 [2]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
269cpλmaximum transcription rate (M/min)0.00000015 estimatehttps://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
270K50IPTGdissociation constant (M)0.0000013 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
271K50LacIdissociation constant (M)0.0000008 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
272K50TetRdissociation constant (M)1.79E-10 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
273K50CIdissociation constant (M)0 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
274nIPTGHills coefficient2 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
275nLacIHills coefficient2 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
276nTetRHills coefficient3 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
277nCIHills coefficient2 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
278dLacIdegradation rate (M/min)0.1386 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
279dTetRdegradation rate (M/min)0.1386 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
280dCIdegradation rate (M/min)0.042 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
281dRFPdegradation rate (M/min)0.0063 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
282dGFPdegradation rate (M/min)0.0063 [3]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
283dmRNAdegradation rate (M/min)0.029 [4]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
284αtranslation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used)16 - 57 [5]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
285kIPTGrate constant for IPTG diffusion into cell0.92 [6]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
286ASurface area available (mm2)1735 Area of 0.2μm filter used in conjugation tests.https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
287r0initial colony radius (μm)0.8 [7]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
288gnspecific growth rate (1/hr)0.99 Determined experimentally for R751 containing cells.https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
289grcolony radial specific growth rate (μm/hr)30 [8]https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
290Ndinitial number of donors10000 Estimatehttps://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
291Nrinitial number of donors10000 Estimatehttps://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
292λintensity (CFU/mm2)5.76 Calculated using Nr/A.https://2009.igem.org/Team:TUDelft/Modeling_ParametersTUDelft
293KLacILacI repressor dissociation constant0.1 - 1 [pM] OR 800 [nM] https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
294KIPTGIPTG-LacI repressor dissociation constant1.3 [?µM] https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
295KtetRTetR repressor dissociation constant179 [pM] https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
296KcIcI repressor dissociation constant8 [pM] OR 50 [nM] https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
297KHSLHSL-LuxR activator dissociation constant0.09 - 1 [?µM] https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
298KLacIDissociation constant for LacI to LacO DNA site~1*10 -12 M OR ~1.8*10-12 M Mitchel Lewis (2005) The Lac repressor. C. R. Biologies 328 (2005) 521?€“548; Falcon C.M and Matthews K.S. (2000) Operator DNA sequence Variation Enhances High Affinity Binding by Hinge Helix Mutants of Lactose Repressor Protein. Biochemistry. 39, 11074-11084https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
299KIPTGDissociation constant for IPTG to LacI1*10-6 M "Uri Alon, An introduction to systems Biology, p244
"https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
300KtetRDissociation constant for TetR to TetO(5.6 ?± 2) ?— 10-9 M OR 1.53*10-8 M Nucleic Acids Res. 2004; 32(2): 842?€“847. Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor Annette Kamionka, Joanna Bogdanska-Urbaniak, Oliver Scholz, and Wolfgang Hillen; Volume 272, Number 11, Issue of March 14, 1997 pp. 6936-6942, The Role of the Variable Region in Tet Repressor for Inducibility by Tetracycline, Christian Berens , Dirk Schnappinger and Wolfgang Hillenhttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
301KcIDissocitation constant for cI to DNA site50 * 10-9 M https://2007.igem.org/wiki/index.php?title=ETHZ/Parametershttps://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1Aberdeen Scotland
302αTetRTetR max. production rate3.93 μM/min, updated to 1 μM/min [5]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
303αCCI max. production rate1 μM/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
304αL1LacI max. production rate1 μM/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
305αL2LacIM1 max. production rate1 μM/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
306αGGFP max. production rate2 μM/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
307αLuxILuxI max. production rate1 μM/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
308ks1AHLi production rate0.01 1/min [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
309ρRLuxR-AHL dimerization rate0.5 1/(μM3*min) [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
310αRFPRFP max. production rate1 μM/min assumptionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
311βAcAAcetaldehyde repression coefficient7.124 μM [5]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
312βTTetR repression coefficient0.01 μM, updated to 0.1 μM/min assumptionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
313βCCI repression coefficient0.008 μM [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
314βLLacI repression coefficient0.8 μM [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
315θRLuxR-AHL repression coefficient0.01 μM [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
316γTetRTetR degradation rate0.0692 1/min assumptionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
317γCCI degradation rate0.0692 1/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
