Team:Brown/Modeling/Parameters

From 2010.igem.org

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{{:Team:Brown/templates/header}}
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==Parameters==
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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.  
As our circuit is relatively complex, we have many factors and thus many parameters with which to describe the function of these factors mathematically.  
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# K_m represents the ligand’s dissociation constant
# K_m represents the ligand’s dissociation constant
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<iframe src ="http://www.brownigem.com/latexconverted.html" width="100%" height="2200" frameborder="1" scrolling="yes">
 
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iGEM's MediaWiki did not support any LaTeX or Math extensions as far as we can tell, so we have embedded the parameters from our external website
 
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For a complete list of values and sensitivities, please see our soon-to-be updated [http://brownigem.com/parameters_2010.ods spreadsheet of parameters and sensitivities].
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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].
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{| {{table}}
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| align="center" style="background:#f0f0f0;"|'''Brown iGEM 2010 – Modeling Parameters'''
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| align="center" style="background:#f0f0f0;"|''''''
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| align="center" style="background:#f0f0f0;"|''''''
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| align="center" style="background:#f0f0f0;"|''''''
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|-
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| ||||||
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|-
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| Parameter Name||Value||Units||Source
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|-
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| ||||||
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|-
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| 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
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|-
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| T7ptag rate of maximum synthesis||7.0208E-015||nanomoles/min||Determined as explained in Brown 2010 wiki
 +
|-
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| GAL4 rate of maximum synthesis||2.9175E-013||nanomoles/min||Determined as explained in Brown 2010 wiki
 +
|-
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| S1 rate of maximum synthesis||9.6899E-014||nanomoles/min||Determined as explained in Brown 2010 wiki
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|-
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| ||||||
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|-
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| LovTAP rate of basal synthesis||1.0643E-015||nanomoles/min||Determined as explained in Brown 2010 wiki
 +
|-
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| 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
 +
|-
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| SupD rate of basal synthesis||2.7149E-014||nanomoles/min||Determined as explained in Brown 2010 wiki
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|-
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| T7ptag rate of basal synthesis||7.0208E-017||nanomoles/min||Determined as explained in Brown 2010 wiki
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|-
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| 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
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|-
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| ||||||
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|-
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| LovTAP degradation rate||6.6667E-002||1/sec||Determined as explained in Brown 2010 wiki
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|-
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| LovTAP* degradation rate||6.6667E-002||1/sec||Determined as explained in Brown 2010 wiki
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|-
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| tetR degradation rate||6.6667E-002||1/sec||Determined as explained in Brown 2010 wiki
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|-
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| 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
 +
|-
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| CI degradation rate||5.6061E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| CI434 degradation rate||1.2424E-001||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| SupD degradation rate||6.6667E-002||1/sec||As explained in wiki
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|-
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| T7ptag degradation rate||6.6667E-002||1/sec||As explained in wiki
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|-
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| T7 polymerase degradation rate||5.8333E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| GAL4 degradation rate||6.6667E-002||1/sec||As explained in wiki
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|-
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| S1 degradation rate||5.0000E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| S2 degradation rate||5.0000E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| S3 degradation rate||5.0000E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| S4 degradation rate||5.0000E-002||1/sec||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| ||||||
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|-
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| LovTAP* hill coefficient||1||||Estimate
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|-
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| tetR hill coefficient||3||||https://2007.igem.org/ETHZ/Parameters
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|-
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| CI hill coefficient||2||||https://2007.igem.org/ETHZ/Parameters
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|-
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| CI434 hill coefficient||2||||PKU 2009 wiki
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|-
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| GAL4 hill coefficient||2||||PKU 2009 wiki
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|-
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| AraC hill coefficient||2||||PKU 2009 wiki
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|-
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| T7 hill coefficient||2||||PKU 2009 wiki
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|-
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| LacI hill coefficient||2||||PKU 2009 wiki
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|-
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| Mnt hill coefficient||1||||PKU 2009 wiki
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|-
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| ||||||
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|-
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| LovTAP* dissociation constant||142.000||nanomoles||Light-activated DNA binding in a designed allosteric protein,Devin Strickland, Keith Moffat, and Tobin R. Sosnick
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|-
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| tetR dissociation constant||0.179||nanomoles||https://2007.igem.org/ETHZ/Parameters
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|-
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| CI dissociation constant||50.000||nanomoles||https://2007.igem.org/ETHZ/Parameters
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|-
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| CI434 dissociation constant||40.000||nanomoles||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| GAL4 dissociation constant||0.500||nanomoles||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| AraC dissociation constant||14.000||nanomoles||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| T7 dissociation constant||2.000||nanomoles||https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
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|-
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| LacI dissociation constant||800.000||nanomoles||https://2007.igem.org/ETHZ/Parameters
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|-
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| Mnt dissociation constant||50.000||nanomoles||Estimate
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|-
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| ||||||
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|-
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| LovTAP → LovTAP* reaction rate||0.100||1/sec||Estimate
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|-
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| SupD + T7ptag → T7 reaction rate||0.100||1/sec||Estimate
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|-
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|
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|}

