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From 2012.igem.org

A large scale simulation

The initial state is as following:

Edge of cube: 50 units

The number of A: 2000

The number of B: 0

The number of C: 0

The number of E1: 50

The number 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

The number of A: 1417             The number of A: 1470

The number of B: 436             The number of B: 451

The number of C: 147             The number of C: 79

The number of E1: 50             The number of E1: 50

The number of E2: 50             The number of E2: 50

Figure 4. Result of scaffold system for large scale simulation. After 1200 iterations, there are 436 B and 147 C.

Figure 5. Result of non-scaffold system for large scale simulation. After 1200 iterations, there are 451 B and 79 C.

 

Comparison between scaffold system and non-scaffold 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).

Figure 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.