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<div id="globalnav">
<div id="globalnav" class="simu">
<ul>
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<li><a href="/wiki/Biomod/2014/Sendai/temp/0821">Home</a></li>
<li id="gn-home"><a href="/wiki/Biomod/2014/Sendai/temp/0821">Home</a></li>
<li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Introduction">Introduction</a></li>
<li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Introduction">Introduction</a></li>
<li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Design">Design</a></li>
<li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Design">Design</a></li>
<li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li>
<li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li>
<li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li>
<li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li>
<li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li>
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<div id="main">
<div id="main">
<h1>Simulation</h1>
<h1>Simulation</h1>
<section>
<h2>1-a.Enzyme system</h2>
<p>Simulation (wiki)
<h3>Results</h3>
酵素使用システム
1.目的
システムが時間間隔を開けて順番に出力を出すことを確認するために，シミュレーションにより出力DNAの濃度の変化をもとめる．


2. 方法
<p>
システムを形成する反応式から濃度の支配方程式（微分方程式）を立て，Scilabを用いて方程式を解く．
Our system gave outputs with time intervals in order.<br><br>
3.条件
</p>
シミュレーションを反応はprotocolに示す。
 
入力DNA濃度10nM
<div class="blockleft">
テンプレート1: 10nM
<figure>
テンプレート2: 10nM
<img src="http://openwetware.org/images/4/44/0823tetsuya-01.png">
リポソーム1: 10nM
<figcaption>Fig.1#</figcaption>
リポソーム2: 10nM
</figure>
ゲート1: 10nM
</div>
ゲート2: 10nM
<div class="blockright">
シミュレーション時間:100[sec]
<span>Our system gave, first, A-outputs, second, B-output with about 10sec interval when we code A-B in the input DNA.</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>Our system gave first, B-outputs second, A-output with about 10sec interval when we code B-A in the input DNA.</span>
</div>
 
<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>Our system gave no outputs when the system accepted no inputs. We need the inputs DNA to start the system.</span>
</div>


反応速度定数の値は次のものを使用した
<p>Our system can change the time intervals by changing concentration’s of components (input, templates). </p>
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


ゲートとkeyDNAの反応のみトーホールドが短いため、反応速度定数を1.0×10^6とした。
<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>


4.結果
<div class="blockleft">
図3.1に酵素使用ゲートのシミュレーション結果を示す。
<figure>
赤：出力リポソーム1
<img src="http://openwetware.org/images/c/cf/0827simulation09-01.png">
青：出力リポソーム2
<figcaption>Fig.7#</figcaption>
緑：テンプレート1
</figure>
水：テンプレート2
</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>
 
<br>
<h3>Method</h3>
<p>
Our system behaved properly in scilico, that is , following can be said.<br><br>
 
・Our system gives outputs as coded in the input DNA. <br>
・Our system gives outputs with time intervals and the interval can be tuned by changing concentrations of the components of the system.<br>
</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>
<img src="http://openwetware.org/images/4/44/0823tetsuya-01.png">


<p>結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく結果についてあれこれかく</p>
<p>
<img src="http://openwetware.org/images/1/1b/写真_2014-08-22_16_11_48.jpg">
Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short.
<p>詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード詳しいソースコード</p>
</p>
</section>


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<body> <div id="globalnav" class="simu"> <ul> <li id="gn-home"><a href="/wiki/Biomod/2014/Sendai/temp/0821">Home</a></li> <li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Introduction">Introduction</a></li> <li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Design">Design</a></li> <li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li> <li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li> <!--<li id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li>--> <li id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Discussion">Discussion</a></li> <li id="gn-team"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Team">Team</a></li> <li id="gn-end"><a href="#"></a></li> </ul> </div> <div id="main"> <h1>Simulation</h1> <h2>1-a.Enzyme system</h2> <h3>Results</h3>

<p> Our system gave outputs with time intervals in order.<br><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>Our system gave, first, A-outputs, second, B-output with about 10sec interval when we code A-B in the input DNA.</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>Our system gave first, B-outputs second, A-output with about 10sec interval when we code B-A in the input DNA.</span> </div>

<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>Our system gave no outputs when the system accepted no inputs. We need the inputs DNA to start the system.</span> </div>

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

<br> <h3>Method</h3> <p> Our system behaved properly in scilico, that is , following can be said.<br><br>

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