Latest revision as of 20:28, 18 September 2015

Technion 2015 HS Team's Wiki

The Constants Database

	name	description	value	unit	Source	url	team
1	k1A	Transcription Rate of Lac I gene	21		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
2	k1C	Transcription Rate of E7 + Imm gene	2.470588		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
3	d1A	Degradation Rate of Lac I mRNA	0.76246		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
4	d1C	Transcription Rate of E7 + Imm mRNA	0.0897		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
5	k2A	Translation Rate of Lac I mRNA	36		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
6	k2C	Translation Rate of E7 + Imm mRNA	4.23539		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
7	d2A,d2C	Protein Degradation Rate	0.03465		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
8	nC	Hill coefficeint for E7 + Imm	1		This is obtained on the assumption that one Repressor Protein binds to one Lactose molecule complex	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
9	KC	Dissociation Constant for E7 + Imm	0.8		[1]	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
10	aC	Constitutive Portion for E7 + Imm	0.5		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/Parameter	NTU-Singapore
11	k3AB	Complex 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/Parameter	NTU-Singapore
12	kPF	Phosphorylation Rate of Ai-2	1		Estimate	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
13	kPB	Dephosphorylation Rate of Ai-2	1		Estimate	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
14	k1C	Transcription Rate of LsrR gene	4.402517		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
15	k1D	Transcription Rate of SupD gene	46.667		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
16	k1E	Transcription Rate of t7pTag gene	1.5556		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
17	k1F	Transcription Rate of Lysis gene	28		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
18	d1C	Degradation Rate of LsrR mRNA	0.159845		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
19	d1D	Degradation Rate of SupD mRNA	1.694359		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
20	d1E	Degradation Rate of t7pTag mRNA	0.056478		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
21	d1F	Degradation Rate of Lysis mRNA	1.0166		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
22	k2C	Translation Rate of LsrR Protein	7.54716		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
23	k2E	Translation Rate of t7 pTag Protein	2.6667		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
24	k2F	Translation Rate of Lysis Protein	48		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
25	d2C,d2E,d2F	Protein Degradation Rate	0.03465		Made using Earlier assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
26	nD	Hill coefficeint for SupD	50		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
27	nE	Hill coefficeint for t7 pTag	1		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/Parameter	NTU-Singapore
28	nF	Hill coefficeint for Lysis	1		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/Parameter	NTU-Singapore
29	KD	Dissociation Constant for SupD	15		[2]	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
30	KE	Dissociation Constant for t7 pTag	1		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
31	KF	Dissociation Constant for Lysis	1		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
32	aD	Constitutive Portion for SupD	0.01		Trial and Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
33	aE	Constitutive Portion for t7 pTag	0.01		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
34	aF	Constitutive Portion for Lysis	0.0001		Trial and Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
35	k3BC	Complex Formation Rate Between LsrR Repressor and Ai-2-Phosphorylated	0.01		Trial and Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
36	k3DE	Complex Formation Rate Between SupD tRNA and t7 pTag mRNA	0.000000001		Trial and Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
37	S	Amount of Protein Kinase	28.747		From Earlier Assumptions	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
38	kf	Forward Reaction rate of Complex	1.2		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
39	kr	Reverse Reaction rate of Complex	0.5		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
40	r	Rate of Logistic Growth	0.01		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
41	A & B	Varying Capacity	1 & 0.9		Trial And Error	https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter	NTU-Singapore
42	k_n	Population and culture	3.85e-3		[1] observed division rate	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
43	N_max	Population and culture; carrying capacity	1e8		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
44	V	Population and culture;	1e-11		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
45	k_dil	Population and culture; dilution rate	varied		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
46	k_assoc	IP binding to receptor	5e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
47	k_dissoc	IP binding to receptor	4.55e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
48	k_s1	Synthesis of CRE1, YPD1, SKN7 species	6.16e-5		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
49	k_s2	Synthesis of CRE1, YPD1, SKN7 species	6.00e-4		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
50	k_s3	Synthesis of CRE1, YPD1, SKN7 species	2.46e-4		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
51	k_dimer	Synthesis of CRE1, YPD1, SKN7 species	20		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
52	k_p1	Phosphorylation/Dephosphorylation reactions;	0.1		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
53	k_p2	Phosphorylation/Dephosphorylation reactions;	1243		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
54	k_p3	Phosphorylation/Dephosphorylation reactions;	56		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
55	k_p-3	Phosphorylation/Dephosphorylation reactions;	4.8		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
56	k_dp1	Phosphorylation/Dephosphorylation reactions;	5.33e-2		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
57	k_dp3	Phosphorylation/Dephosphorylation reactions;	2.89e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
58	k_dp3	Phosphorylation/Dephosphorylation reactions;	4.80e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
59	k_d1	Decay constants;	5.33e-2		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
60	k_d2	Decay constants;	2.89e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
61	k_d3	Decay constants;	4.80e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
62	k_dip	Decay constants;	5e-4		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
63	k_dgfp	Decay constants;	5.77e-3		[1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
64	k_dtet	Decay constants;	3.85e-3		Cell division rate (assumed stable)	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
65	k_dckx	Decay constants;	<=3.85e-3		Cell division rate, or lower if diffusion is significant.	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
66	k_bgfp, k_btet, k_bckx	Basal expression;	6e-6		adapted from [1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
67	k_tdim	Basal expression;	1e3		arbitrary	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
68	k_gfp	Induced expression;	6e-3		adapted from [1]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
69	k_tet	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
70	k_ckx	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
71	K_g, K_t, K_c	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
72	α_g, α_t α_c	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
73	K_i	Induced expression;	5e-6		K_ass = 2e11 M^-1 [2], [3]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
74	β	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
75	k_ipt4	Induced expression;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
76	k_sip	IPT4 enzyme kinetics;	varied		-	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
77	CKX enzyme kinetics	IPT4 enzyme kinetics;				https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
78	K_m	IPT4 enzyme kinetics;	40 ?µM		[4]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
79	k_cat	IPT4 enzyme kinetics;	0.5-1000 s^-1		[5], [6]	https://2008.igem.org/Team:University_of_Ottawa/Modeling/Parameters	University of Ottawa
80	Length of e.coli		2μm		"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-Parameters	BCCS-Bristol
81	Diameter e. coli		0.8μm		University of Alberta	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
82	Shape e. coli	Actually rod-like. A circle with r= 0.714μm will have equivalent surface area to rod-like.	Circle r =0.714μm		University of Alberta	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
83	Mass e. coli	Given 1x10^-12g for cell wet weight. Dividing this by gravity (=9.81) gives mass.	1.02x10^-13g		University of Alberta	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
84	Swimming 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-Parameters	BCCS-Bristol
85	Aspartate concentration detected by E. coli	Related 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 K_d 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-Parameters	BCCS-Bristol
