Biomod/2014/Sendai/Simulation/sandbox

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Simulation

1-1.Enzyme system

Results

Our system’s strong points are that it gives outputs in order with time intervals. We can program order as we want.
Here we examine whether our system behaves properly in the simulation.

Fig.1#
First, we simulated the behavior when the system had no input. Of course, the system gave no outputs (Fig.1). This system needs some inputs to start the actions.
Fig.2#
Second, we gave A-B input to the system. Our design is correct, the system gives at first, A-output, secondly B-output. In the simulation, we got the result as we expected, that is, the system gave A-output first, B-output second.(Fig.2)

These results above show that the system seems to behave properly, but we need to check that the system changes order of outputs to actually say its behavior is proper. So third, we simulated how the system works when system accepts B-A input.

Fig.3#
The behavior when we coded B-A to the input DNA is shown in Fig.3.
As we designed, the system gave B then A outputs in order. This prove our system can recognize input DNA and change its outputs as we coded.
Moreover, We wanted to know the relations of time intervals between concentration of input, templates, and gates to control the system more precisely.
Each concentration related to the system, so we checked the behavior of time intervals when the concentrations of each component are changed.
Following are the results of simulations when concentration of input, templates, gates were changed (Fig.4,5,6,7). Each result shows that time interval can be arranged by concentration of components.
Fig.4#
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Fig.5#
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Fig.6#
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Fig.7#
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Fig.8#
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In these simulations, the system can be controlled from perspective of order and time intervals and we concluded followings.
・Our system gives outputs as coded in the input DNA in order.
・Our system gives outputs with time intervals and the interval can be arranged by changing concentrations of the components of the system.

Method

Our system is described by differential equations obtained from chemical reaction formulas. We solved them by using numerical software (Scilab).

Condition

Condition of simulating is as follows.

Input DNA concentration: 10nM
Template1 concentration: 10nM
Template2 concentration: 10nM
Liposome1 concentration: 10nM
Liposome2 concentration: 10nM
Gate1 concentration: 10nM
Gate2 concentration: 10nM
Simulation time: 100[sec]

Values of chemical parameters are as follows.

Hybridization:kh=5.0*10^6
Denaturation:kd=1.0*10^3
Branch migration:kb=1.0*10^-1
Polymerase:kp:=17
Nickase:kn=3.0
Restriction enzyme:kr=3.0

Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short.

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