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<h1>Simulation</h1>
<h1>Simulation</h1>
<section>
<h2>1-a.Enzyme system</h2>
<p>Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.</p>
<h3>Results</h3>
<img src="#.png" width="900" height="600">
 
<p>Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.Quick brown fox jumped over the lazy dog.</p>
<p>
<img src="http://openwetware.org/images/e/e0/Graph_dummy-01.png">
Our system gave outputs with time intervals in order.<br><br>
</section>
</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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Latest revision as of 08:30, 27 August 2014

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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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