318γLLacI degradation rate0.0231 1/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
319γGGFP degradation rate0.0692 1/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
320γLuxILuxI degradation rate0.0167 1/min [3]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
321ks0AHLi degradation rate1 1/min [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
322kseAHLe degradation rate1 1/min [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
323γRLuxR-AHL degradation rate0.0231 1/min [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
324γRFPRFP degradation rate0.0041 1/min [4]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
325n1LacI cooperativity coefficient2 [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
326n2CI cooperativity coefficient2 [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
327n3TetR cooperativity coefficient2 [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
328n4LuxR-AHL cooperativity coefficient1 [1]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
329n5AlcR-AcA cooperativity coefficient1.352 [5]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
330n7XylR cooperativity coefficient5 [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
331ηDiffusion rate across the cell membrane2 [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
332ηextAverage diffusion rate for all cells1 [2]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
333NNumber of cells1 assumptionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
334aXylRXylR max. production rate95.5 μM/min [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
335γXylRiXylRi degradation rate0.03553 1/min [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
336γXylRaXylRa degradation rate0.04527 1/min [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
337KXylRXylR activation coefficient1.419*10-3 μM [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
338rXylRXylRi oligomerization constant0.04315e-3 1/(μM*min) [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
339rRXylRXylRa dissociation constant0.1301e-3 1/(μM*min) [6]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
340zendMicrofluidics channel length5 cm Choice in diffusion modelhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
341RChannelMicrofluidics channel radius1 mm Choice in diffusion modelhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
342VeColiE. coli average volume2 μm3 [13] [14]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
343cdOD600, undilutedE. coli Cell Density at OD600 = 11e9 1/ml [13] [16]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
344cDilutionDilution of cell culture in microfludics channel01-אוג Choice in diffusion modelhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
345cdRelOD600, undilutedRelative E. coli Cell Density at OD600 = 1, undiluted0.001 Derived from VeColi, cdOD600, undilutedhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
346cdRelOD600, dilutedRelative E. coli Cell Density at OD600 = 1, diluted0.000125 Derived from cdRelOD600, undiluted, cDilutionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
347CAgaroseScaling coefficient for diffusion of small molecules in agarose instead of water0.9 assumptionhttps://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
348DAcAlAcetaldehyde Diffusion Constant1.23e-5 cm2/s [8]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
349mAcAlAcetaldehyde Molecular Weight44.05316 u [8]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
350Kcat,AcAlSpecific enzyme activity of acetaldehyde dehydrogenase in E. coli14.1 μmol/(min*mg) [10] [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
351[E]TMean acetaldehyde dehydrogenase enzyme concentration in E. coli1.6659 kg/m3 Estimation from cell extract, [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
352vmax,AcAlMaximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde0.02349 M/min Estimation from cell extract, [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
353KM,AcAlMichaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde10 μM [10] [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
354mADHMolecular mass of acetaldehyde dehydrogenase33442 u [12]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
355nADHMean number of acetaldehyde dehydrogenase protein molecules per E. coli cell28512.2, rounded to 30000 Estimation from cell extract, [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
356[ADH]Extractacetaldehyde dehydrogenase concentration in E. coli cell extract19 mg/ml [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
357dilExtractE. coli cell extract dilution01-דצמ [11]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
358DAHLAHL Diffusion Constant4.9e-6 cm2/s [9]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
359mAHLAHL Molecular Weight297.38990 u [15]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
360γAHL,extAHL cell-external degradation8.0225e-006/s Derived from 1 day half-life at pH 7 [7]https://2011.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
361Concentration of XNAmolecules
per cell		Notation conventionhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
362Delay due to protein X production and maturationNAsNotation conventionhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
363Maximal production rate of pVeg promoter (constitutive)0.02molecules.s-1
or pops		Estimated, see the justificationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
364Maximal production rate of pHyperSpank promoter0.02molecules.s-1
or pops		Estimated, see the justificationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
365Maximal production rate of pT7 promoter0.02molecules.s-1
or pops		Estimated, see the justificationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
366Maximal production rate of pComK promoter0.049molecules.s-1
or pops		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
367Maximal production rate of pComS promoter0.057molecules.s-1
or pops		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
368Maximal production rate of pComG promoter0.02molecules.s-1