86	Temporal comparison of chemotactic gradient	Related 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 c_1-4 to the average receptor occupancy during the last second c_0-1 . Hence b= c_0-1 - c_1-4 . If b>0, the cell reduces the tumbling rate to T_tumbling 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-Parameters	BCCS-Bristol
87	Tumbling angle	Related 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-Parameters	BCCS-Bristol
88	Tumble angle direction	Related 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-Parameters	BCCS-Bristol
89	Tumbling time	Related 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-Parameters	BCCS-Bristol
90	Relationship between tumbling angle and time	Related to Run Tumble Motion.				https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
91	Speed while Tumbling	Related 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-Parameters	BCCS-Bristol
92	Drift during run	Related 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-Parameters	BCCS-Bristol
93	Thrust	Related 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-Parameters	BCCS-Bristol
94	Isotropic run lengths	Related 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 distribution	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
95	Run length UP Aspartate gradient	Related 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-Parameters	BCCS-Bristol
96	Run length DOWN Aspartate gradient	Related 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 distribution	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
97	Viscosity	Related 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-Parameters	BCCS-Bristol
98	C_pMax	Maximal CpxR protein concentration	Unknown (varied in the program)			https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
99	k_Cp	Maximal transcription rate of pCpxR promoter	0.075min^{-1^ESTIMATED}		Surface Sensing and Adhesion of Escherichia Coli controlled by the cpx-signalling pathway.	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
100	theta_Cpx	Threshold for pCpxR promoter Hill Function	1 x 10^-9 M ESTIMATED		iGEM 2008 KULeuven	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
101	m_Cpx	Co-operativity of pCpxR promoter Hill function	1			https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
102	d_Im	Degradation rate of GFP mRNA	3.6 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-Parameters	BCCS-Bristol
103	k_Ip	Rate of LuxI protein translation	9.6 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-Parameters	BCCS-Bristol
104	d_Ip	Degradation rate of LuxI protein	1.67 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-Parameters	BCCS-Bristol
105	d_Gm	Degradation rate of GFP protein	1.65 x 10^-3 min^-1		Efficient GFP mutations profoundly affect mRNA transcription and translation rates	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
106	k_Gp	Rate of GFP protein translation	2.4 x 10^-1 min^-1		Quantitative measurement of green fluorescent protein expression	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
107	d_Gp	Degradation rate of GFP protein	2.14 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-Parameters	BCCS-Bristol
108	A_prod	AHL production rate per LuxI enzyme	3.6 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-Parameters	BCCS-Bristol
109	d_A	Degradation rate of AHL molecule	1 x 10^-2 min^-1		A synthetic multicellular system for programmed pattern formation	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
110	D_A	Diffusion coefficient of AHL	0.23s^-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-Parameters	BCCS-Bristol
111	k_Tp	Maximal Transcription rate of ptetR promoter	0.08min^-1		iGEM 2007Imperial College London	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
112	d_Rm	Degradation rate of LuxR mRNA	3.6 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-Parameters	BCCS-Bristol
113	k_Rp	Rate of Lux protein translation	9.6 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-Parameters	BCCS-Bristol
114	d_Rp	Degration rate of LuxR protein	2.31 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-Parameters	BCCS-Bristol
115	k_LuxR	Maximal transcription rate of LuxR promoter	0.11 min^-1		iGEM 2008 KULeuven	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
116	theta_LuxR	Threshold for LuxR pR promoter Hill function	1.5 x 10^-9 M		iGEM 2008 KULeuven	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
117	m_LuxR	Co-operativity of LuxpR promoter Hill function	1.6		iGEM 2008 KULeuven	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
118	rho_C	LuxR/AHL dimerisation	0.5 micro M^-3 min^-1		A synthetic multicellular system for programmed pattern formation	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
119	d_C	Degradation rate of mCherry mRNA	0.0231 min^-1		A synthetic multicellular system for programmed pattern formation	https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters	BCCS-Bristol
120	d_Mm	Degradation rate of LuxR/AHL complex	1.65 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-Parameters	BCCS-Bristol
121	k_Mp	Rate of mCherry protein translation	2.4 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-Parameters	BCCS-Bristol
122	d_Mp	Degradation rate of mCherry protein	2.14 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-Parameters	BCCS-Bristol
123		Rate of production of HSL from LuxI	0.45	1/s	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
124	_HSL	Rate of diffusion of HSL in/out of the cell	0.4	1/s	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
125	_IPTG	Rate of diffusion of IPTG in/out of the cell	0.014	1/s	[3]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
126	p_production	Number of plasmids	10		medium copy plasmid number; decided within the team	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
127	p_latch	Number of plasmids	10		medium copy plasmid number; decided within the team	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
128	p_lysis	Number of plasmids	10		medium copy plasmid number; decided within the team	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
129	p_anti-lysis	Number of plasmids	10		medium copy plasmid number; decided within the team	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
130	p_QS	Number of plasmids	10		medium copy plasmid number; decided within the team	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
131	_{max_production}	Maximal production rate of lux box promoter	0.44	pops	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
132	_{min_production}	Minimal production rate of lux box promoter	0.013	pops	estimated	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
133	_latch	Maximal production rate of latch promoter	0.28	pops	See Below	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
134	_lysis	Maximal production rate of lysis promoter	0.0426	pops	See Below	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
135	_anti-lysis	Maximal production rate of anti-lysis promoter	0.0066	pops	See Below	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
136	_QS	Maximal production rate of QS promoter	0.018	pops	See Below	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
137	K_LacI	Dissociation constant for LacI to LacO	700	m	See Explanation	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
138	K_LacI-IPTG	Dissociation constant for IPTG to LacI	1200	m	See Explanation	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
139	K_TetR	Dissociation constant for TetR to TetO	7000	m	See Explanation	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
140	K_cI	Dissociation constant for cI to operon	7000	m	See Explanation	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
141	K_P	Dissociation constant for P to lux box	700	m	See Explanation	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
142	n_LacI	Hill coefficient	2		[10]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
143	n_cI	Hill coefficient	2		[11]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
144	n_TetR	Hill coefficient	3		[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
145	n_P	Hill coefficient	2		[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
146	_mRNA	Degradation of mRNA	0.00288	1/s	[2]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
147	_X	Degradation of X	0.00000802	1/s	[5]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
148	_Y	Degradation of Y	0.00000802	1/s	[5]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
149	_λ-CI	Degradation of lambda CI	0.002888	1/s	[5]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
150	_LacI	Degradation of LacI	0.001155	1/s	[8]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
151	_TetR	Degradation of TetR	0.00288811	1/s	tagged; half-life of 4 min	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
152	_Holin	Degradation of Holin	0.0002	1/s	estmated; half-life of an hour	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
153	_Endolysin	Degradation of Endolysin	0.0002	1/s	estimated; half-life of an hour	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
154	_Antiholin	Degradation of Antiholin	0.0002	1/s	estimated; half-life of an hour	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
155	_LuxI	Degradation of LuxI	0.002888	1/s	tagged; half-life of 4 min	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
156	_LuxR	Degradation of LuxR	0.0002	1/s	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
157	_HSL	Degradation of HSL	0.00016667	1	[8]; value for AHL	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
