Template:ETH Sim Input Rate
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* ''E.coli'' cytoplasm volume is approximately <tt>6.7*10<sup>-16</sup> l</tt> | * ''E.coli'' cytoplasm volume is approximately <tt>6.7*10<sup>-16</sup> l</tt> | ||
* average number of mRNA molecules: <tt>10<br/>→ concentration<sub>mRNA</sub> = 10/(6.7*10<sup>-16</sup> * 6.022*10<sup>23</sup>) M = 0.0248 μM</tt> | * average number of mRNA molecules: <tt>10<br/>→ concentration<sub>mRNA</sub> = 10/(6.7*10<sup>-16</sup> * 6.022*10<sup>23</sup>) M = 0.0248 μM</tt> | ||
| - | * at equilibrum, mRNA rate and degredation balance each other. Assuming half life period of 30min for mRNA, the result is<br/><tt>→rate<sub>mRNA</sub> = concentration<sub>mRNA</sub> * log(2)/30 μM/min = 5.7265e-04 μM/min</tt> | + | * at equilibrum, mRNA rate and degredation balance each other. Assuming half life period of 30min for mRNA, the result is<br/><tt>→ rate<sub>mRNA</sub> = concentration<sub>mRNA</sub> * log(2)/30 μM/min = 5.7265e-04 μM/min</tt> |
Amplifying/damping the input rates by small constant factors has influence on the qualitative outcome of the simulation. | Amplifying/damping the input rates by small constant factors has influence on the qualitative outcome of the simulation. | ||
Revision as of 09:14, 30 October 2006
The input rates (PoPS) have been chosen in the range of mRNA transcription rate, which was estimated according to the following assumptions:
- E.coli cytoplasm volume is approximately 6.7*10-16 l
- average number of mRNA molecules: 10
→ concentrationmRNA = 10/(6.7*10-16 * 6.022*1023) M = 0.0248 μM - at equilibrum, mRNA rate and degredation balance each other. Assuming half life period of 30min for mRNA, the result is
→ ratemRNA = concentrationmRNA * log(2)/30 μM/min = 5.7265e-04 μM/min
Amplifying/damping the input rates by small constant factors has influence on the qualitative outcome of the simulation.
- it is thus important to know how strong the input of the gate has to be.
- we can regulate this by choosing/designing the predecessor gate accordingly or
- by changing the ribosome binding sites to strengthen/weaken the input signal.
We accounted for this by adding restriction enzyme sites to the DNA.
