Biomod/2012/TeamSendaiA/Simulation

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<h2>Simulation</h2>

<!--目次 --> <div id="mokuji"> <h2>Contents</h2> <ol> <li><a href="#Calculation">Calculation</a></li> <li><a href="#Model&Fomula">Model&Fomula</a></li> <li><a href="#Electric Potential">Electric Potential</a></li>

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<a name="Calculation"></a><h2>Calculation</h2> <p>

A phosphodiester bond make up the backbone of each helical strand of DNA. <br> The phosphate groups in the phosphodiester bond are negatively-charged.<br> Because gate is produced by DNA, we can not ignore the influence of the Coulomb force.<br> So we calculate the electric potential near the gate.

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<a name="Model&Fomula"></a><h2>Model&Fomula</h2> <p> <br> Sets the coordinates as follows.<br>

<img src="http://openwetware.org/images/9/90/Cy.png" width="350px" height="300px"> <img src="http://openwetware.org/images/6/66/Lin.jpg" width="420px" height="300px"><br> <br><br><br> And we use follow fomula to calculate electric potential.<br><br> Debye–Hückel equation<br> <img src="http://openwetware.org/images/e/ec/Potential_fomula.png" width="300px" height="90px"><br> <br> Debye length<br> <img src="http://openwetware.org/images/9/9f/Debye.png" width="330px" height="100px"><br>


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<a name="Electric Potential"></a><h2>Electric Potential</h2> <p> <br> Electric potential changing z-axis at x-axis and y-axis is 0.<br>

<img src="http://openwetware.org/images/0/09/1014x0y0potential.png" width="620px" height="450px"><br> the length of the gate is 88bp, 30nm.


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