158	_Protein	Translation rate of Protein	0.1	1/s	[2]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
159	_P	Rate of formation of the HSL-LuxI complex	0.0001	1/ms	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
160	_-P	Rate of dissociation of the HSL-LuxI complex	0.003	1/s	[1]	https://2009.igem.org/Team:Aberdeen_Scotland/parameters	Aberdeen Scotland
161	k_1	Max Transcription rate of tRNA	46.67	nM/min	Assumption, sensitivity:0.19	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
162	k_2	Synthesis rate of Aa-tRNA	0.08	min^-1	Sensitivity: 0.09	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
163	k_3	Max Transcription rate of T7RNAP	1.5625	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
164	k_4	Max Translation rate of T7RNAP	2.68*0.05	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
165	k_5	Max Transcription rate of trigger CI	5.6	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
166	k_6	Transcription rate of bistable CI	5.6	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
167	k_6'	Transcription rate of bistable CI	1	nM/min	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
168	k_7	Transcription rate of T3RNAP	1.75	nM/min	Assumption, sensitivity:1.34	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
169	k_7'	Transcription rate of T3RNAP	1	nM/min	Sensitivity: Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
170	k_8	Translation rate of trigger CI	9.6*0.045	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
171	k_8'	Translation rate of bistable CI	9.6*0.3	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
172	k_9	Max Transcription rate of CI434	5.92	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
173	k_10	Transcription rate of CI434	10.14*0.5	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
174	k_11	Max Translation rate of T3RNAP	3*0.15	min^-1	Assumption, sensitivity:1.34	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
175	k_12	Max Transcription rate of GFP from Sal	5.25	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
176	k_12'	Max Trasncription rate of GFP from T3RNAP	5.25	nM/min	Assumption, sensitivity:1.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
177	k_13	Translation rate of GFP	9*0.6	min^-1	Assumption, sensitivity:1.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
178	k_s	rate of AND Gate 1	0.3	nM^-1	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
179	k_s'	rate of AND Gate 2	0.3	nM^-1	Sensitivity: 0.18	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
180	K_1	dissociation constant of AraC,tRNA	14	nM	Sensitivity: 0.03	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
181	K_3	dissociation constant of Sal,T7RNAP	0.5	nM	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
182	K_5	dissociation constant of T7RNAP,trigger CI	3	nM	Ref	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
183	K_6	dissociation constant of CI,bistable CI	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
184	K_6'	dissociation constant of CI434,bistable CI	50	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
185	K_7	dissociation constant of CI,T3RNAP	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
186	K_7'	dissociation constant of CI434,T3RNAP	50	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
187	K_9	dissociation constant of CI,CI434	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
188	K_12	dissociation constant of Sal,GFP	0.5	nM	Sensitivity: Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
189	K_12'	dissociation constant of T3RNAP,GFP	55	nM	Ref: The FEBS journal 2006,273:17	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
190	n_1	Hill co-effiency of AraC,tRNA	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
191	n_3	Hill co-effiency of Sal,T7RNAP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
192	n_5	Hill co-effiency of T7RNAP,CI	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
193	n_6	Hill co-effiency of CI,bistable CI	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
194	n_6'	Hill co-effiency of CI434,bistable CI	2		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
195	n_7	Hill co-effiency of CI,T3RNAP	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
196	n_7'	Hill co-effiency of CI434,T3RNAP	2		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
197	n_9	Hill co-effiency of CI,CI434	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
198	n_12	Hill co-effiency of Sal,GFP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
199	n_12'	Hill co-effiency of T3RNAP,GFP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
200	γ_1	Degradation rate of tRNA	1/30+1/60	min^-1	Since half life of tRNA is very long, we decided to use 60 mins instead	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
201	γ_2	Degradation rate of Aa-tRNA	1/30+1/40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
202	γ_2'	Real Degradation rate of Aa-tRNA	ינו-40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
203	γ_3	Degradation rate of T7RNAP mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
204	γ_4	Degradation rate of T7RNAP	1/30+1/40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
205	γ_5	Degradation rate of trigger CI mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
206	γ_6	Degradation rate of bistable CI mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
207	γ_7	Degradation rate of T3RNAP mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
208	γ_8	Degradation rate of CI	1/30+1/44	min^-1	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
209	γ_9	Degradation rate of CI434 mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
210	γ_10	Degradation rate of CI434	1/30+1/11	min^-1	Ref: iGEM 2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
211	γ_11	Degradation rate of T3RNAP	1/30+1/30	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
212	γ_12	Degradation rate of GFP mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
213	γ_13	Degradation rate of GFP	1/30+1/60	min^-1	Since half life of GFP is very long, we use 60 mins instead	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
214	k_1	Max Transcription rate of tRNA	46.67	nM/min	Assumption, sensitivity:1.41	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
215	k_2	Synthesis rate of Aa-tRNA	0.08	min^-1	Sensitivity: 0.81	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
216	k_3	Max Transcription rate of T7RNAP	1.5625	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
217	k_4	Max Translation rate of T7RNAP	2.68*0.05	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
218	k_5	Max Transcription rate of trigger CI	5.6	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
219	k_6	Transcription rate of bistable CI	5.6	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
220	k_6'	Transcription rate of bistable CI	1	nM/min	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
221	k_7	Transcription rate of P2	16.8	nM/min	Assumption, sensitivity:1.23	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
222	k_7'	Transcription rate of P2	1	nM/min	Sensitivity: Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
223	k_8	Translation rate of trigger CI	9.6*0.05	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
224	k_8'	Translation rate of bistable CI	9.6*0.5	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
225	k_9	Max Transcription rate of CI434	5.92	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
226	k_10	Transcription rate of CI434	10.14*1	min^-1	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
227	k_11	Max Translation rate of P2	28.8*0.0045	min^-1	Assumption, sensitivity:1.23	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
228	k_12	Max Transcription rate of GFP from Sal	5.25	nM/min	Assumption, sensitivity:0.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
229	k_12'	Max Trasncription rate of GFP from P2	5.25	nM/min	Assumption, sensitivity:1.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
230	k_13	Translation rate of GFP	9*0.6	min^-1	Assumption, sensitivity:1.00	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
231	k_s	rate of AND Gate 1	0.3	nM^-1	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
232	k_s'	rate of AND Gate 2	0.01	nM^-1	Sensitivity: 1.29	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
233	K_1	dissociation constant of AraC,tRNA	14	nM	Sensitivity: 0.2	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
234	K_3	dissociation constant of Sal,T7RNAP	0.5	nM	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
235	K_5	dissociation constant of T7RNAP,trigger CI	3	nM	Ref	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
236	K_6	dissociation constant of CI,bistable CI	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
237	K_6'	dissociation constant of CI434,bistable CI	50	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
238	K_7	dissociation constant of CI,P2	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
239	K_7'	dissociation constant of CI434,P2	50	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
240	K_9	dissociation constant of CI,CI434	40	nM	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
241	K_12	dissociation constant of Sal,GFP	0.5	nM	Sensitivity: 0	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
242	K_12'	dissociation constant of P2,GFP	35	nM	Sensitivity: 1.29	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