Latest revision as of 22:14, 27 October 2010

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 NameValueUnitsSource
LovTAP rate of maximum synthesis1.0643E-013nanomoles/minDetermined as explained in Brown 2010 wiki
tatR rate of maximum synthesis1.1532E-013nanomoles/minDetermined as explained in Brown 2010 wiki
Mnt rate of maximum synthesis6.0562E-013nanomoles/minDetermined as explained in Brown 2010 wiki
AraC rate of maximum synthesis5.9999E-014nanomoles/minDetermined as explained in Brown 2010 wiki
LacI rate of maximum synthesis3.9479E-014nanomoles/minDetermined as explained in Brown 2010 wiki
CI rate of maximum synthesis8.9302E-014nanomoles/minDetermined as explained in Brown 2010 wiki
CI434 rate of maximum synthesis1.2236E-013nanomoles/minDetermined as explained in Brown 2010 wiki
SupD rate of maximum synthesis2.7149E-012nanomoles/minDetermined as explained in Brown 2010 wiki
T7ptag rate of maximum synthesis7.0208E-015nanomoles/minDetermined as explained in Brown 2010 wiki
GAL4 rate of maximum synthesis2.9175E-013nanomoles/minDetermined as explained in Brown 2010 wiki
S1 rate of maximum synthesis9.6899E-014nanomoles/minDetermined as explained in Brown 2010 wiki
LovTAP rate of basal synthesis1.0643E-015nanomoles/minDetermined as explained in Brown 2010 wiki
tatR rate of basal synthesis1.1532E-015nanomoles/minDetermined as explained in Brown 2010 wiki
Mnt rate of basal synthesis6.0562E-015nanomoles/minDetermined as explained in Brown 2010 wiki
AraC rate of basal synthesis5.9999E-016nanomoles/minDetermined as explained in Brown 2010 wiki
LacI rate of basal synthesis3.9479E-016nanomoles/minDetermined as explained in Brown 2010 wiki
CI rate of basal synthesis8.9302E-016nanomoles/minDetermined as explained in Brown 2010 wiki
CI434 rate of basal synthesis1.2236E-015nanomoles/minDetermined as explained in Brown 2010 wiki
SupD rate of basal synthesis2.7149E-014nanomoles/minDetermined as explained in Brown 2010 wiki
T7ptag rate of basal synthesis7.0208E-017nanomoles/minDetermined as explained in Brown 2010 wiki
GAL4 rate of basal synthesis2.9175E-015nanomoles/minDetermined as explained in Brown 2010 wiki
S1 rate of basal synthesis9.6899E-016nanomoles/minDetermined as explained in Brown 2010 wiki
LovTAP degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
LovTAP* degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
tetR degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
Mnt degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
AraC degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
LacI degradation rate6.6667E-0021/secDetermined as explained in Brown 2010 wiki
CI degradation rate5.6061E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
CI434 degradation rate1.2424E-0011/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
SupD degradation rate6.6667E-0021/secAs explained in wiki
T7ptag degradation rate6.6667E-0021/secAs explained in wiki
T7 polymerase degradation rate5.8333E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
GAL4 degradation rate6.6667E-0021/secAs explained in wiki
S1 degradation rate5.0000E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S2 degradation rate5.0000E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S3 degradation rate5.0000E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
S4 degradation rate5.0000E-0021/sechttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
LovTAP* hill coefficient1Estimate
tetR hill coefficient3https://2007.igem.org/ETHZ/Parameters
CI hill coefficient2https://2007.igem.org/ETHZ/Parameters
CI434 hill coefficient2PKU 2009 wiki
GAL4 hill coefficient2PKU 2009 wiki
AraC hill coefficient2PKU 2009 wiki
T7 hill coefficient2PKU 2009 wiki
LacI hill coefficient2PKU 2009 wiki
Mnt hill coefficient1PKU 2009 wiki
LovTAP* dissociation constant142.000nanomolesLight-activated DNA binding in a designed allosteric protein,Devin Strickland, Keith Moffat, and Tobin R. Sosnick
tetR dissociation constant0.179nanomoleshttps://2007.igem.org/ETHZ/Parameters
CI dissociation constant50.000nanomoleshttps://2007.igem.org/ETHZ/Parameters
CI434 dissociation constant40.000nanomoleshttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
GAL4 dissociation constant0.500nanomoleshttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
AraC dissociation constant14.000nanomoleshttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
T7 dissociation constant2.000nanomoleshttps://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
LacI dissociation constant800.000nanomoleshttps://2007.igem.org/ETHZ/Parameters
Mnt dissociation constant50.000nanomolesEstimate
LovTAP → LovTAP* reaction rate0.1001/secEstimate
SupD + T7ptag → T7 reaction rate0.1001/secEstimate
Retrieved from "http://2010.igem.org/Team:Brown/Modeling/Parameters"