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Team:Brown/Modeling/Parameters
From 2010.igem.org
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# n represents a ligand’s hill coefficient. | # n represents a ligand’s hill coefficient. | ||
# K_m represents the ligand’s dissociation constant | # K_m represents the ligand’s dissociation constant | ||
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For a complete, up-to-date list of values and sensitivities, please see our current [http://brownigem.com/parameters_2010.ods spreadsheet of parameters and sensitivities]. | For a complete, up-to-date list of values and sensitivities, please see our current [http://brownigem.com/parameters_2010.ods spreadsheet of parameters and sensitivities]. | ||
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| + | Alternatively, please see our prettier [http://brownigem.com/parameters_2010.pdf typeset PDF file] | ||
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Revision as of 21:41, 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:
- δ is a function designed to represent the presence/absence of light in a Boolean fashion. δ=0 without light and 1 with light.
- c_1 represents the rate of conformational change from LovTAP to LovTAP* when irradiated with 470nm light.
- c_2 represents the rate of SupD + T7ptag --> T7 polymerase
- α represents the maximum protein synthesis rate in nanomoles/sec.
- β represents the basal synthesis rate. We assume ∀x β_x= .01α_x
- μ represents the protein degradation rate.
- n represents a ligand’s hill coefficient.
- K_m represents the ligand’s dissociation constant
For a complete, up-to-date list of values and sensitivities, please see our current [http://brownigem.com/parameters_2010.ods spreadsheet of parameters and sensitivities].
Alternatively, please see our prettier [http://brownigem.com/parameters_2010.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 |