or pops		Estimated, see the justificationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
369Basal production rate of pComK promoter0.0028molecules.s-1
or pops		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
370Basal production rate of pComG promoter0.028molecules.s-1
or pops		Is roughly one order of magnitude higher than production rate of pComK[4]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
371Dissociation constant for IPTG to LacI1200molecules
per cell		Aberdeen 2009 wikihttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
372Dissociation constant for LacI to LacO (pLac)700molecules
per cell		Aberdeen 2009 wikihttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
373Dissociation constant for T7 RNA polymerase to pT710molecules
per cell		We used the classic assumption 1nM=1 molecule per cell and [1]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
374Dissociation constant for ComK to pComK110molecules
per cell		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
375Dissociation constant for ComK to pComS100molecules
per cell		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
376ComK concentration for half maximal degradation500molecules
per cell		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
377ComS concentration for half maximal degradation50molecules
per cell		[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
378Hill coefficient for LacI/IPTG interaction2NAAberdeen 2009 wikihttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
379Hill coefficient for LacI/pHyperSpank interaction2NAAberdeen 2009 wikihttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
380Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction2NA[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
381Hill coefficient for ComK/pComS (negative feedback) interaction5NA[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
382Translation rate of proteins0.9s-1Estimated, see the justificationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
383Dilution rate in exponential phase2.88x10-4s-1Calculated with a 40 min generation time. See explanationhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
384Unrepressed degradation rate of ComK1.4x10-3s-1[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
385Unrepressed degradation rate of ComS1.4x10-3s-1[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
386Degradation rate of mRNA2.88x10-3s-1[4]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
387Degradation rate of GFP10-4s-1BioNumbershttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
388Degradation rate of RFP10-4s-1Estimated equal to GFP degradation ratehttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
389Delay due to CFP production and maturation360sEstimated equal to GFP delay (similar molecules)https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
390Delay due to YFP production and maturation360sEstimated equal to GFP delay (similar molecules)https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
391Delay due to ComK production and maturation300sArbitraryhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
392Delay due to ComS production and maturation300sArbitraryhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
393Delay for ComS repression by ComK714s[3]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
394Delay due tT7 RNA polymerase production and maturation300s[2]https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
395Delay due GFP production and maturation360sBioNumbershttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
396Delay due RFP production and maturation360sEstimated equal to GFP delay (similar molecules)https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
397Delay due to mRNA production30sBioNumbers with an approximation: all our contructs are around 1-2kbhttps://2011.igem.org/Team:Paris_Bettencourt/Modeling/ParametersParis Bettencourt
398Ltail length0.8cm[1]https://2012.igem.org/Team:Evry/parametersEvry
399lmax tail width0.07cm[1]https://2012.igem.org/Team:Evry/parametersEvry
400rhead radius0.3cm[1]https://2012.igem.org/Team:Evry/parametersEvry
401Tskinskin thickness35μm[1]https://2012.igem.org/Team:Evry/parametersEvry
402Vtailtail volume0.001cm3herehttps://2012.igem.org/Team:Evry/parametersEvry
403Vheadhead volume0.1131cm3herehttps://2012.igem.org/Team:Evry/parametersEvry
404Vtadpole volume0.1141cm3herehttps://2012.igem.org/Team:Evry/parametersEvry
405Vskinskin volume0.0041cm3herehttps://2012.igem.org/Team:Evry/parametersEvry
406Vreceptorreceptor compartment volumexxxxcm3herehttps://2012.igem.org/Team:Evry/parametersEvry
407PX<->Ypermeability between tissues X and Y10-5cm.min-1[3]https://2012.igem.org/Team:Evry/parametersEvry
408Stadpolesum of the external surfaces of the tail and the head1.219cm2herehttps://2012.igem.org/Team:Evry/parametersEvry
409Sskinskin internal surface1.1839cm2herehttps://2012.igem.org/Team:Evry/parametersEvry
410Sreceptorblood-receptor exchange surface0.0781cm2herehttps://2012.igem.org/Team:Evry/parametersEvry
411Dauxinauxin diameter0.766nm[2]https://2012.igem.org/Team:Evry/parametersEvry
412sunnatural sun light  n/ahttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
413roomsun*0.3, (UV<350nm)*0.05, (UV>=350nm)*0,90  n/ahttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
414bulb200WIncandescent light bulb  1 mhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
415k_UVR8_hvLight dependent dissociation rate UVR8 dimer2.08?·10-3 s-1 from gelshttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
416k_UVR8_decayDimerization rate UVR8 monomer8.4?·10-10 nM-1 s-1 estimatehttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
417KM_TetRTetR repression coefficient100 nM assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
418n_TetRTetR cooperativity coefficient1 [GarciaOjalvo2004]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
419k_PtetTet promoter expression strength1.1 nM s-1 optimisedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
