Team:KULeuven/Model/Filter

(Difference between revisions)

Revision as of 11:45, 14 August 2008

dock/undock dropdown

*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)

Matlab diagram for the filter system:

Discussion of the simulation:

1. AND gate of the filter

 ribokey (dark blue) --> T7 (red)--> |
     |                               | --> lactonase (blue)
     |-----------------------------> |

todo: add extra comment

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

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        |-----------------------------> |
-todo: add extra comment
+<b>todo:</b> add extra comment
 . Filtering in practice