243	n_1	Hill co-effiency of AraC,tRNA	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
244	n_3	Hill co-effiency of Sal,T7RNAP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
245	n_5	Hill co-effiency of T7RNAP,CI	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
246	n_6	Hill co-effiency of CI,bistable CI	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
247	n_6'	Hill co-effiency of CI434,bistable CI	2		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
248	n_7	Hill co-effiency of CI,P2	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
249	n_7'	Hill co-effiency of CI434,P2	2		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
250	n_9	Hill co-effiency of CI,CI434	4		Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
251	n_12	Hill co-effiency of Sal,GFP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
252	n_12'	Hill co-effiency of P2,GFP	2			https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
253	γ_1	Degradation rate of tRNA	1/30+1/60	min^-1	Since half life of tRNA is very long, we decided to use 60 mins instead	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
254	γ_2	Degradation rate of Aa-tRNA	1/30+1/40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
255	γ_2'	Real Degradation rate of Aa-tRNA	ינו-40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
256	γ_3	Degradation rate of T7RNAP mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
257	γ_4	Degradation rate of T7RNAP	1/30+1/40	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
258	γ_5	Degradation rate of trigger CI mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
259	γ_6	Degradation rate of bistable CI mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
260	γ_7	Degradation rate of P2 mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
261	γ_8	Degradation rate of CI	1/30+1/44	min^-1	Ref: iGEM2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
262	γ_9	Degradation rate of CI434 mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
263	γ_10	Degradation rate of CI434	1/30+1/11	min^-1	Ref: iGEM 2007 PKU Team	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
264	γ_11	Degradation rate of P2	1/30+1/30	min^-1		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
265	γ_12	Degradation rate of GFP mRNA	1/30+1/4.4	min^-1	Assumption	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
266	γ_13	Degradation rate of GFP	1/30+1/60	min^-1	Since half life of GFP is very long, we use 60 mins instead	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	PKU Beijing
267	c_pLac	maximum transcription rate (M/min)	5E-10		[1]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
268	c_pTet	maximum transcription rate (M/min)	0.00000015		[2]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
269	c_pλ	maximum transcription rate (M/min)	0.00000015		estimate	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
270	K₅₀^IPTG	dissociation constant (M)	0.0000013		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
271	K₅₀^LacI	dissociation constant (M)	0.0000008		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
272	K₅₀^TetR	dissociation constant (M)	1.79E-10		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
273	K₅₀^CI	dissociation constant (M)	0		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
274	n_IPTG	Hills coefficient	2		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
275	n_LacI	Hills coefficient	2		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
276	n_TetR	Hills coefficient	3		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
277	n_CI	Hills coefficient	2		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
278	d_LacI	degradation rate (M/min)	0.1386		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
279	d_TetR	degradation rate (M/min)	0.1386		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
280	d_CI	degradation rate (M/min)	0.042		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
281	d_RFP	degradation rate (M/min)	0.0063		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
282	d_GFP	degradation rate (M/min)	0.0063		[3]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
283	d_mRNA	degradation rate (M/min)	0.029		[4]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
284	α	translation 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_Parameters	TUDelft
285	k_IPTG	rate constant for IPTG diffusion into cell	0.92		[6]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
286	A	Surface area available (mm²)	1735		Area of 0.2μm filter used in conjugation tests.	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
287	r₀	initial colony radius (μm)	0.8		[7]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
288	g_n	specific growth rate (1/hr)	0.99		Determined experimentally for R751 containing cells.	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
289	g_r	colony radial specific growth rate (μm/hr)	30		[8]	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
290	N_d	initial number of donors	10000		Estimate	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
291	N_r	initial number of donors	10000		Estimate	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
292	λ	intensity (CFU/mm²)	5.76		Calculated using N_r/A.	https://2009.igem.org/Team:TUDelft/Modeling_Parameters	TUDelft
293	K_LacI	LacI repressor dissociation constant	0.1 - 1 [pM] OR 800 [nM]		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
294	K_IPTG	IPTG-LacI repressor dissociation constant	1.3 [?µM]		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
295	K_tetR	TetR repressor dissociation constant	179 [pM]		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
296	K_cI	cI repressor dissociation constant	8 [pM] OR 50 [nM]		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
297	K_HSL	HSL-LuxR activator dissociation constant	0.09 - 1 [?µM]		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
298	K_LacI	Dissociation constant for LacI to LacO DNA site	~110 -12 M OR ~1.810-12 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, 11074-11084	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
299	K_IPTG	Dissociation constant for IPTG to LacI	1*10-6 M		"Uri Alon, An introduction to systems Biology, p244
"	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
300	K_tetR	Dissociation 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 Hillen	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
301	K_cI	Dissocitation constant for cI to DNA site	50 * 10-9 M		https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1	Aberdeen Scotland
302	α_TetR	TetR max. production rate	3.93 μM/min, updated to 1 μM/min		[5]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
303	α_C	CI max. production rate	1 μM/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
304	α_L1	LacI max. production rate	1 μM/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
305	α_L2	LacI_M1 max. production rate	1 μM/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
306	α_G	GFP max. production rate	2 μM/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
307	α_LuxI	LuxI max. production rate	1 μM/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
308	k_s1	AHL_i production rate	0.01 1/min		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
309	ρ_R	LuxR-AHL dimerization rate	0.5 1/(μM³*min)		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
310	α_RFP	RFP max. production rate	1 μM/min		assumption	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
311	β_AcA	Acetaldehyde repression coefficient	7.124 μM		[5]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
312	β_T	TetR repression coefficient	0.01 μM, updated to 0.1 μM/min		assumption	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
313	β_C	CI repression coefficient	0.008 μM		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
314	β_L	LacI repression coefficient	0.8 μM		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
315	θ_R	LuxR-AHL repression coefficient	0.01 μM		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
316	γ_TetR	TetR degradation rate	0.0692 1/min		assumption	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
317	γ_C	CI degradation rate	0.0692 1/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
318	γ_L	LacI degradation rate	0.0231 1/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
319	γ_G	GFP degradation rate	0.0692 1/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
320	γ_LuxI	LuxI degradation rate	0.0167 1/min		[3]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
321	k_s0	AHL_i degradation rate	1 1/min		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
322	k_se	AHL_e degradation rate	1 1/min		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
323	γ_R	LuxR-AHL degradation rate	0.0231 1/min		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
324	γ_RFP	RFP degradation rate	0.0041 1/min		[4]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
325	n₁	LacI cooperativity coefficient	2		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
326	n₂	CI cooperativity coefficient	2		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
327	n₃	TetR cooperativity coefficient	2		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
328	n₄	LuxR-AHL cooperativity coefficient	1		[1]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
329	n₅	AlcR-AcA cooperativity coefficient	1.352		[5]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
330	n₇	XylR cooperativity coefficient	5		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