420ABasal expression fraction0.05 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
421nHill-like pABA cooperativity coefficient10-5 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
422k_degProtein degradation rate3.85?·10-5 s-1 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
423KM_PabABPabAB Michaelis constant960?·103 nM [Roux1992]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
424k_catPabAB catalysis rate0.65 s-1 [Roux1992]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
425Chor0Intracellular chorismate concentration100 mM assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
426k_outpABA outflux rate3.85?·10-4 s-1 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
427k_Cph8_hvLight dependent activation rates-1 from photoinduction modelhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
428KM_LOVLOV repression coefficient142 nM [Strickland2007]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
429KM_Cph8Cph8 activation coefficient1000 nM estimatehttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
430KM_LacILacI repression coefficient800 nM [Basu2005]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
431KM_cIcI repression coefficient8 nM [Basu2005]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
432KM_TetRTetR repression coefficient100 nM assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
433n_LacILacI cooperativity coefficient2 [Basu2005]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
434n_cIcI cooperativity coefficient2 [Basu2005]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
435n_TetRTetR cooperativity coefficient1 [GarciaOjalvo2004]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
436n_Cph8Cph8 cooperativity coefficient1 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
437n_LOVLOV cooperativity coefficient1 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
438k_LOV_decayDark decay rate of active LOV5.8?·10-3 s-1 [Drepper2007]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
439k_Cph8_decayDark decay rate of active Cph85.8?·10-3 s-1 estimatehttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
440k_PtrpTrp promoter expression strength2.23 nM s-1 optimizedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
441k_PompCOmpC promoter expression strength3.454?·10-1 nM s-1 optimizedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
442k_P_RLambda P_R expression strength4.21?·10-2 nM s-1 optimizedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
443k_P_LLambda P_L expression strength3.0?·10-2 nM s-1 optimizedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
444ABasal expression fraction0.05 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
445k_degProtein degradation rate1.9?·10-3 s-1 assumedhttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
446ecoli_vVolume of E.coli2.0e-18 m3 Bionumbershttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
447ecoli_extcoeffExtinction coefficient of E.coli at 600nm6.022e10 m2 mol-1 Computed via OD600https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
448ecoli_absorptionAbsorption spectrum E.coliETH modeling abs ecoli.png [Kiefer2010]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
449pABA_extcoeffExtinction coefficient of pABA at 290nm1.9e3 m2 mol-1 [Quinlivan2003]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
450pABA_absorptionAbsorption spectrum pABAETH modeling abs paba.png [EC2006]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
451pABA_molarweightMolar weight of pABA137.14 g mol-1 Datasheethttps://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
452layer_heightHeight of sunscreen layer2e-5 m [Vainio2001]https://2012.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
453\(\alpha_{TetR} \)TetR max. production rate\(0.8~\mu \text{M}\cdot\text{min}^{-1} \) [5] Wilfried Weber, Markus Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique Aubel, Cornelia C Weber & Martin Fussenegger, Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology, volume 22, number 11, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
454\(\alpha_{FadR} \)FadR max. production rate\(100~\mu\text{M}\cdot\text{min}^{-1} \) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
455\(\alpha_{GLP-1} \)GLP-1 max. production rate\(1.23~\mu\text{M}\cdot\text{min}^{-1} \) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
456\(\alpha_{LacI} \)LacI? max. production rate\(0.8~\mu\text{M}\cdot\text{min}^{-1} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
457\(k_{s1} \)AHL i production rate\(0.01~\text{min}^{-1} \) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
458\(\rho_R \)LuxR-AHL dimerization rate\(0.5~\mu\text{M}^{-3}\cdot \text{min}^{-1} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
459\(\beta_{TetR} \)TetR repression coefficient\(0.13~\mu\text{M} \) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
460\(\beta_{FA} \)FA repression coefficient\(10~\mu\text{M} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
461\(\beta_{FadR} \)FadR repression coefficient\(0.13~\mu\text{M} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
462\(\beta_{LacI} \)LacI repression coefficient\(0.8~\mu\text{M} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
463\(\beta_R \)LuxR-AHL repression coefficient\(0.01~\mu\text{M} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
464\(\gamma_{TetR} \)TetR degradation rate\(0.0692~\text{min}^{-1} \) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
465\(\gamma_{LacI} \)LacI degradation rate\(0.0231~\text{min}^{-1} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
466\(\gamma_{GLP-1} \)GLP-1 degradation rate\(0.0731~\text{min}^{-1} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
467\(\gamma_{LuxI} \)LuxI degradation rate\(0.0167~\text{min}^{-1} \) [3] MIT igem 2010https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
468\(k_{s0} \)AHLi? degradation rate\(1~\text{min}^{-1} \) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
469\(k_{se} \)AHLe? degradation rate\(1~\text{min}^{-1} \) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
