Biomod/2014/Sendai/Discussion: Difference between revisions

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scalability. To achieve our goals, we created two types of system, Enzyme system and  
scalability. To achieve our goals, we created two types of system, Enzyme system and  
Enzyme-free system. In both of these systems, programmability and scalability are  
Enzyme-free system. In both of these systems, programmability and scalability are  
confirmed through simulations. Results of the simulation are shown below.
confirmed through simulations. Results of the simulation are shown below.<br />
<p>
Both Enzyme and Enzyme-free systems have a common limitation, which is that the same  
Both Enzyme and Enzyme-free systems have a common limitation, which is that the same  
output cannot be released again. In concrete terms, input coded A-B-A is not accepted  
output cannot be released again. In concrete terms, input coded A-B-A is not accepted  
while input coded A-B-C is accepted.
while input coded A-B-C is accepted.</p><br />
The reaction rate constant is planned to be optimized by feed-backing the result of  
The reaction rate constant is planned to be optimized by feed-backing the result of  
chemical reaction.
chemical reaction.
(1) Enzyme system
<br /><br /><b>(1) Enzyme system</b><br />
First we verified the programmability of Enzyme system. When information of input  
<p>First we verified the programmability of Enzyme system. When information of input  
was a-b, output A-B was released in order. The same thing applies to input coded b-
was a-b, output A-B was released in order. The same thing applies to input coded b-
a. We can conclude that Enzyme system has programmability. By adjusting initial  
a. We can conclude that Enzyme system has programmability. By adjusting initial  
concentration, the time interval of the output was changed.
concentration, the time interval of the output was changed.</p>
However, we found it difficult to adjust the time interval of the output arbitrarily. We  
<p>However, we found it difficult to adjust the time interval of the output arbitrarily. We  
are searching for solution for this problem.
are searching for solution for this problem.<br />
The simulation in which information of input was a-b-c to show the scalability is  
The simulation in which information of input was a-b-c to show the scalability is  
now proceeding by extending ordinary differential equations.
now proceeding by extending ordinary differential equations.</p><br />
(2) Enzyme-free system
<b>(2) Enzyme-free system</b><br />
In the same manner as Enzyme system, we carried out the simulation of Enzyme-
<p>In the same manner as Enzyme system, we carried out the simulation of Enzyme-
free system. When information of input was a-b, output A-B was released in order.  
free system. When information of input was a-b, output A-B was released in order.  
The same result of the simulation was obtained when information of input was b-a as  
The same result of the simulation was obtained when information of input was b-a as  
well. Subsequently, we simulated the scalability. When information of the input was a-
well. Subsequently, we simulated the scalability. When information of the input was a-
b-c, output A-B-C was released. We can conclude that Enzyme-free system has both  
b-c, output A-B-C was released. We can conclude that Enzyme-free system has both  
programmability and scalability.
programmability and scalability.<br />
We found that a slight difference in the concentrations of components has a  
We found that a slight difference in the concentrations of components has a  
great effect on the intervals of output releasing, which makes it difficult to tune the  
great effect on the intervals of output releasing, which makes it difficult to tune the  
whole reactions in detail.
whole reactions in detail.</p>
<p>
We have to make experiments to confirm that the two systems have  
We have to make experiments to confirm that the two systems have  
programmability, and Enzyme-free system has scalability. We have already finished  
programmability, and Enzyme-free system has scalability. We have already finished  
designing the sequence of DNA. We have prepared all the materials and are about  
designing the sequence of DNA. We have prepared all the materials and are about  
to go on experiments to prove these features.
to go on experiments to prove these features.
</p>
</p>
</p>
</section>
</section>

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<div id="homebutton"> <li id="stamp"><a href="http://openwetware.org/wiki/Biomod/2014/Sendai">Home</a></li> </div>


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<div id="main"> <h1>Conclusion&Discussion</h1> <section> <p> In our project, we proposed a system that releases molecules following the information written on DNA. The features of this system are programmability and scalability. To achieve our goals, we created two types of system, Enzyme system and Enzyme-free system. In both of these systems, programmability and scalability are confirmed through simulations. Results of the simulation are shown below.<br /> <p> Both Enzyme and Enzyme-free systems have a common limitation, which is that the same output cannot be released again. In concrete terms, input coded A-B-A is not accepted while input coded A-B-C is accepted.</p><br /> The reaction rate constant is planned to be optimized by feed-backing the result of chemical reaction. <br /><br /><b>(1) Enzyme system</b><br /> <p>First we verified the programmability of Enzyme system. When information of input was a-b, output A-B was released in order. The same thing applies to input coded b- a. We can conclude that Enzyme system has programmability. By adjusting initial concentration, the time interval of the output was changed.</p> <p>However, we found it difficult to adjust the time interval of the output arbitrarily. We are searching for solution for this problem.<br /> The simulation in which information of input was a-b-c to show the scalability is now proceeding by extending ordinary differential equations.</p><br /> <b>(2) Enzyme-free system</b><br /> <p>In the same manner as Enzyme system, we carried out the simulation of Enzyme- free system. When information of input was a-b, output A-B was released in order. The same result of the simulation was obtained when information of input was b-a as well. Subsequently, we simulated the scalability. When information of the input was a- b-c, output A-B-C was released. We can conclude that Enzyme-free system has both programmability and scalability.<br /> We found that a slight difference in the concentrations of components has a great effect on the intervals of output releasing, which makes it difficult to tune the whole reactions in detail.</p> <p> We have to make experiments to confirm that the two systems have programmability, and Enzyme-free system has scalability. We have already finished designing the sequence of DNA. We have prepared all the materials and are about to go on experiments to prove these features. </p> </p> </section> </div> <div style="background-color:#5b2d01; margin-top:30px; padding-top:15px; width:100% ;height:100px; color:#fff; font-size: 125%; position: absolute; bottom: 0; display: inline;"> 

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(C)Copyright Biomod 2014 Team Sendai<br /> E-MAIL:<a href="mailto:teamsendai2014@gmail.com"><span style="color:white">teamsendai2014@gmail.com</span></a> 

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