Team:KULeuven/Model/Filter

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Revision as of 09:19, 17 August 2008

dock/undock dropdown

Filter

Position in the system

todo

Describing the system

ODE's

Parameters

*Parameter values Filter*
Name	Value	Comments	Reference
Degradation rates
d_{pT7_tag}	0.00155 s^-1	tag added to speed up degradation of otherwise too stable T7 polymerase	[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link]
d_{mRNA_RIBOKEY}	0.00462 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{closed_mRNA_T7}	0.00462 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{open_mRNA_T7}	0.00231 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{open_mRNA_T7_complex}	0.00231 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Equilibrium constants
K_{eq_1}	0,015 [M]	closed and open mRNA
K_{eq_2}	0.0212 [M]	closed and key (binded with ribokey) complex mRNA
Transcription rates
k_{mRNA_RIBOKEY}	Input dependent
k_{mRNA_T7}	0,0011 s^-1

Remark: The key-lock system can be enhanced to 0.3%-14% (todo: Jonas/Dries)

Models

CellDesigner (SBML file)

Matlab (SBML file)

Simulations

Discussion of the simulation:

1. AND gate of the filter

In the simulation we can clearly see this series of events:

when dark blue(ribokey) starts to increase, red (T7) also starts to increase, giving rise to an increasing amount of lactonase (blue) = AND-GATE.
when dark blue(ribokey) starts to decrease, red (T7) also starts to decrease, but much slower. The lactonase also starts to decrease, as it should be.

The short lifetime of the ribokey compared to the lifetime of the T7-protein, guarantees that the AND-GATE always works perfectly fine: when there's no more input, the ribokey will rapidly decrease (and disappear) and makes sure that the AND-GATE is not activated anymore, even when the T7-protein is slowly decreasing.

2. Filtering in practice

First Lightpulse: 300s
- small peak of lactonase
- no influence on the timer
Second Lightpulse: 1000s
- medium peak of lactonase
- influences the timer by levelling the timing capabilities, but it doesn't reset the timer
Third Lightpulse: 5000s
- huge peak of lactonase
- reset of the timer: amount of complex goes to zero

Sensitivity Analysis

@@ Line 95: / Line 95: @@
 ==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====
-Matlab diagram for the filter system:
 [[Image:Filter_Matlab.jpg|center]]
 === Simulations ===