470\(\gamma_R \)LuxR-AHL degradation rate\(0.0231~\text{min}^{-1} \) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
471\(\gamma_{RFP} \)RFP degradation rate\(0.0041~\text{min}^{-1} \) [4] 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, 2007https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
472\(n_1\)FadR cooperativity coefficient\(3\) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
473\(n_2\)FA cooperativity coefficient\(2\) a.https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
474\(n_3\)LuxR-AHL cooperativity coefficient\(3\) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
475\(n_5\)TetR cooperativity coefficient\(2\) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
476\(n_6\)LacI cooperativity coefficient\(4\) [1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
477\(\eta\)AHL Diffusion rate across the cell membrane\(2\) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
478\(\eta\)extAverage diffusion rate for all cells\(1\) [2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
479\([E]_t \)Total active enzyme\(50~\text{U}\text{mL}^{-1} \) [8] Bengt Borgstrom, Luminal Digestion of Fats, Handbook of Physiology, The Gastrointestinal System, Intestinal Absorption and Secretion, 1991
[9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973
[11] M Lingumsky, E Granot, D Branski, H Stankiewicz, R Goldstein, Isolated lipase and colipase deficiency in two brothers, Gut, 1990		https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
480\(K_m \)Reaction rate constant\(47.9\) [6] Sulaiman Al-Zuhair, Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of palm oil by lipase, Process Biochemistry Volume 38, Issue 8, 2003
[7] Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6?€“7, 2004		https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
481\(D_{FA} \)FA Diffusion Constant\( 6.46 \times 10^{-10}~\text{m}^2\text{s}^{-1} \) [9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
482\(d\)Thickness of the unstirred water layer\( 190~\mu\text{m} \) [9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
483\( K_{cat}\)Catalytic Rate constant\(1.3\times10^{-5}\text{min}^{-1}\) [6] Sulaiman Al-Zuhair, Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of palm oil by lipase, Process Biochemistry Volume 38, Issue 8, 2003
[7] Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6?€“7, 2004		https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
484\( cd \)Relative E. coli Cell Density\( 0.1 \)  https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
485\( D_{FA} \)FA Diffusion Constant\( 6.46 \times 10^{-10}\text{m}^2\text{s}^{-1} \) [9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
486\(D_{AHL} \)AHL Diffusion Constant\( 4.9\times10^{-6}~\text{cm}^2\text{s}^{-1} \) [9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
487\( \gamma_{AHL,ext} \)AHL cell-external degradation\( 8.0225\times10^{6}~\text{s}^{-1} \) Derived from 1 day half-life at pH 7. [7] [7] Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6?€“7, 2004https://2012.igem.org/Team:NTU-Taida/Modeling/ParametersNTU-Taida
488DAHLAHL diffusion constant4.9 x 10-6 cm2/s  Stewart P.S., 2003https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
489CagarReduced diffusion coefficient0.9 Fatin-Rouge et al., 2004https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
490αAHLAHL synthesis rate0.01 min-1  Garcia-Ojalvo et. al., 2004https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
491dAHLAHL degradation rate (intracellular)0.01 min-1 Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
492dAHL,eAHL extracellular decay4.8135 x 10-4 min-1 Horswill et al., 2007https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
493ηAHLDiffusion rate across the cell membrane2  Garcia-Ojalvo et. al., 2004https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
494ηextAverage diffusion rate for all cells1.3333  Garcia-Ojalvo et. al., 2004https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
495αLuxILuxI synthesis rate1 μM/min Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
496dLuxILuxI degradation rate0.0167 min-1  MIT iGEM 2010https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
497kCell growth rate0.888 h-1 estimated from experimental datahttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
498αLuxRLuxR synthesis rate0.005 μ M/min Basu et al., 2005 https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
499dLuxRLuxR degradation rate0.01 min-1 Manefield et al., 2002https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
500ρRLuxR/AHL dimerization0.5 μM-3min-1 Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
501dRDimer LuxR/AHL degradation rate0.0231 min-1 Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
502KRLuxR/AHL activation coefficient0.013 nM estimated from experimental data (scaled)https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
503nHill coefficient1 Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
504αGFPGFP synthesis rate2 μM min-1 Basu et al., 2005https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
505dGFPGFP degradation rate4.4432 x 10-4 min-1 Corish and Tyler-Smith, 1999 https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
506αGusAGusA synthesis rate1 μM min-1 estimatedhttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
507dGusAGusA degradation (half-life 55oC 2 hr)9.6270-5 s-1 Jefferson, 1995https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
508KR1AHL activation coefficient4.45 nM estimated from experimental datahttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
509n1Hill coefficient1.7 estimated from experimental datahttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
510kleakyGusA basal expression0.0375 estimatedhttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
511αAESAES synthesis rate1 μM min-1 estimatedhttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
512dAESAES degradation (half-life 55oC 2 hr)9.6270-5 s-1 Jefferson, 1995https://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
