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Modeling Parameters

As our circuit is relatively complex, we have many factors and thus many parameters with which to describe the function of these factors mathematically.

These parameters are as follows:

1. δ is a function designed to represent the presence/absence of light in a Boolean fashion. δ=0 without light and 1 with light.
2. c_1 represents the rate of conformational change from LovTAP to LovTAP* when irradiated with 470nm light.
3. c_2 represents the rate of SupD + T7ptag --> T7 polymerase
4. α represents the maximum protein synthesis rate in nanomoles/sec.
5. β represents the basal synthesis rate. We assume ∀x β_x= .01α_x
6. μ represents the protein degradation rate.
7. n represents a ligand’s hill coefficient.
8. K_m represents the ligand’s dissociation constant

For a complete, up-to-date list of values and sensitivities, please see our current [http://www.brownigem.com/2010_parameters.ods spreadsheet of parameters and sensitivities] (or http://www.brownigem.com/2010_parameters.xls here for closed source Microsoft Excel format).

Alternatively, please see our prettier [http://www.brownigem.com/2010_parameters.pdf typeset PDF file]

Brown iGEM 2010 – Modeling Parameters	'	'	'
Parameter Name	Value	Units	Source
LovTAP rate of maximum synthesis	1.0643E-013	nanomoles/min	Determined as explained in Brown 2010 wiki
tatR rate of maximum synthesis	1.1532E-013	nanomoles/min	Determined as explained in Brown 2010 wiki
Mnt rate of maximum synthesis	6.0562E-013	nanomoles/min	Determined as explained in Brown 2010 wiki
AraC rate of maximum synthesis	5.9999E-014	nanomoles/min	Determined as explained in Brown 2010 wiki
LacI rate of maximum synthesis	3.9479E-014	nanomoles/min	Determined as explained in Brown 2010 wiki
CI rate of maximum synthesis	8.9302E-014	nanomoles/min	Determined as explained in Brown 2010 wiki
CI434 rate of maximum synthesis	1.2236E-013	nanomoles/min	Determined as explained in Brown 2010 wiki
SupD rate of maximum synthesis	2.7149E-012	nanomoles/min	Determined as explained in Brown 2010 wiki
T7ptag rate of maximum synthesis	7.0208E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
GAL4 rate of maximum synthesis	2.9175E-013	nanomoles/min	Determined as explained in Brown 2010 wiki
S1 rate of maximum synthesis	9.6899E-014	nanomoles/min	Determined as explained in Brown 2010 wiki
LovTAP rate of basal synthesis	1.0643E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
tatR rate of basal synthesis	1.1532E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
Mnt rate of basal synthesis	6.0562E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
AraC rate of basal synthesis	5.9999E-016	nanomoles/min	Determined as explained in Brown 2010 wiki
LacI rate of basal synthesis	3.9479E-016	nanomoles/min	Determined as explained in Brown 2010 wiki
CI rate of basal synthesis	8.9302E-016	nanomoles/min	Determined as explained in Brown 2010 wiki
CI434 rate of basal synthesis	1.2236E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
SupD rate of basal synthesis	2.7149E-014	nanomoles/min	Determined as explained in Brown 2010 wiki
T7ptag rate of basal synthesis	7.0208E-017	nanomoles/min	Determined as explained in Brown 2010 wiki
GAL4 rate of basal synthesis	2.9175E-015	nanomoles/min	Determined as explained in Brown 2010 wiki
S1 rate of basal synthesis	9.6899E-016	nanomoles/min	Determined as explained in Brown 2010 wiki
LovTAP degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
LovTAP* degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
tetR degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
Mnt degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
AraC degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
LacI degradation rate	6.6667E-002	1/sec	Determined as explained in Brown 2010 wiki
CI degradation rate	5.6061E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
CI434 degradation rate	1.2424E-001	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
SupD degradation rate	6.6667E-002	1/sec	As explained in wiki
T7ptag degradation rate	6.6667E-002	1/sec	As explained in wiki
T7 polymerase degradation rate	5.8333E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
GAL4 degradation rate	6.6667E-002	1/sec	As explained in wiki
S1 degradation rate	5.0000E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S2 degradation rate	5.0000E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S3 degradation rate	5.0000E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S4 degradation rate	5.0000E-002	1/sec	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
LovTAP* hill coefficient	1		Estimate
tetR hill coefficient	3		http://parts.mit.edu/igem07/index.php/ETHZ/Parameters
CI hill coefficient	2		http://parts.mit.edu/igem07/index.php/ETHZ/Parameters
CI434 hill coefficient	2		PKU 2009 wiki
GAL4 hill coefficient	2		PKU 2009 wiki
AraC hill coefficient	2		PKU 2009 wiki
T7 hill coefficient	2		PKU 2009 wiki
LacI hill coefficient	2		PKU 2009 wiki
Mnt hill coefficient	1		PKU 2009 wiki
LovTAP* dissociation constant	142.000	nanomoles	Light-activated DNA binding in a designed allosteric protein,Devin Strickland, Keith Moffat, and Tobin R. Sosnick
tetR dissociation constant	0.179	nanomoles	http://parts.mit.edu/igem07/index.php/ETHZ/Parameters
CI dissociation constant	50.000	nanomoles	http://parts.mit.edu/igem07/index.php/ETHZ/Parameters
CI434 dissociation constant	40.000	nanomoles	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
GAL4 dissociation constant	0.500	nanomoles	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
AraC dissociation constant	14.000	nanomoles	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
T7 dissociation constant	2.000	nanomoles	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
LacI dissociation constant	800.000	nanomoles	http://parts.mit.edu/igem07/index.php/ETHZ/Parameters
Mnt dissociation constant	50.000	nanomoles	Estimate
LovTAP → LovTAP* reaction rate	0.100	1/sec	Estimate
SupD + T7ptag → T7 reaction rate	0.100	1/sec	Estimate