Difference between revisions of "Team:Valencia UPV/Modeling/Simulations"

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<p>Hello world</p>
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<p>Before studying saturation when light pulses were given, we must take in advice that first level (producing A, B, C and D), starts expressing from minute 0. Activation of next level is directly proportional to the amount of those proteins that were produced firstly, as they are binding domains of secondly activated constructions. Thus, more expression will be obtained as more binding domains are synthetized.</p>
 +
We determine the moment when constitutive expression reaches its plateau by simulating the zero input response of our system during 10000 minutes. </p>
 +
Light Inputs: </p>
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<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/4/4a/Valencia_upv_saturation1.png/800px-Valencia_upv_saturation1.png" ></div></p>
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<p><div style="text-align:center;"><h5><b>Figure 1.</b></h5></div></p>
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 +
Outputs:</p>
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<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/1/17/Valencia_upv_saturation2.png" ></div></p>
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 +
<p><div style="text-align:center;"><h5><b>Figure 2.</b></h5></div></p>
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 +
Protein production behaves like a first order system after a step input. In this case, the step from 0 to 1 is the beginning of the protein production inside the cell. Thus, the moment when it will saturate is approx. 5·τ, where τ is the time constant of this process, given by the moment at which production has reached the 63% of its saturation level. </p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/a/a7/Valencia_upv_saturation3.png/800px-Valencia_upv_saturation3.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 3. </b></h5></div></p>
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Searching again with the data cursor:</p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/3/35/Valencia_upv_equations1.png/800px-Valencia_upv_equations1.png" ></div></p>
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 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/e/ee/Valencia_upv_saturation4.png/800px-Valencia_upv_saturation4.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 4.</b></h5></div></p>
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 +
Now we can fix the beginning of light irradiation in 250 min, and the initial concentrations of proteins BD1-PIF6, PhyB-VP16, BD2-LOV2 and ePDZ-VP16 in 250 nM. This is the reason why all our inputs will have the structure:</p>
 +
input_red =[zeros(251,1);… ;zeros(100,1)];
 +
input_blue=[zeros(251,1);… ;zeros(100,1)];
 +
 
 +
The final vector of zeros is added in order to appreciate the effect of degradation when lights are switched off. This could give a qualitative idea of how much of the production can be lost during the extraction of the product for its ingestion. </p>
 +
 
 +
Switches level.</p>
 +
We opted to make the light pulse “infinitely” long in order to notice until when does production rise and its saturation point.
 +
Firstly, we did only a red pulse of 10000 minutes, so the final product should be alpha.</p>
 +
t_final=10000; % with input_t=(0:Ts:t_final)' (minutes)</p>
 +
 
 +
input_red =[zeros(251,1);red_intensity*ones(length (input_t)-351,1) ;zeros(100,1)];</p>
 +
input_blue=[zeros(251,1); zeros(length (input_t)-351,1) ;zeros(100,1)];</p>
 +
 
 +
Following graphics let us determine the moment when second and last levels of production, reach their plateau </p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/d/da/Valencia_upv_saturation5.png/800px-Valencia_upv_saturation5.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 5.</b></h5></div></p>
 +
 
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/d/d1/Valencia_upv_saturation6.png/800px-Valencia_upv_saturation6.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 6.</b></h5></div></p>
 +
 
 +
Inputs are on the top of the graphics. Second line belongs to second level expression and green curves represent the outputs performance.  Using the data cursor in both elements whose production was being induced (protein E and alpha): </p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/4/46/Valencia_upv_equations2.png/799px-Valencia_upv_equations2.png" ></div></p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/2/26/Valencua_upv_equations3.png/800px-Valencua_upv_equations3.png" ></div></p>
 +
 
 +
 
 +
Searching again with the data cursor:
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/7/74/Valencia_upv_saturation9.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 7.</b></h5></div></p>
 +
 
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/5/5c/Valencia_upv_equations4.png/799px-Valencia_upv_equations4.png" ></div></p>
 +
 
 +
With inputs of 250 minutes, the plateau will be reached. If carry on with the irradiation after 250 minutes or not, relies on the efficiency of recombinases. </p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/8/85/Valencia_upv_saturation10.png/800px-Valencia_upv_saturation10.png" ></div></p>
 +
 
 +
<p><div style="text-align:center;"><h5><b>Figure 8.</b></h5></div></p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/2/23/Valencia_upv_equations5.png/800px-Valencia_upv_equations5.png" ></div></p>
 +
 
 +
 
 +
With inputs of 2510 minutes, maximum output production can be reached. Then:</p>
 +
<p><div style="text-align:center;"><img width=600em src=" https://static.igem.org/mediawiki/2015/thumb/7/76/Valencia_upv_equations6.png/800px-Valencia_upv_equations6.png" ></div></p>
 +
 
 +
 
 +
 
 +
This will be the duration considered in next simulations.</p>
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</p>
  
 
<br/>
 
<br/>

Revision as of 04:48, 18 September 2015

Valencia UPV iGEM 2015

Saturation

Before studying saturation when light pulses were given, we must take in advice that first level (producing A, B, C and D), starts expressing from minute 0. Activation of next level is directly proportional to the amount of those proteins that were produced firstly, as they are binding domains of secondly activated constructions. Thus, more expression will be obtained as more binding domains are synthetized.

We determine the moment when constitutive expression reaches its plateau by simulating the zero input response of our system during 10000 minutes.

Light Inputs:

Figure 1.

Outputs:

Figure 2.

Protein production behaves like a first order system after a step input. In this case, the step from 0 to 1 is the beginning of the protein production inside the cell. Thus, the moment when it will saturate is approx. 5·τ, where τ is the time constant of this process, given by the moment at which production has reached the 63% of its saturation level.

Figure 3.

Searching again with the data cursor:

Figure 4.

Now we can fix the beginning of light irradiation in 250 min, and the initial concentrations of proteins BD1-PIF6, PhyB-VP16, BD2-LOV2 and ePDZ-VP16 in 250 nM. This is the reason why all our inputs will have the structure:

input_red =[zeros(251,1);… ;zeros(100,1)]; input_blue=[zeros(251,1);… ;zeros(100,1)]; The final vector of zeros is added in order to appreciate the effect of degradation when lights are switched off. This could give a qualitative idea of how much of the production can be lost during the extraction of the product for its ingestion.

Switches level.

We opted to make the light pulse “infinitely” long in order to notice until when does production rise and its saturation point. Firstly, we did only a red pulse of 10000 minutes, so the final product should be alpha.

t_final=10000; % with input_t=(0:Ts:t_final)' (minutes)

input_red =[zeros(251,1);red_intensity*ones(length (input_t)-351,1) ;zeros(100,1)];

input_blue=[zeros(251,1); zeros(length (input_t)-351,1) ;zeros(100,1)];

Following graphics let us determine the moment when second and last levels of production, reach their plateau

Figure 5.

Figure 6.

Inputs are on the top of the graphics. Second line belongs to second level expression and green curves represent the outputs performance. Using the data cursor in both elements whose production was being induced (protein E and alpha):

Searching again with the data cursor:

Figure 7.

With inputs of 250 minutes, the plateau will be reached. If carry on with the irradiation after 250 minutes or not, relies on the efficiency of recombinases.

Figure 8.

With inputs of 2510 minutes, maximum output production can be reached. Then:

This will be the duration considered in next simulations.


Recombinases action

Hello world

Action for stablished inputs. How do they behave?

Influence of gene copy number

Light stimuli

Hello world

Pause between pulses

Inputs combination: Sequences

Inputs choice for each output