513KR2AHL activation coefficient12555 nM estimated from experimental datahttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
514n2Hill coefficient0.8 estimated from experimental datahttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
515kGFPHydrolases basal expression0.0375 estimatedhttps://2013.igem.org/Team:ETH_Zurich/ParameterETH Zurich
516Transcription rate of cI4200/Gene Length (nM/min)5.6  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
517Translation rate of cI2400RBS/Protein Length9.6  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
518Transcription rate of VIP4200/Gene Length (nM/min)1.74129353  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
519Translation rate of VIP2400RBS/Protein Length2.985075  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
520Transcription rate of GFP4200/Gene Length (nM/min)5.53359684  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
521Translation rate of GFP2400RBS/Protein Length9.486166  https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
522Degradation rate of cI (mRNAHalf life = 6.8 min, Division time = 30 min0.18063836 (Selinger, GW, et al., 2003)https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
523Degradation rate of cI (protein)Half life > 10 h; division time = 30 min0.03885825 (Varshavsky, (1997) and Tobias et al., 1991)https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-ParametersCIDEB-UANL Mexico
524αLuxRProduction rate of LuxR0.005 μMmin-1 Literature [20]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
525kRLuxRate of formation of RLux from LuxAHL and LuxR0.1 nM-1min-1 Literature [19]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
526k-RLuxDissociation rate of RLux10 min-1 Literature [19]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
527KmLuxLumped parameter for the Lux system10 nM Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
528dLuxAHLExternal degradation rate of LuxAHL (30C6HSL)0.004 min-1 Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
529dLuxRDegradation rate of LuxR0.0231 min-1 Literature [21]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
530dRLuxDegradation rate of RLux0.0231 min-1 Literature [20]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
531dmRNABxb1Degradation rate of mRNABxb10.2773 min-1 Literature [22]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
532dBxb1Degradation rate of Bxb10.01 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
533LPLuxLeakiness after using riboswitch for Plux0.01463 nMmin-1 Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
534KmRNABxb1Rate of transcription of Bxb15 nMmin-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
535kBxb1Rate of formation of Bxb10.1 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
536αLasRProduction rate of LasR0.005 μMmin-1 Literature [20](Assumed to be the same as Lux system)https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
537kRLasRate of formation of RLas from LasAHL and LasR0.1 nM-1min-1 Literature [19] (Assumed to be the same as Lux system)https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
538k-RLasDissociation rate of RLas10 min-1 Literature [19](Assumed to be the same as Lux system)https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
539KmLasLumped parameter for the Las system0.45 nM Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
540dLasAHLDegradation rate of LasAHL (30C12HSL)0.004 min-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
541dLasRDegradation rate of LasR0.0231 min-1 Literature [21] (Assumed to be the same as Lux system)https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
542dRLasDegradation rate of RLas0.0231 min-1 Literature [20] (Assumed to be the same as 
Lux system)
https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
543dmRNAϕc31Degradation rate of mRNAϕc310.2773 min-1 Literature [22]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
544dϕc31Degradation rate of ϕC310.01 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
545LPLasLeakiness after using riboswitch for Plas0.02461 nMmin-1 Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
546KmRNAϕc31Rate of transcription of ϕc315 nMmin-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
547kϕc31Rate of formation of ϕc310.1 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
548kDBxb1Dimerization rate of Bxb11 nM-1min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
549k-DBxb1Dissociation rate of DBxb110-6 min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
550kSABxb1Rate of formation of SABxb1 from DBxb1 and SIBxb11 nM-1min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
551k-SABxb1Dissociation rate of SABxb110-6 min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
552dDBxb1Degradation rate of DBxb10.02 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
553kDϕc31Dimerization rate of ϕc311 nM-1min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
554k-Dϕc31Rate of dissociation of Dϕc3110-6 min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
555kSAϕc31Rate of formation of SAϕc31 from Dϕc31 and SIϕc311 nM-1min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
556k-SAϕc31Rate of dissociation of SAϕc3110-6 min-1 Fittedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
557dDϕc31Degradation rate of Dϕc310.02 min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
558kToffBxb1Rate of flipping of Ton,i to ToffBxb10.1 nM-2min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
559k-ToffBxb1Rate of flipping of ToffBxb1 to Ton,f0.1 nM-2min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
560kToffϕc31Rate of flipping of Ton,i to Toffϕc310.1 nM-2min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
561k-Toffϕc31Rate of flipping of Toffϕc31 to Ton,f0.1 nM-2min-1 Assumedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
562kmRNAGFPProduction rate of mRNAGFP5 nMmin-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
