Difference between revisions of "Biomod/2012/TeamSendai/Simulation"

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<div id="Container">
 
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<!-- Menu -->
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<h1>Project</h1>
<ul id="menu">
 
<li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Top</a></li>
 
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li>
 
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a>
 
</li>
 
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a>
 
<ul>
 
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Method">Method</a>
 
<ul>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li>
 
<li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a>
 
</li>
 
</ul>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result">Result</a>
 
<ul>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li>
 
<li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a>
 
</li>
 
</ul>
 
</li>
 
</ul>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Achievement">Achievement</a>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a>
 
</li>
 
<li>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/FAQ">FAQ</a>
 
</li>
 
</ul>
 
 
 
<!--目次 -->
 
<div id="mokuji">
 
<h2>Contents</h2>
 
<ol>
 
<li><a href="#Numerical Calculation for Electric Potential">Electric Potential Numerical Calculation</a></li>
 
<ol>
 
<li><a href="#Model">Model</a></li>
 
<li><a href="#">Results</a></li>
 
</ol>
 
 
 
<li><a href="#MD Simulation">MD Simulation</a></li>
 
<ol>
 
<li><a href="#DNA Model">DNA Model</a></li>
 
<ol>
 
<li><a href="#Results">Results</a></li>
 
</ol>
 
 
 
<li><a href="#Comparison of capture ability">Comparison of capture ability</a></li>
 
<ol>
 
<li><a href="#Results">Results</a></li>
 
</ol>
 
<li><a href="#Reference">Reference</a></li>
 
</ol>
 
 
 
</ol>
 
</div>
 
 
 
 
<p>
 
<p>
<br><br>
+
Our project is to create a new designable channel with a high selectivity and activity. We named the channel; Cell Gate. (Cell Gateが出てくるのが唐突だと思う) We make the Cell Gate of DNA.
 
+
</p>
  
 
+
<h1>Why do we use DNA?</h1>
</p>
 
<a name="Numerical Calculation"></a><h2>Numerical Calculation</h2>
 
 
<p>
 
<p>
 
+
・自然界にあるチャネルは(タンパク質でできていて?)人間の手で作り変えたりして自在に扱うということは難しい。だから、デザインが可能でsiRNAなどの生体分子と相互作用を持つDNAを使って、チャネルを作ることができれば、チャネル設計(?)の幅が広がるというようなことをまとめていただけると…。(タンパク質とDNAの対比表とか対比図があるとわかりやすい)
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.
 
 
 
 
</p>
 
</p>
  
<a name="Model"></a><h2>Model</h2>
+
<h1>How do we penetrate the Gate to membrane?</h1>
 +
<img src=" http://openwetware.org/images/e/e6/Format_gate_no_tukikata_project.jpg " alt="coreste&tutu " align="left" width="450px" height="290px" >
 
<p>
 
<p>
<br>
+
Lipidと親和性のあるコレステロールを使えばいいということを面白おかしく論理的に説明.
Sets the coordinates as follows.<br>
+
どのように貫通するかなど。</br>
 
+
(画像はプレゼン用のを拝借したので修正必要。特にHexagonalとかsmall tube とか。絵自体もまだまだ分かりやすくできそうな気が。数式みたいな絵じゃなく、もっと動きのあるものに(アニメーションにしろというわけではない))
<img src="http://openwetware.org/images/9/90/Cy.png" width="350px" height="300px">
+
<br clear="left">
<img src="http://openwetware.org/images/6/66/Lin.jpg" width="420px" height="300px"><br>
 
<br><br><br>
 
 
 
Point-charge model is used.<br>
 
Assumesd the phosphate groups negative charge,and<br>
 
negative charge circles the axis of the double helix once every 10.4 base pairs like DNA.<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/f/f9/Debyelen.png" width="400px" height="250px"><br><br>
 
 
 
 
 
 
 
 
 
Add all potential by negative charge DNA which compose gate have.<br>
 
(used C language to output the numbers)<br><br>
 
<img src="http://openwetware.org/images/4/45/Helix.gif" width="500px" height="290px"><br>
 
 
 