331	η	Diffusion rate across the cell membrane	2		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
332	η_ext	Average diffusion rate for all cells	1		[2]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
333	N	Number of cells	1		assumption	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
334	a_XylR	XylR max. production rate	95.5 μM/min		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
335	γ_XylRi	XylRi degradation rate	0.03553 1/min		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
336	γ_XylRa	XylRa degradation rate	0.04527 1/min		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
337	K_XylR	XylR activation coefficient	1.419*10-3 μM		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
338	r_XylR	XylRi oligomerization constant	0.04315e-3 1/(μM*min)		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
339	r_RXylR	XylRa dissociation constant	0.1301e-3 1/(μM*min)		[6]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
340	z_end	Microfluidics channel length	5 cm		Choice in diffusion model	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
341	R_Channel	Microfluidics channel radius	1 mm		Choice in diffusion model	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
342	V_eColi	E. coli average volume	2 μm³		[13] [14]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
343	cd_{OD600, undiluted}	E. coli Cell Density at OD₆₀₀ = 1	1e9 1/ml		[13] [16]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
344	c_Dilution	Dilution of cell culture in microfludics channel	01-אוג		Choice in diffusion model	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
345	cdRel_{OD600, undiluted}	Relative E. coli Cell Density at OD₆₀₀ = 1, undiluted	0.001		Derived from V_eColi, cd_{OD600, undiluted}	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
346	cdRel_{OD600, diluted}	Relative E. coli Cell Density at OD₆₀₀ = 1, diluted	0.000125		Derived from cdRel_{OD600, undiluted}, c_Dilution	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
347	C_Agarose	Scaling coefficient for diffusion of small molecules in agarose instead of water	0.9		assumption	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
348	D_AcAl	Acetaldehyde Diffusion Constant	1.23e-5 cm²/s		[8]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
349	m_AcAl	Acetaldehyde Molecular Weight	44.05316 u		[8]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
350	K_cat,AcAl	Specific enzyme activity of acetaldehyde dehydrogenase in E. coli	14.1 μmol/(min*mg)		[10] [11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
351	[E]^T	Mean acetaldehyde dehydrogenase enzyme concentration in E. coli	1.6659 kg/m³		Estimation from cell extract, [11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
352	v_max,AcAl	Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde	0.02349 M/min		Estimation from cell extract, [11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
353	K_M,AcAl	Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde	10 μM		[10] [11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
354	m_ADH	Molecular mass of acetaldehyde dehydrogenase	33442 u		[12]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
355	n_ADH	Mean number of acetaldehyde dehydrogenase protein molecules per E. coli cell	28512.2, rounded to 30000		Estimation from cell extract, [11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
356	[ADH]_Extract	acetaldehyde dehydrogenase concentration in E. coli cell extract	19 mg/ml		[11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
357	dil_Extract	E. coli cell extract dilution	01-דצמ		[11]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
358	D_AHL	AHL Diffusion Constant	4.9e-6 cm²/s		[9]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
359	m_AHL	AHL Molecular Weight	297.38990 u		[15]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
360	γ_AHL,ext	AHL cell-external degradation	8.0225e-006/s		Derived from 1 day half-life at pH 7 [7]	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
361		Concentration of X	NA	molecules per cell	Notation convention	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
362		Delay due to protein X production and maturation	NA	s	Notation convention	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
363		Maximal production rate of pVeg promoter (constitutive)	0.02	molecules.s^-1 or pops	Estimated, see the justification	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
364		Maximal production rate of pHyperSpank promoter	0.02	molecules.s^-1 or pops	Estimated, see the justification	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
365		Maximal production rate of pT7 promoter	0.02	molecules.s^-1 or pops	Estimated, see the justification	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
366		Maximal production rate of pComK promoter	0.049	molecules.s^-1 or pops	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
367		Maximal production rate of pComS promoter	0.057	molecules.s^-1 or pops	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
368		Maximal production rate of pComG promoter	0.02	molecules.s^-1 or pops	Estimated, see the justification	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
369		Basal production rate of pComK promoter	0.0028	molecules.s^-1 or pops	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
370		Basal production rate of pComG promoter	0.028	molecules.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/Parameters	Paris Bettencourt
371		Dissociation constant for IPTG to LacI	1200	molecules per cell	Aberdeen 2009 wiki	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
372		Dissociation constant for LacI to LacO (pLac)	700	molecules per cell	Aberdeen 2009 wiki	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
373		Dissociation constant for T7 RNA polymerase to pT7	10	molecules per cell	We used the classic assumption 1nM=1 molecule per cell and [1]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
374		Dissociation constant for ComK to pComK	110	molecules per cell	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
375		Dissociation constant for ComK to pComS	100	molecules per cell	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
376		ComK concentration for half maximal degradation	500	molecules per cell	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
377		ComS concentration for half maximal degradation	50	molecules per cell	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
378		Hill coefficient for LacI/IPTG interaction	2	NA	Aberdeen 2009 wiki	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
379		Hill coefficient for LacI/pHyperSpank interaction	2	NA	Aberdeen 2009 wiki	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
380		Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction	2	NA	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
381		Hill coefficient for ComK/pComS (negative feedback) interaction	5	NA	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
382		Translation rate of proteins	0.9	s^-1	Estimated, see the justification	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
383		Dilution rate in exponential phase	2.88x10^-4	s^-1	Calculated with a 40 min generation time. See explanation	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
384		Unrepressed degradation rate of ComK	1.4x10^-3	s^-1	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
385		Unrepressed degradation rate of ComS	1.4x10^-3	s^-1	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
386		Degradation rate of mRNA	2.88x10^-3	s^-1	[4]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
387		Degradation rate of GFP	10^-4	s^-1	BioNumbers	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
388		Degradation rate of RFP	10^-4	s^-1	Estimated equal to GFP degradation rate	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
389		Delay due to CFP production and maturation	360	s	Estimated equal to GFP delay (similar molecules)	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
390		Delay due to YFP production and maturation	360	s	Estimated equal to GFP delay (similar molecules)	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
391		Delay due to ComK production and maturation	300	s	Arbitrary	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
392		Delay due to ComS production and maturation	300	s	Arbitrary	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
393		Delay for ComS repression by ComK	714	s	[3]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
394		Delay due tT7 RNA polymerase production and maturation	300	s	[2]	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
395		Delay due GFP production and maturation	360	s	BioNumbers	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
396		Delay due RFP production and maturation	360	s	Estimated equal to GFP delay (similar molecules)	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
397		Delay due to mRNA production	30	s	BioNumbers with an approximation: all our contructs are around 1-2kb	https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters	Paris Bettencourt
398	L	tail length	0.8	cm	[1]	https://2012.igem.org/Team:Evry/parameters	Evry
399	l	max tail width	0.07	cm	[1]	https://2012.igem.org/Team:Evry/parameters	Evry
400	r	head radius	0.3	cm	[1]	https://2012.igem.org/Team:Evry/parameters	Evry
401	T_skin	skin thickness	35	μm	[1]	https://2012.igem.org/Team:Evry/parameters	Evry