563kGFPRate of formation of folded GFP1 min-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
564dmRNAGFPDegradation rate of mRNAGFP0.2773 min-1 Literature [22]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
565dGFPDegradation rate of GFP0.0049 min-1 Fitted to experimental datahttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
566kmRNALasIProduction rate of mRNALasI5 nMmin-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
567kLasIRate of formation of LasI20 min-1 Estimatedhttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
568dmRNALasIDegradation rate of mRNALasI0.2773 min-1 Literature [22]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
569dLasIDegradation rate of LasI0.0167 min-1 Literature [21]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
570kLasAHLProduction rate of LasAHL (30C12HSL) from the LasI0.04 min-1 Literature [19]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
571θKm value for the production of mRNAGFP and mRNALasI0.01 μM Literature [20] (approximation)https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
572DAHLextDiffusion coefficient of extracellular AHL in liquid4.9 10-6 cm2/s Literature [27]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
573DmDiffusion rate of AHL through the membrane100 min-1 Estimated from literature [27]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
574rGrowth rate of E. coli in our alginate beads0.006 min-1  https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
575αRatio of E. coli volume to the volume of one bead100 min-1 V E. coli from literature [28], bead volume from experimental setuphttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
576N0Initial number of cells per bead107 cells Experimental setuphttps://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
577NmMaximum number of cells per bead8 107 cells Estimated from literature [29]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
578CbeadsCorrection factor (a priori) for diffusion of LuxAHL in alginate beads1 Estimated from literature [30]https://2014.igem.org/Team:ETH_Zurich/modeling/parametersETH Zurich
579\(K_{d,\text{LuxRAHL}}\)Dissociation constant between luxR and AHL100 nM Weber, 2013https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
580\(\text{LuxR}_\text{tot}\)Total concentration of LuxR0.0025 μM estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
581\(a_\mathrm{LuxI}\)Maximal production rate of LuxI1 μM.min-1 Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
582\(a_\mathrm{LuxI,ribo}\)Maximal production rate of LuxI0.1 μM.min-1 ETHZ 2014https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
583\(k_\mathrm{leaky}\)Coefficient for leakiness dependency on LuxR concentration of PLuxR promoter0.0375 μM-1  ETHZ 2013 https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
584\(K_\mathrm{a,LuxRAHL}\)Activation coefficient of LuxRAHL0.45 nM ETHZ 2014https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
585\(K_\mathrm{LuxRAHL,ribo}\)Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter285 nM ETHZ 2014https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
586\(L_\mathrm{lux,ribo}\)Leakiness after using riboswitch for Plux0.01463 nM.min-1 ETHZ 2014https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
587\(n_\mathrm{lux}\)Hill coefficient for LuxRAHL activation1.7 ETHZ 2014https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
588\(d_\mathrm{LuxI}\)Degradation rate of LuxI0.0167 min-1 MIT 2010https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
589\(a_\mathrm{AHL}\)Production rate of AHL0.04 μM.min-1 Weber, 2013https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
590\(d_\mathrm{AHL}\)Degradation rate of AHL0.01 min-1 Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
591\(v_\mathrm{AiiA}\)Maximal conversion rate of AiiA\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)  https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
592\(k_\mathrm{cat}\)Turnover number of AiiA1.63 103min-1 Wang, 2004https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
593\(C_\mathrm{AiiA}\)Concentration of AiiAvaried  https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
594\(K_\mathrm{M,AiiA}\)Half-maximal rate substrate concentration of AiiA2.95 103 μM Wang, 2004https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
595\(a_\mathrm{GFP}\)Maximal production rate of GFP2 μM.min-1 Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
596\(d_\mathrm{GFP}\)Degradation rate of GFP0.01 min-1 estimated from doubling time of E. colihttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
597\(N_{d}\)Number of E. coli in the doughnut150 Maximal number of E. coli that would fit on the surfacehttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
598\(N_{b,max}\)Maximum number of E. coli in the bulk12798 Considering the maximal OD is 2https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
599\(V_{cell,d}\)Volume around an E. coli in the doughnut6 μm3 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
600\(V_{cell,b,worst}\)Volume around an E. coli in the bulk78 μm3 Worst case, estimated from \(N_{b,max}\)https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
601\(V_{cell,b,norm}\)Volume around an E. coli in the bulk1000 μm3 Normal casehttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
602\(\text{B}\)\(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\)0.000001 - 4  https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
603\(\text{Lac}_{\text{ini}}\)Initial concentration of lactate in the medium0.1 μM - 2 μM Low concentration of lactate in the mediumhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
604\(K_\mathrm{d,DLL}\)Dissociation constant between the dimer of Lldr and Lactate10 μM2 - 10000 μM2  https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
605\(\alpha\)Multiplication factor between the initial concentration of Lactate and Production of normal cells1 - 150 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
606\(F_\mathrm{C}\)Fold change between Lactate production by cancer and normal cells2 - 4 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
