Team:KULeuven/Model/Reset

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(Difference between revisions)
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== Constant Lactonase Production ==
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 +
=== Position in the system ===
 +
 +
The Constant Lactonase Production-system is directly linked to the [[Team:KULeuven/Model/Filter | Filter]].
 +
 +
When the filter indicates that the input is zero (there is no light), the system will (ideally) produce no lactonase. As soon as the output of the filter is one, the system starts producing lactonase and remains doing this untill the light goes off again.
 +
 +
=== Describing the system ===
 +
 +
==== ODE's ====
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<html>
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<body>
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<p>
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<a href="https://static.igem.org/mediawiki/2008/6/6a/Lactonaseproduction.pdf">
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<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60">
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</a>
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</p>
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</body>
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</html>
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==== Parameters ====
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{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
 +
|+ ''Parameter values Constant Lactonase Production''
 +
! width=15% | Name
 +
! width=15% | Value
 +
! width=40% | Comments
 +
! width=10% | Reference
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Constants
 +
|-
 +
| d<sub>lactonase</sub>
 +
| 2.888E-4 s<sup>-1</sup>
 +
|
 +
|
 +
|-
 +
| d<sub>closed_mRNA_lactonase</sub>
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| 0.0046209812 s<sup>-1</sup>
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|
 +
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
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| d<sub>open_mRNA_lactonase</sub>
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| 0.0023104906 s<sup>-1</sup>
 +
|
 +
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| d<sub>open_mRNA_lactonase_complex</sub>
 +
| 0.0023104906 s<sup>-1</sup>
 +
|
 +
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
 +
|-
 +
| k<sub>mRNA_lactonase</sub>
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| 0.03 s<sup>-1</sup>
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|
 +
|
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
 +
|-
 +
| k<sub>lactonase</sub>
 +
| 0.1666667 s<sup>-1</sup>
 +
| RBS is B0032 (efficiency of 0.3)
 +
|
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Equilibrium constants
 +
|-
 +
| K<sub>eq_1</sub>
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| 0.015
 +
| closed and open mRNA
 +
|
 +
|-
 +
| K<sub>eq_2</sub>
 +
| 0.0212 M
 +
| closed and key (binded with ribokey) complex mRNA
 +
|
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Association/Dissociation/Reaction Rates
 +
|-
 +
| k<sub>ass</sub> (closed mRNA lactonase + mRNA Ribokey)
 +
| 2.12 s<sup>-1</sup>
 +
|
 +
|
 +
|-
 +
| k<sub>diss</sub> (closed mRNA lactonase + mRNA Ribokey)
 +
| 100 s<sup>-1</sup>
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|
 +
|
 +
|-
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| k (open mRNA lactonase)
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| 1.5 s<sup>-1</sup>
 +
|
 +
|
 +
|-
 +
| k (closed mRNA lactonase)
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| 100 s<sup>-1</sup>
 +
|
 +
|
 +
|-
 +
|}
 +
 +
=== Models ===
 +
 +
==== CellDesigner ([https://static.igem.org/mediawiki/2008/a/a2/LactonaseProduction.zip SBML file]) ====
 +
The model:
 +
[[Image:LactonaseProduction.png|500px|center]]
 +
Simulation: <br>
 +
The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4. <br>
 +
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.
 +
[[Image:Sim_lactonaseproduction_1.png|700px|center]]

Revision as of 13:15, 29 July 2008

Result:

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Inspirational websites:

  • [http://javascript-array.com/scripts/simple_drop_down_menu/ Most basic dropdown menu, with no submenu's]
  • [http://jquery.com/ The javascript library used to add effects and optimise the dropdown]
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The dropdown has been created and developed by the KULeuven team. 

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					<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
				</div>
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                        <span>
				<a>Components</a>
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					<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
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					<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
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			<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
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					<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
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				<a>Lab Data</a>
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					<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
					<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a>
					<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
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Contents

Pulse Generator

Position in the system

Describing the system

Pulse Generator BioBrick.jpg

ODE's

Parameters

Parameter values (Pulse Generator)
Name Value Comments Reference
Degradation rates
dRNA_cI 0.00462 s-1
dcI 7.0E-4 s-1 [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link]
dRNA_Lac 0.00231 s-1
dLac 2.888E-4 s-1
dRNA_Ribokey:cI 0.00231 s-1
Dissociation constants
KRibokey:cI 0.00212 kass/kdiss for the Ribokey cI complex
KcI 0.00337 binding cI on cI-Promotor [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link]
Transcription rates
kRNA_cI 0.025? s-1 maximal transcription rate RNA cI (no cI repressor present)
kRNA_Lac 0.025? s-1
Translation rates
kcI 0.167? s-1
kLac 0.167 s-1 RBS is B0032 (efficiency 0.3) [http://partsregistry.org/Part:BBa_B0032 link]
Hill cooperativity
ncI 2.0 [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link]

Models

CellDesigner (SBML file)

Pulse Generator

Matlab

The diagram for the pulse generator system is shown below:

Pulse Generator Matlab.jpg

Following figure shows the repons of the pulse generator to a step signal of T7 polymerase.

...


Constant Lactonase Production

Position in the system

The Constant Lactonase Production-system is directly linked to the Filter.

When the filter indicates that the input is zero (there is no light), the system will (ideally) produce no lactonase. As soon as the output of the filter is one, the system starts producing lactonase and remains doing this untill the light goes off again.

Describing the system

ODE's

Parameters

Parameter values Constant Lactonase Production
Name Value Comments Reference
Degradation Constants
dlactonase 2.888E-4 s-1
dclosed_mRNA_lactonase 0.0046209812 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_lactonase 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_lactonase_complex 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Transcription Rates
kmRNA_lactonase 0.03 s-1
Translation Rates
klactonase 0.1666667 s-1 RBS is B0032 (efficiency of 0.3)
Equilibrium constants
Keq_1 0.015 closed and open mRNA
Keq_2 0.0212 M closed and key (binded with ribokey) complex mRNA
Association/Dissociation/Reaction Rates
kass (closed mRNA lactonase + mRNA Ribokey) 2.12 s-1
kdiss (closed mRNA lactonase + mRNA Ribokey) 100 s-1
k (open mRNA lactonase) 1.5 s-1
k (closed mRNA lactonase) 100 s-1

Models

CellDesigner (SBML file)

The model:

LactonaseProduction.png

Simulation:
The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4.
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.

Sim lactonaseproduction 1.png
Retrieved from "http://2008.igem.org/Team:KULeuven/Model/Reset"