402	V_tail	tail volume	0.001	cm³	here	https://2012.igem.org/Team:Evry/parameters	Evry
403	V_head	head volume	0.1131	cm³	here	https://2012.igem.org/Team:Evry/parameters	Evry
404	V	tadpole volume	0.1141	cm³	here	https://2012.igem.org/Team:Evry/parameters	Evry
405	V_skin	skin volume	0.0041	cm³	here	https://2012.igem.org/Team:Evry/parameters	Evry
406	V_receptor	receptor compartment volume	xxxx	cm³	here	https://2012.igem.org/Team:Evry/parameters	Evry
407	P_X<->Y	permeability between tissues X and Y	10^-5	cm.min^-1	[3]	https://2012.igem.org/Team:Evry/parameters	Evry
408	S_tadpole	sum of the external surfaces of the tail and the head	1.219	cm²	here	https://2012.igem.org/Team:Evry/parameters	Evry
409	S_skin	skin internal surface	1.1839	cm²	here	https://2012.igem.org/Team:Evry/parameters	Evry
410	S_receptor	blood-receptor exchange surface	0.0781	cm²	here	https://2012.igem.org/Team:Evry/parameters	Evry
411	D_auxin	auxin diameter	0.766	nm	[2]	https://2012.igem.org/Team:Evry/parameters	Evry
412	sun	natural sun light			n/a	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
413	room	sun0.3, (UV<350nm)0.05, (UV>=350nm)*0,90			n/a	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
414	bulb200W	Incandescent light bulb			1 m	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
415	k_UVR8_hv	Light dependent dissociation rate UVR8 dimer	2.08?·10^-3 s^-1		from gels	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
416	k_UVR8_decay	Dimerization rate UVR8 monomer	8.4?·10^-10 nM^-1 s^-1		estimate	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
417	KM_TetR	TetR repression coefficient	100 nM		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
418	n_TetR	TetR cooperativity coefficient	1		[GarciaOjalvo2004]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
419	k_Ptet	Tet promoter expression strength	1.1 nM s^-1		optimised	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
420	A	Basal expression fraction	0.05		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
421	n	Hill-like pABA cooperativity coefficient	10^-5		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
422	k_deg	Protein degradation rate	3.85?·10^-5 s^-1		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
423	KM_PabAB	PabAB Michaelis constant	960?·10³ nM		[Roux1992]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
424	k_cat	PabAB catalysis rate	0.65 s^-1		[Roux1992]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
425	Chor0	Intracellular chorismate concentration	100 mM		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
426	k_out	pABA outflux rate	3.85?·10^-4 s^-1		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
427	k_Cph8_hv	Light dependent activation rate	s^-1		from photoinduction model	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
428	KM_LOV	LOV repression coefficient	142 nM		[Strickland2007]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
429	KM_Cph8	Cph8 activation coefficient	1000 nM		estimate	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
430	KM_LacI	LacI repression coefficient	800 nM		[Basu2005]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
431	KM_cI	cI repression coefficient	8 nM		[Basu2005]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
432	KM_TetR	TetR repression coefficient	100 nM		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
433	n_LacI	LacI cooperativity coefficient	2		[Basu2005]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
434	n_cI	cI cooperativity coefficient	2		[Basu2005]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
435	n_TetR	TetR cooperativity coefficient	1		[GarciaOjalvo2004]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
436	n_Cph8	Cph8 cooperativity coefficient	1		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
437	n_LOV	LOV cooperativity coefficient	1		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
438	k_LOV_decay	Dark decay rate of active LOV	5.8?·10^-3 s^-1		[Drepper2007]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
439	k_Cph8_decay	Dark decay rate of active Cph8	5.8?·10^-3 s^-1		estimate	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
440	k_Ptrp	Trp promoter expression strength	2.23 nM s^-1		optimized	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
441	k_PompC	OmpC promoter expression strength	3.454?·10^-1 nM s^-1		optimized	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
442	k_P_R	Lambda P_R expression strength	4.21?·10^-2 nM s^-1		optimized	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
443	k_P_L	Lambda P_L expression strength	3.0?·10^-2 nM s^-1		optimized	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
444	A	Basal expression fraction	0.05		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
445	k_deg	Protein degradation rate	1.9?·10^-3 s^-1		assumed	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
446	ecoli_v	Volume of E.coli	2.0e-18 m3		Bionumbers	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
447	ecoli_extcoeff	Extinction coefficient of E.coli at 600nm	6.022e10 m2 mol-1		Computed via OD600	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
448	ecoli_absorption	Absorption spectrum E.coli			[Kiefer2010]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
449	pABA_extcoeff	Extinction coefficient of pABA at 290nm	1.9e3 m2 mol-1		[Quinlivan2003]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
450	pABA_absorption	Absorption spectrum pABA			[EC2006]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
451	pABA_molarweight	Molar weight of pABA	137.14 g mol-1		Datasheet	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
452	layer_height	Height of sunscreen layer	2e-5 m		[Vainio2001]	https://2012.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH 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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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/Parameters	NTU-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/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
459	\(\beta_{TetR} \)	TetR repression coefficient	\(0.13~\mu\text{M} \)		a.	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
464	\(\gamma_{TetR} \)	TetR degradation rate	\(0.0692~\text{min}^{-1} \)		a.	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
467	\(\gamma_{LuxI} \)	LuxI degradation rate	\(0.0167~\text{min}^{-1} \)		[3] MIT igem 2010	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
468	\(k_{s0} \)	AHL_i? 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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
469	\(k_{se} \)	AHL_e? 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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2007	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
472	\(n_1\)	FadR cooperativity coefficient	\(3\)		a.	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
473	\(n_2\)	FA cooperativity coefficient	\(2\)		a.	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2005	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
478	\(\eta\)_ext	Average 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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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/Parameters	NTU-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/Parameters	NTU-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, 1973	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 1973	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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/Parameters	NTU-Taida
484	\( cd \)	Relative E. coli Cell Density	\( 0.1 \)			https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 1973	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 1973	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-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, 2004	https://2012.igem.org/Team:NTU-Taida/Modeling/Parameters	NTU-Taida
488	D_AHL	AHL diffusion constant	4.9 x 10^-6 cm²/s		Stewart P.S., 2003	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
489	C_agar	Reduced diffusion coefficient	0.9		Fatin-Rouge et al., 2004	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
490	α_AHL	AHL synthesis rate	0.01 min^-1		Garcia-Ojalvo et. al., 2004	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
491	d_AHL	AHL degradation rate (intracellular)	0.01 min^-1		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
492	d_AHL,e	AHL extracellular decay	4.8135 x 10^-4 min^-1		Horswill et al., 2007	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
493	η_AHL	Diffusion rate across the cell membrane	2		Garcia-Ojalvo et. al., 2004	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
494	η_ext	Average diffusion rate for all cells	1.3333		Garcia-Ojalvo et. al., 2004	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
495	α_LuxI	LuxI synthesis rate	1 μM/min		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
496	d_LuxI	LuxI degradation rate	0.0167 min^-1		MIT iGEM 2010	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
497	k	Cell growth rate	0.888 h^-1		estimated from experimental data	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
498	α_LuxR	LuxR synthesis rate	0.005 μ M/min		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
499	d_LuxR	LuxR degradation rate	0.01 min^-1		Manefield et al., 2002	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
