Biomod/2012/UTokyo/UT-Komaba/Simulation: Difference between revisions

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[[image:Bistable simulation.jpg|400px]]　
[[image:Bistable simulation.jpg|400px]]　


[image:Biomod-2012-UTokyo-UTKomaba-math8.png|300px]]
[[image:Biomod-2012-UTokyo-UTKomaba-math8.png|300px]]


All the reactions are here.
All the reactions are here.

Revision as of 23:57, 29 August 2012

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<div id="title"><img src="http://openwetware.org/images/4/47/Biomod_2012_UTokyo_UT-Komaba_Top.png" alt="DNA tablet" width="800" height="120" onClick="this.src='http://openwetware.org/images/7/7d/BIOMOD_2012_UTokyo_UT-Komaba_title-animation.gif'"/></div>

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 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba">Home</a></li>
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 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Simulation">Simulation</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment">Experiment</a></li>
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Bistable system

Using the bistable system, you can realize two different states, state"A" and state"B".

State"A"has many staple strands of type A and few of type B.

In contrast, "B"has few staple strands of type A and many of type B.

Please note that we'll represent state"X" as "X", and staple strands of type X as X.


So, how do concentrations of A and B change?

In this section, we will show you the results of the simulations.

Bistable simulation without "switch"

　

All the reactions are here.

But as you'll see later, these are simplified.

If you have no idea about these reactions, please refer to"Idea" section.

For example, first reaction formula shows A is doubled by template [math]\displaystyle{ T_{A} }[/math]

You should care that, A, B, iA, and iB naturally decreases because exonuclease gradually decomposes these staple strands.

To set up equations, let's close up some reactions.

First of all, let's consider the reactions among A, iA and [math]\displaystyle{ T_{A} }[/math]

[math]\displaystyle{ T_{A} }[/math]has three states.

We considered A increases in proportion to [math]\displaystyle{ T_{A}/n }[/math]

By these equations, you can get this conclusion.

Bistable simulation with "switch"

DNA tablet

5×5 origami simulation

{{#widget:YouTube|id=BLX8pDfZ2Ek}}


15×15 origami simulation

{{#widget:YouTube|id=5PmS2_7T44A}}
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