Biomod/2014/Sendai/Simulation: Difference between revisions

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<li><a href="/wiki/Biomod/2014/Sendai">Home</a></li>
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<h1>Simulation</h1>
<h1>Simulation</h1>
<h2>1-1.Enzyme system</h2>
<h3>Results</h3>
<p>
Our system’s strong points are that it gives outputs in order with time intervals. We can program order as we want.<br>
Here we examine whether our system behaves properly in the simulation.<br>
</p>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/4/44/0823tetsuya-01.png">
<figcaption>Fig.1#</figcaption>
</figure>
</div>
<div class="blockright">
<span>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.</span>
</div>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png">
<figcaption>Fig.2#</figcaption>
</figure>
</div>
<div class="blockright">
<span>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)</span>
</div>
<p>
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.
</p>
<div class="blockleft">
<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>
</div>
<div class="blockright">
<span>The behavior when we coded B-A to the input DNA is shown in Fig.3.<br>
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.
<span>
</div>
<p>Moreover, We wanted to know the relations of time intervals between concentration of input, templates, and gates to control the system more precisely.</p>
<p>
Each concentration related to the system, so we checked the behavior of time intervals when the concentrations of each component are changed.
</p>
<p>
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.
</p>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/5/59/0824simulation04-01.png">
<figcaption>Fig.4#</figcaption>
</figure>
</div>
<div class="blockright">
<span>Time intervals changed by changing templates.
Time interval increased when the concentration of template-A(Fig.4) or template-B(Fig.5) decreased.
</span>
</div>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/e/e7/0824simulation03-01.png">
<figcaption>Fig.5#</figcaption>
</figure>
</div>
<div class="blockright">
<span>#</span>
</div>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/9/91/0827simulation08-01.png" width="610px" height="460px">
<figcaption>Fig.6#</figcaption>
</figure>
</div>
<div class="blockright">
<span>Time interval changed by changing the concentration of gate. (Fig6)</span>
</div>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/c/cf/0827simulation09-01.png">
<figcaption>Fig.7#</figcaption>
</figure>
</div>
<div class="blockright">
<span>#</span>
<br>
<p>
Note that outputs DNA didn’t decrease if input DNA did
</p>
</div>
<div class="blockleft">
<figure>
<img src="http://openwetware.org/images/6/6e/0824simulation05-01.png">
<figcaption>Fig.8#</figcaption>
</figure>
</div>
<div class="blockright">
<span>Time interval changed when the concentration of input DNA decreased. (Fig.8)</span>
<br>
<p>
Note that outputs DNA didn’t decrease if input DNA did
</p>
</div>
In these simulations, the system can be controlled from perspective of order and time intervals and we concluded followings.<br>
・Our system gives outputs as coded in the input DNA in order. <br>
・Our system gives outputs with time intervals and the interval can be arranged by changing concentrations of the components of the system.<br>
<h3>Method</h3>
<p>
Our system is described by differential equations obtained from chemical reaction formulas. We solved them by using numerical software (Scilab).
</p>
<h3>Condition</h3>
<p>
Condition of simulating is as follows.<br><br>
Input DNA concentration: 10nM<br>
Template1 concentration: 10nM<br>
Template2 concentration: 10nM<br>
Liposome1 concentration: 10nM<br>
Liposome2 concentration: 10nM<br>
Gate1 concentration: 10nM<br>
Gate2 concentration: 10nM<br>
Simulation time: 100[sec]<br>
</p>
<p>
Values of chemical parameters are as follows.<br><br>
Hybridization:kh=5.0*10^6<br>
Denaturation:kd=1.0*10^3<br>
Branch migration:kb=1.0*10^-1<br>
Polymerase:kp:=17<br>
Nickase:kn=3.0<br>
Restriction enzyme:kr=3.0<br>
</p>
<p>
Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short.
</p>
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Revision as of 17:51, 27 August 2014

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<body> <div id="globalnav" class="simu"> <ul> <li id="gn-home"><a href="/wiki/Biomod/2014/Sendai">Home</a></li> <li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/Introduction">Introduction</a></li> <li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/Design">Design</a></li> <li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/Simulation">Simulation</a></li> <li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/Experiment">Experiment</a></li> <!--<li id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/Protocol">Protocol</a></li>--> <li id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/Discussion">Discussion</a></li> <li id="gn-team"><a href="/wiki/Biomod/2014/Sendai/Team">Team</a></li> <li id="gn-end"><a href="#"></a></li> </ul> </div> <div id="main"> <h1>Simulation</h1> <h2>1-1.Enzyme system</h2> <h3>Results</h3>

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

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

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

<p> 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. </p>

<div class="blockleft"> <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> </div> <div class="blockright"> <span>The behavior when we coded B-A to the input DNA is shown in Fig.3.<br> 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. <span> </div>

<p>Moreover, We wanted to know the relations of time intervals between concentration of input, templates, and gates to control the system more precisely.</p> <p> Each concentration related to the system, so we checked the behavior of time intervals when the concentrations of each component are changed. </p> <p> 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. </p>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/5/59/0824simulation04-01.png"> <figcaption>Fig.4#</figcaption> </figure> </div> <div class="blockright"> <span>Time intervals changed by changing templates. Time interval increased when the concentration of template-A(Fig.4) or template-B(Fig.5) decreased. </span> </div>

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

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/9/91/0827simulation08-01.png" width="610px" height="460px"> <figcaption>Fig.6#</figcaption> </figure> </div> <div class="blockright"> <span>Time interval changed by changing the concentration of gate. (Fig6)</span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/cf/0827simulation09-01.png"> <figcaption>Fig.7#</figcaption> </figure> </div> <div class="blockright"> <span>#</span> <br> <p> Note that outputs DNA didn’t decrease if input DNA did </p> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/6/6e/0824simulation05-01.png"> <figcaption>Fig.8#</figcaption> </figure> </div> <div class="blockright"> <span>Time interval changed when the concentration of input DNA decreased. (Fig.8)</span> <br> <p> Note that outputs DNA didn’t decrease if input DNA did </p> </div>


In these simulations, the system can be controlled from perspective of order and time intervals and we concluded followings.<br> ・Our system gives outputs as coded in the input DNA in order. <br> ・Our system gives outputs with time intervals and the interval can be arranged by changing concentrations of the components of the system.<br>


<h3>Method</h3> <p> Our system is described by differential equations obtained from chemical reaction formulas. We solved them by using numerical software (Scilab). </p>

<h3>Condition</h3> <p> Condition of simulating is as follows.<br><br>

Input DNA concentration: 10nM<br> Template1 concentration: 10nM<br> Template2 concentration: 10nM<br> Liposome1 concentration: 10nM<br> Liposome2 concentration: 10nM<br> Gate1 concentration: 10nM<br> Gate2 concentration: 10nM<br> Simulation time: 100[sec]<br> </p>

<p> Values of chemical parameters are as follows.<br><br>

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

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

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