Team:ZJU-China/model s2 3.htm

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<p align="justify">The initial state is as following:</p>
<p align="justify">The initial state is as following:</p>
<p align="justify">Edge of cube: 50 units</p>
<p align="justify">Edge of cube: 50 units</p>
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<p align="justify">The number of A: 2000</p>
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<p align="justify">The amount of A: 2000</p>
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<p align="justify">The number of B: 0</p>
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<p align="justify">The amount of B: 0</p>
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<p align="justify">The number of C: 0</p>
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<p align="justify">The amount of C: 0</p>
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<p align="justify">The number of E1: 50</p>
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<p align="justify">The amount of E1: 50</p>
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<p align="justify">The number of E2: 50</p>
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<p align="justify">The amount of E2: 50</p>
<p align="justify">The distance between E1 and E2 for RNA scaffold: 2 units</p>
<p align="justify">The distance between E1 and E2 for RNA scaffold: 2 units</p>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
<p align="justify">After 1200 iterations, the scaffold and non-scaffold results are as following:</p>
<p align="justify">After 1200 iterations, the scaffold and non-scaffold results are as following:</p>
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<p align="justify">Scaffold &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Non-scaffold</p>
 
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<p align="justify">The number of A: 1417 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The number of A: 1470</p>
 
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<p align="justify">The number of B: 436 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The number of B: 451</p>
 
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<p align="justify">The number of C: 147 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The number of C: 79</p>
 
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<p align="justify">The number of E1: 50 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The number of E1: 50</p>
 
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<p align="justify">The number of E2: 50 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The number of E2: 50</p>
 
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<div><img src="http://www.jiajunlu.com/igem/zju_model2_4.jpg"></div>
 
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<p align="justify">Figure 4. Result of scaffold system for large scale simulation. After 1200 iterations, there are 436 B and 147 C.</p>
 
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<div><img src="http://www.jiajunlu.com/igem/zju_model2_5.jpg"></div>
 
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<p align="justify">Figure 5. Result of non-scaffold system for large scale simulation. After 1200 iterations, there are 451 B and 79 C.</p>
 
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
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<h2>Comparison between scaffold system and non-scaffold system</h2>
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<table align="center">
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<p align="justify">As the iteration increasing, the number of A is decreasing and the number of B and C are increasing. We record the number of B and C for both scaffold system and non-scaffold system as iteration grows to watch the reaction rate of pathway (i.e. the number of C).</p>
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<tr>
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<div><img src="http://www.jiajunlu.com/igem/zju_model2_6.jpg"></div>
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<th></th>
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<p align="justify">Figure 6. The number of B and C as iteration grows.</p>
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<th>Scaffold</th>
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<th>Non-scaffold</th>
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</tr>
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<tr>
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<td>A (Substrate)</td>
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<td>1417</td>
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<td>1470</td>
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</tr>
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<tr>
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<td>B (Intermediate)</td>
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<td>436</td>
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<td>451</td>
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</tr>
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<tr>
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<td>C (Product)</td>
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<td>147</td>
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<td>79</td>
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</tr>
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<tr>
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<td>E1 (Enzyme1)</td>
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<td>50</td>
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<td>50</td>
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</tr>
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<tr>
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<td>E2 (Enzyme2)</td>
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<td>50</td>
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<td>50</td>
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</tr>
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</table>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
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<p align="justify">From figure 4.5.6, it is obvious that the number of C for scaffold system is more than that for non-scaffold system and the number of B for scaffold system is less than that for non-scaffold system. This phenomenon can be interpreted as that the probability that B meets an E2 is highly increased since their distance is closer. Therefore, it is safely to draw a conclusion that the reaction rate of pathway has been speed up because of the scaffold bringing two enzymes closer.</p>
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<table class="tm" align="center">
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<tr>
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<td class="tm"><img src="https://static.igem.org/mediawiki/2012/3/3a/Scaffold.gif" width="350px" /></td>
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<td class="tm"><img src="https://static.igem.org/mediawiki/2012/a/ab/Nonscaffold.gif" width="350px" /></td>
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</tr>
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</table>
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<p class="fig" align="justify"><b>Fig 4.(Left)</b> Result of scaffold system for large scale simulation. After 1200 iterations, there are 436 B and 147 C.<br/>
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<b>Fig 5.(Right)</b> Result of non-scaffold system for large scale simulation. After 1200 iterations, there are 451 B and 79 C.</p>
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<p align="justify">&nbsp;</p>
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<h2>Comparison between the two system</h2>
 +
<p align="justify">As the iteration increasing, the number of A is decreasing and the number of B and C are increasing. We record the number of B and C for both scaffold system and non-scaffold system as iteration grows to watch the reaction rate of pathway (i.e. the number of C).</p>
 +
<div class="floatC"><img src="http://www.jiajunlu.com/igem/zju_model2_6.jpg" width="400px">
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<p class="fig"><b>Fig 6.</b> The number of B and C as iteration grows.</p>
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</div>
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<p align="justify">From figure 4.5.6, it is obvious that the number of C for scaffold system is more than that for non-scaffold system and the number of B for scaffold system is less than that for non-scaffold system. This phenomenon can be interpreted as that the probability that B meets an E2 is highly increased since their distance is closer. Therefore, it is safely to draw a conclusion that the reaction rate of pathway has been speed up because of the scaffold bringing two enzymes closer.</p>
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Latest revision as of 19:58, 26 October 2012

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A large scale simulation

The initial state is as following:

Edge of cube: 50 units

The amount of A: 2000

The amount of B: 0

The amount of C: 0

The amount of E1: 50

The amount of E2: 50

The distance between E1 and E2 for RNA scaffold: 2 units

 

After 1200 iterations, the scaffold and non-scaffold results are as following:

 

Scaffold Non-scaffold
A (Substrate) 1417 1470
B (Intermediate) 436 451
C (Product) 147 79
E1 (Enzyme1) 50 50
E2 (Enzyme2) 50 50

 

Fig 4.(Left) Result of scaffold system for large scale simulation. After 1200 iterations, there are 436 B and 147 C.
Fig 5.(Right) Result of non-scaffold system for large scale simulation. After 1200 iterations, there are 451 B and 79 C.

 

Comparison between the two system

As the iteration increasing, the number of A is decreasing and the number of B and C are increasing. We record the number of B and C for both scaffold system and non-scaffold system as iteration grows to watch the reaction rate of pathway (i.e. the number of C).

Fig 6. The number of B and C as iteration grows.

From figure 4.5.6, it is obvious that the number of C for scaffold system is more than that for non-scaffold system and the number of B for scaffold system is less than that for non-scaffold system. This phenomenon can be interpreted as that the probability that B meets an E2 is highly increased since their distance is closer. Therefore, it is safely to draw a conclusion that the reaction rate of pathway has been speed up because of the scaffold bringing two enzymes closer.


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