500	ρ_R	LuxR/AHL dimerization	0.5 μM^-3min^-1		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
501	d_R	Dimer LuxR/AHL degradation rate	0.0231 min^-1		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
502	K_R	LuxR/AHL activation coefficient	0.013 nM		estimated from experimental data (scaled)	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
503	n	Hill coefficient	1		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
504	α_GFP	GFP synthesis rate	2 μM min^-1		Basu et al., 2005	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
505	d_GFP	GFP degradation rate	4.4432 x 10^-4 min^-1		Corish and Tyler-Smith, 1999	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
506	α_GusA	GusA synthesis rate	1 μM min^-1		estimated	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
507	d_GusA	GusA degradation (half-life 55^oC 2 hr)	9.6270^-5 s^-1		Jefferson, 1995	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
508	K_R1	AHL activation coefficient	4.45 nM		estimated from experimental data	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
509	n₁	Hill coefficient	1.7		estimated from experimental data	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
510	k_leaky	GusA basal expression	0.0375		estimated	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
511	α_AES	AES synthesis rate	1 μM min^-1		estimated	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
512	d_AES	AES degradation (half-life 55^oC 2 hr)	9.6270^-5 s^-1		Jefferson, 1995	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
513	K_R2	AHL activation coefficient	12555 nM		estimated from experimental data	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
514	n₂	Hill coefficient	0.8		estimated from experimental data	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
515	k_GFP	Hydrolases basal expression	0.0375		estimated	https://2013.igem.org/Team:ETH_Zurich/Parameter	ETH Zurich
516	Transcription rate of cI	4200/Gene Length (nM/min)	5.6		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
517	Translation rate of cI	2400RBS/Protein Length	9.6		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
518	Transcription rate of VIP	4200/Gene Length (nM/min)	1.74129353		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
519	Translation rate of VIP	2400RBS/Protein Length	2.985075		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
520	Transcription rate of GFP	4200/Gene Length (nM/min)	5.53359684		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
521	Translation rate of GFP	2400RBS/Protein Length	9.486166		https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
522	Degradation rate of cI (mRNA	Half life = 6.8 min, Division time = 30 min	0.18063836		(Selinger, GW, et al., 2003)	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
523	Degradation rate of cI (protein)	Half life > 10 h; division time = 30 min	0.03885825		(Varshavsky, (1997) and Tobias et al., 1991)	https://2013hs.igem.org/Team:CIDEB-UANL_Mexico/Math-Parameters	CIDEB-UANL Mexico
524	α_LuxR	Production rate of LuxR	0.005 μMmin^-1		Literature ^[20]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
525	k_RLux	Rate of formation of RLux from LuxAHL and LuxR	0.1 nM^-1min^-1		Literature ^[19]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
526	k_-RLux	Dissociation rate of RLux	10 min^-1		Literature ^[19]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
527	K_mLux	Lumped parameter for the Lux system	10 nM		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
528	d_LuxAHL	External degradation rate of LuxAHL (30C6HSL)	0.004 min^-1		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
529	d_LuxR	Degradation rate of LuxR	0.0231 min^-1		Literature ^[21]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
530	d_RLux	Degradation rate of RLux	0.0231 min^-1		Literature ^[20]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
531	d_mRNABxb1	Degradation rate of mRNA_Bxb1	0.2773 min^-1		Literature ^[22]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
532	d_Bxb1	Degradation rate of Bxb1	0.01 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
533	L_PLux	Leakiness after using riboswitch for P_lux	0.01463 nMmin^-1		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
534	K_mRNABxb1	Rate of transcription of Bxb1	5 nMmin^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
535	k_Bxb1	Rate of formation of Bxb1	0.1 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
536	α_LasR	Production rate of LasR	0.005 μMmin^-1		Literature ^[20](Assumed to be the same as Lux system)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
537	k_RLas	Rate of formation of RLas from LasAHL and LasR	0.1 nM^-1min^-1		Literature ^[19] (Assumed to be the same as Lux system)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
538	k_-RLas	Dissociation rate of RLas	10 min^-1		Literature ^[19](Assumed to be the same as Lux system)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
539	K_mLas	Lumped parameter for the Las system	0.45 nM		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
540	d_LasAHL	Degradation rate of LasAHL (30C12HSL)	0.004 min^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
541	d_LasR	Degradation rate of LasR	0.0231 min^-1		Literature ^[21] (Assumed to be the same as Lux system)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
542	d_RLas	Degradation rate of RLas	0.0231 min^-1		Literature ^[20] (Assumed to be the same as Lux system)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
543	d_mRNAϕc31	Degradation rate of mRNA_ϕc31	0.2773 min^-1		Literature ^[22]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
544	d_ϕc31	Degradation rate of ϕC31	0.01 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
545	L_PLas	Leakiness after using riboswitch for P_las	0.02461 nMmin^-1		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
546	K_mRNAϕc31	Rate of transcription of ϕc31	5 nMmin^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
547	k_ϕc31	Rate of formation of ϕc31	0.1 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
548	k_DBxb1	Dimerization rate of Bxb1	1 nM^-1min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
549	k_-DBxb1	Dissociation rate of DBxb1	10^-6 min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
550	k_SABxb1	Rate of formation of SA_Bxb1 from DBxb1 and SI_Bxb1	1 nM^-1min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
551	k_-SABxb1	Dissociation rate of SA_Bxb1	10^-6 min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
552	d_DBxb1	Degradation rate of DBxb1	0.02 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
553	k_Dϕc31	Dimerization rate of ϕc31	1 nM^-1min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
554	k_-Dϕc31	Rate of dissociation of Dϕc31	10^-6 min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
555	k_SAϕc31	Rate of formation of SA_ϕc31 from Dϕc31 and SI_ϕc31	1 nM^-1min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
556	k_-SAϕc31	Rate of dissociation of SA_ϕc31	10^-6 min^-1		Fitted	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
557	d_Dϕc31	Degradation rate of Dϕc31	0.02 min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
558	k_ToffBxb1	Rate of flipping of T_on,i to T_offBxb1	0.1 nM^-2min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
559	k_-ToffBxb1	Rate of flipping of T_offBxb1 to T_on,f	0.1 nM^-2min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
560	k_Toffϕc31	Rate of flipping of T_on,i to T_offϕc31	0.1 nM^-2min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
561	k_-Toffϕc31	Rate of flipping of T_offϕc31 to T_on,f	0.1 nM^-2min^-1		Assumed	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
562	k_mRNAGFP	Production rate of mRNA_GFP	5 nMmin^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
563	k_GFP	Rate of formation of folded GFP	1 min^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
564	d_mRNAGFP	Degradation rate of mRNA_GFP	0.2773 min^-1		Literature ^[22]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
565	d_GFP	Degradation rate of GFP	0.0049 min^-1		Fitted to experimental data	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
566	k_mRNALasI	Production rate of mRNA_LasI	5 nMmin^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
567	k_LasI	Rate of formation of LasI	20 min^-1		Estimated	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
568	d_mRNALasI	Degradation rate of mRNA_LasI	0.2773 min^-1		Literature ^[22]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
569	d_LasI	Degradation rate of LasI	0.0167 min^-1		Literature ^[21]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
570	k_LasAHL	Production rate of LasAHL (30C12HSL) from the LasI	0.04 min^-1		Literature ^[19]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
571	θ	K_m value for the production of mRNA_GFP and mRNA_LasI	0.01 μM		Literature ^[20] (approximation)	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
572	D_AHLext	Diffusion coefficient of extracellular AHL in liquid	4.9 10^-6 cm²/s		Literature ^[27]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
573	D_m	Diffusion rate of AHL through the membrane	100 min^-1		Estimated from literature ^[27]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
574	r	Growth rate of E. coli in our alginate beads	0.006 min^-1			https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
575	α	Ratio of E. coli volume to the volume of one bead	100 min^-1		V_{E. coli} from literature ^[28], bead volume from experimental setup	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