607\(a_1\)\(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)0.05 - 1000  https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
608\( a_\mathrm{LacI}\)Maximal production rate of LacI0.05 μM.min-1 - 1 μM.min-1 Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
609\( d_\mathrm{LacI}\)Degradation rate of LacI0.01 min-1 - 0.1 min-1 Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
610\( K_\mathrm{R,LacI}\)Repression coefficient of LacI0.1 μM - 10 μM Basu, 2005https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
611\( \gamma_1\)\( \frac{L_\mathrm{2tot}}{K_\mathrm{R,L}}\)5 - 10000 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
612\( L_\mathrm{2tot}\)Total concentration of LldR dimer0.5 μM - 10 μM estimated from paxdbhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
613\( K_\mathrm{R,L}\)Repression coefficient of LldR0.001 μM - 0.1 μM estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
614\( \gamma_2\)\(\frac{IPTG_{tot}}{K_{IL}}\)0 - 500 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
615\( \frac{a_1}{\gamma_2+1}\) 0.001 - 1000 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
616\( n_1\)Hill coefficient of LldR0.5 - 2.5 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
617\( n_2\)Hill coefficient of LacI1.5 - 2.5 estimatedhttps://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
618\(D_\text{AHL,agar}\)Diffusion coefficient of AHL in agar\(3.0\times 10^{-10} m^2/s\) - \(4.41\times 10^{-10} m^2/s\) Trovato, 2014
Fatin-Rouge, 2004		https://2015.igem.org/Team:ETH_Zurich/Modeling/ParametersETH Zurich
619c1max0.01 [mM/h]max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Estimatehttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
620c2max0.01 [mM/h]max. transcription rate of LuxR-activated promoter (per gene) Estimatehttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
621lhi25high-copy plasmid number Estimatehttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
622llo5low-copy plasmid number Estimatehttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
623a0.01basic production levels Estimatehttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
624dLacI2.31e-3 [1/s]degradation of LacI Ref. [10] Tuttle et al. "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
625dTetR1e-5 [1/s] 2.31e-3 [1/s]degradation of TetR [9] Becskei A and Serrano L "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[10] Tuttle et al. "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
626dLuxR1e-3 - 1e-4 [1/s]degradation of LuxR Ref: [6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
627dCI7e-4 [1/s]degradation of CI Ref. [7] Arkin A et al. "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
628dP22CII degradation of P22CII  https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
629dYFP6.3e-3 [1/min]degradation of YFP suppl. mat. to Ref. [8] corresponding to a half life of 110min. [8] Colman-Lerner A et al. "Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates", Cell 107(6): 739-750, 2001 (supplementary material)
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
630dGFP6.3e-3 [1/min]degradation of GFP in analogy to YFPhttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
631dRFP6.3e-3 [1/min]degradation of RFP in analogy to YFPhttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
632dCFP6.3e-3 [1/min]degradation of CFP in analogy to YFPhttps://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
633KLacI0.1 - 1 [pM] 800 [nM]LacI repressor dissociation constant Ref. [2] Setty Y et al. "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
Ref. [12]		https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
634KIPTG1.3 [?µM]IPTG-LacI repressor dissociation constant Ref. [2] Setty Y et al. "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
635KTetR179 [pM]TetR repressor dissociation constant Ref. [1] Weber W et al. "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
636KATC893 [pM]ATC-TetR repressor dissociation constant Ref. [1] Weber W et al. "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
637KLuxR55 - 520 [nM]LuxR activator dissociation constant Ref: [6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
638KAHL0.09 - 1 [?µM]AHL-LuxR activator dissociation constant Ref:[6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
639KCI8 [pM] 50 [nM]CI repressor dissociation constant Ref. [12] Basu S et al. "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005

starting with values of Ref.[6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
and using Ref. [3] Braun D et al. "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
640KP22CII0.577 [?µM]P22CII repressor dissociation constant Ref. [11] McMillen LM et al. "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
641nLacI1;2LacI repressor Hill cooperativity Ref. [5] Iadevaia S and Mantzais NV "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
; Ref. [12]		https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
642nIPTG2IPTG-LacI repressor Hill cooperativity Ref. [5] Iadevaia S and Mantzais NV "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
643nTetR3TetR repressor Hill cooperativity Ref. [3] Braun D et al. "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
644nATC2 (1.5-2.5)ATC-TetR repressor Hill cooperativity Ref. [3] Braun D et al. "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
645nLuxR2LuxR activator Hill cooperativity Ref: [6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
646nAHL1AHL-LuxR activator Hill cooperativity Ref. [3] Braun D et al. "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
647nCI2CI repressor Hill cooperativity Ref. [12] Basu S et al. "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005

https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ
648nP22CII4P22CII repressor Hill cooperativity Ref. [11] McMillen LM et al. "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
https://2007.igem.org/wiki/index.php?title=ETHZ/ParametersETHZ