Biomod/2014/Sendai/temp/0821/Simulation

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<body>

Simulation

1-a.Enzyme system

Results

Our system gave outputs with time intervals in order.

<figure> <img src="http://openwetware.org/images/4/44/0823tetsuya-01.png"> <figcaption>Fig.1#</figcaption> </figure>

Our system gave, first, A-outputs, second, B-output with about 10sec interval when we code A-B in the input DNA.

<figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.2#</figcaption> </figure>

Our system gave first, B-outputs second, A-output with about 10sec interval when we code B-A in the input DNA.

<figure> <img src="http://openwetware.org/images/3/3e/Ab%28インプットなし%29-01.png"> <figcaption>Fig.3#</figcaption> </figure>

Our system gave no outputs when the system accepted no inputs. We need the inputs DNA to start the system.

Our system can change the time intervals by changing concentration’s of components (input, templates).

<figure> <img src="http://openwetware.org/images/5/59/0824simulation04-01.png"> <figcaption>Fig.4#</figcaption> </figure>

Time intervals changed by changing templates. Time interval increased when the concentration of template-A(Fig.4) or template-B(Fig.5) decreased.

<figure> <img src="http://openwetware.org/images/e/e7/0824simulation03-01.png"> <figcaption>Fig.5#</figcaption> </figure>

#

<figure> <img src="http://openwetware.org/images/9/91/0827simulation08-01.png" width="610px" height="460px"> <figcaption>Fig.6#</figcaption> </figure>

Time interval changed by changing the concentration of gate. (Fig6)

<figure> <img src="http://openwetware.org/images/c/cf/0827simulation09-01.png"> <figcaption>Fig.7#</figcaption> </figure>

#

Note that outputs DNA didn’t decrease if input DNA did

<figure> <img src="http://openwetware.org/images/6/6e/0824simulation05-01.png"> <figcaption>Fig.8#</figcaption> </figure>

Time interval changed when the concentration of input DNA decreased. (Fig.8)

Note that outputs DNA didn’t decrease if input DNA did


Method

Our system behaved properly in scilico, that is , following can be said.

・Our system gives outputs as coded in the input DNA.
・Our system gives outputs with time intervals and the interval can be tuned by changing concentrations of the components of the system.

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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