576	N₀	Initial number of cells per bead	10⁷ cells		Experimental setup	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
577	N_m	Maximum number of cells per bead	8 10⁷ cells		Estimated from literature ^[29]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
578	C_beads	Correction factor (a priori) for diffusion of LuxAHL in alginate beads	1		Estimated from literature ^[30]	https://2014.igem.org/Team:ETH_Zurich/modeling/parameters	ETH Zurich
579	\(K_{d,\text{LuxRAHL}}\)	Dissociation constant between luxR and AHL	100 nM		Weber, 2013	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
580	\(\text{LuxR}_\text{tot}\)	Total concentration of LuxR	0.0025 μM		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
581	\(a_\mathrm{LuxI}\)	Maximal production rate of LuxI	1 μM.min^-1		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
582	\(a_\mathrm{LuxI,ribo}\)	Maximal production rate of LuxI	0.1 μM.min^-1		ETHZ 2014	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
583	\(k_\mathrm{leaky}\)	Coefficient for leakiness dependency on LuxR concentration of P_LuxR promoter	0.0375 μM^-1		ETHZ 2013	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
584	\(K_\mathrm{a,LuxRAHL}\)	Activation coefficient of LuxRAHL	0.45 nM		ETHZ 2014	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
585	\(K_\mathrm{LuxRAHL,ribo}\)	Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter	285 nM		ETHZ 2014	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
586	\(L_\mathrm{lux,ribo}\)	Leakiness after using riboswitch for P_lux	0.01463 nM.min^-1		ETHZ 2014	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
587	\(n_\mathrm{lux}\)	Hill coefficient for LuxRAHL activation	1.7		ETHZ 2014	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
588	\(d_\mathrm{LuxI}\)	Degradation rate of LuxI	0.0167 min^-1		MIT 2010	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
589	\(a_\mathrm{AHL}\)	Production rate of AHL	0.04 μM.min^-1		Weber, 2013	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
590	\(d_\mathrm{AHL}\)	Degradation rate of AHL	0.01 min^-1		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH 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/Parameters	ETH Zurich
592	\(k_\mathrm{cat}\)	Turnover number of AiiA	1.63 10³min^-1		Wang, 2004	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
593	\(C_\mathrm{AiiA}\)	Concentration of AiiA	varied			https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
594	\(K_\mathrm{M,AiiA}\)	Half-maximal rate substrate concentration of AiiA	2.95 10³ μM		Wang, 2004	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
595	\(a_\mathrm{GFP}\)	Maximal production rate of GFP	2 μM.min^-1		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
596	\(d_\mathrm{GFP}\)	Degradation rate of GFP	0.01 min^-1		estimated from doubling time of E. coli	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
597	\(N_{d}\)	Number of E. coli in the doughnut	150		Maximal number of E. coli that would fit on the surface	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
598	\(N_{b,max}\)	Maximum number of E. coli in the bulk	12798		Considering the maximal OD is 2	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
599	\(V_{cell,d}\)	Volume around an E. coli in the doughnut	6 μm³		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
600	\(V_{cell,b,worst}\)	Volume around an E. coli in the bulk	78 μm³		Worst case, estimated from \(N_{b,max}\)	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
601	\(V_{cell,b,norm}\)	Volume around an E. coli in the bulk	1000 μm³		Normal case	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
602	\(\text{B}\)	\(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\)	0.000001 - 4			https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
603	\(\text{Lac}_{\text{ini}}\)	Initial concentration of lactate in the medium	0.1 μM - 2 μM		Low concentration of lactate in the medium	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
604	\(K_\mathrm{d,DLL}\)	Dissociation constant between the dimer of Lldr and Lactate	10 μM² - 10000 μM²			https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
605	\(\alpha\)	Multiplication factor between the initial concentration of Lactate and Production of normal cells	1 - 150		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
606	\(F_\mathrm{C}\)	Fold change between Lactate production by cancer and normal cells	2 - 4		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH 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/Parameters	ETH Zurich
608	\( a_\mathrm{LacI}\)	Maximal production rate of LacI	0.05 μM.min^-1 - 1 μM.min^-1		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
609	\( d_\mathrm{LacI}\)	Degradation rate of LacI	0.01 min^-1 - 0.1 min^-1		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
610	\( K_\mathrm{R,LacI}\)	Repression coefficient of LacI	0.1 μM - 10 μM		Basu, 2005	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
611	\( \gamma_1\)	\( \frac{L_\mathrm{2tot}}{K_\mathrm{R,L}}\)	5 - 10000		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
612	\( L_\mathrm{2tot}\)	Total concentration of LldR dimer	0.5 μM - 10 μM		estimated from paxdb	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
613	\( K_\mathrm{R,L}\)	Repression coefficient of LldR	0.001 μM - 0.1 μM		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
614	\( \gamma_2\)	\(\frac{IPTG_{tot}}{K_{IL}}\)	0 - 500		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
615	\( \frac{a_1}{\gamma_2+1}\)		0.001 - 1000		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
616	\( n_1\)	Hill coefficient of LldR	0.5 - 2.5		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH Zurich
617	\( n_2\)	Hill coefficient of LacI	1.5 - 2.5		estimated	https://2015.igem.org/Team:ETH_Zurich/Modeling/Parameters	ETH 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/Parameters	ETH Zurich
619	c₁^max	0.01 [mM/h]	max. transcription rate of constitutive promoter (per gene)		promoter no. J23105; Estimate	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
620	c₂^max	0.01 [mM/h]	max. transcription rate of LuxR-activated promoter (per gene)		Estimate	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
621	l^hi	25	high-copy plasmid number		Estimate	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
622	l^lo	5	low-copy plasmid number		Estimate	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
623	a	0.01	basic production levels		Estimate	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
624	d_LacI	2.31e-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/Parameters	ETHZ
625	d_TetR	1e-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/Parameters	ETHZ
626	d_LuxR	1e-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/Parameters	ETHZ
627	d_CI	7e-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/Parameters	ETHZ
628	d_P22CII		degradation of P22CII			https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
629	d_YFP	6.3e-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/Parameters	ETHZ
630	d_GFP	6.3e-3 [1/min]	degradation of GFP		in analogy to YFP	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
631	d_RFP	6.3e-3 [1/min]	degradation of RFP		in analogy to YFP	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
632	d_CFP	6.3e-3 [1/min]	degradation of CFP		in analogy to YFP	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
633	K_LacI	0.1 - 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/Parameters	ETHZ
634	K_IPTG	1.3 [?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/Parameters	ETHZ
635	K_TetR	179 [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/Parameters	ETHZ
636	K_ATC	893 [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/Parameters	ETHZ
637	K_LuxR	55 - 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/Parameters	ETHZ
638	K_AHL	0.09 - 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/Parameters	ETHZ
639	K_CI	8 [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/Parameters	ETHZ
640	K_P22CII	0.577 [?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/Parameters	ETHZ
641	n_LacI	1;2	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 ; Ref. [12]	https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters	ETHZ
642	n_IPTG	2	IPTG-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/Parameters	ETHZ
643	n_TetR	3	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/Parameters	ETHZ
644	n_ATC	2 (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/Parameters	ETHZ
645	n_LuxR	2	LuxR 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/Parameters	ETHZ
646	n_AHL	1	AHL-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/Parameters	ETHZ
647	n_CI	2	CI 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/Parameters	ETHZ
648	n_P22CII	4	P22CII 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/Parameters	ETHZ

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-<h1><font color="#800080"> The Constants Database</font></h1>
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 <div style="position:absolute;right:20px;font-size:30px;top:15;font-family:arial"><a href="LINK_TO_EXPLANATION">Explanation and Documentation</a></div>
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Difference between revisions of "Team:Technion HS Israel/Constants Database"

Latest revision as of 20:28, 18 September 2015

The Constants Database