# Team:ETH Zurich/modeling/whole

(Difference between revisions)
 Revision as of 09:26, 17 October 2014 (view source)Eledieu (Talk | contribs)m (→Ideal case)← Older edit Revision as of 09:49, 17 October 2014 (view source)Eledieu (Talk | contribs) mNewer edit → Line 268: Line 268: - + - However, if we measure the fluorescence at around 400 mins, we observe a good and acceptable XOR behaviour. Therefore, one of the solutions we propose is to kill or freeze the cells in each row after 6.5 hours. + However, if we measure the fluorescence at around 400 mins, the effect of leakiness becomes negligible: in the case with null inputs, the level of the output concentration, GFP, is negligible compared to the level of the GFP concentration produced when the cell receives only one type of AHL. At this point, our model behaves like an XOR gate. Therefore, one of the solutions we propose is to kill or freeze the cells in each row after 6.5 hours. - Initially from our model we observed that the feedback was rapid and hence, the amplification was much higher. However, from literature [[Team:ETH_Zurich/project/references|[9]]] we see that the XOR module is relatively slow. We were able to correct this by modelling transcription and translation steps. The delay introduced seems more reliable although we do not have our own experimental data to validate the same. Further, we use a dilution factor (DF) which represents the density of the cells in the bead. By choosing and appropriate DF we can get a more delayed response. + Initially from our model we observed that the feedback was rapid and hence, the amplification was much higher. However, from literature [[Team:ETH_Zurich/project/references|[9]]] we see that the XOR module is relatively slow. We were able to correct this by modelling transcription and translation steps. The delay introduced seems more realistic although we do not have our own experimental data to validate the same. Further, we use a dilution factor (DF) which represents the density of the cells in the bead. By choosing and appropriate DF we can get a more delayed response. $$DF = \frac{No. of cells * V_{E.coli}}{V_{Bead}}$$ $$DF = \frac{No. of cells * V_{E.coli}}{V_{Bead}}$$ Line 298: Line 298:

- Here, we present the simulation results. The four possibilities of the XOR gate are presented in the following figure. The system was the one with a feedback corresponding to the metabolite pathway. The metabolite parameter taken was the one of xylose, which is supposed to be generic for all models + Here, we present the simulation results. The four possibilities of the XOR gate are presented in the following figure. The system was the one with a feedback corresponding to the metabolite pathway.

## Revision as of 09:49, 17 October 2014

iGEM ETH Zurich 2014