 
 
 
 
Condition<br>
 
Temperature 298[K]<br>
 
Na+ 50mM<br>
 
 
 
<img src="http://openwetware.org/images/f/fc/Add2.png" width="500px" height="180px"><br>
 
 
 
 
 
 
 
 
</p>
 
</p>
  
<a name="Results"></a><h2>Results</h2>
+
<h1>穴開けただけでチャネル(細胞膜間輸送?)って呼べるの?</h1>
 
<p>
 
<p>
<br>
+
クーロン力があるから物質だだ漏れにはならない。Gateの内部にDNAの一本鎖並べて、DNAの特異性を利用することで、狙いの分子だけを、一本鎖DNAとの結合エネルギーポテンシャルの坂道に乗せることができる。その一本鎖DNAの列をPoaterと呼ぶことにする。PorterがCellGateのエンジン。みたいなことをうまくまとめる。ここでPorterの説明を終えるつもりで。画像に関してはとりあえず津沢のポテンシャルエネルギーのグラフは必須。
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.
 
 
 
Target base pair 25 を点電荷と仮定する
 
 
</p>
 
</p>
  
 
+
<h1>クーロン力があるならGateに近づけないんじゃない?</h1>
<a name="MD Simulation"></a><h2>MD Simulation</h2>
 
 
<p>
 
<p>
We carried out molecular dynamics simulation to examine the the mechanism and
+
Porterの一番目を伸ばせばいいみたいなことをキャッチ―な図とともに。筒井さんのシミュレーション映像を貼る。
the effectiveness of our structure “Cell Gate”.
 
 
 
 
</p>
 
</p>
  
<a name="DNA Model"></a><h2>DNA Model</h2>
+
<h1>私たちが実験で目指したもの</h1>
 +
<img src=" http://openwetware.org/images/c/c8/Format_cell_gate.jpg " alt="hybrid graph" align="left" width="465px" height="315px" >
 
<p>
 
<p>
For simplicity, course-grained DNA model is used in our simulation. <br>
+
ここで初めてMembrane登場? 細胞のモデルとして使っただけ?本物の細胞どうして使わなかったのかという疑問が生まれそう。何かいい理由はないものか。画像はプレゼン用のやつそのままなので改善の余地あり
One DNA nucleotide is represented by one bead in the model and each bead can be<br>
 
hybridized with complementary bead.<br>
 
  <<モデル載せる>><br><br>
 
The potential energy of the system includes 5 distinct contributions.<br>
 
  <<ポテンシャル載せる>><br><br><br>
 
The first three terms are intramolecular interactions , bonds , bond angles, and<br>
 
dihedral angles. In order to express “tether like structure”, only bond interactions<br>
 
are active in our DNA model.<br>
 
And the latter two are non-bonded interactions. Coulomb interactions are taken into<br>
 
account using the Debye-Huckel approximation which enables to internalize<br>
 
counterions contribution.<br>
 
Constants of these potentials are achieved from references.<br>
 
The force on bead i is given by a Langevin equation<br><br><br>
 
 
 
Langevin equation<br><br>
 
 
<img src="http://openwetware.org/images/1/11/Langevin.png" width="220px" height="80px"><br><br>
 
<img src="http://openwetware.org/images/2/23/F%3D.png" width="150px" height="80px"><br>
 
 
 
The first term donates a conservative force derived from the potential U and the<br>
 
second is a viscosity dependent friction.<br>
 
The third term is a white Gaussian noise and effects of solvent molecules are<br>
 
internalized in this term.<br>
 
Langevin equation is integrated using a Velocity-Verlet method.<br><br><br>
 
Toehold displacement of dsDNA<br>
 
In order to test predictive capability of the model, here we carried out a simulation<br>
 
of Toehold displacement between two strands.<br>
 
Length of strands and simulation situation was as follows.<br><br>
 
Target strand/Toehold A/Toehold B : 25nt / 9nt (+10nt spacer) / 13nt (+10nt
 
spacer)<br>
 
Temperature : 300K<br>
 
Time-step size / simulation length : 0.01ps / 100ns<br>
 
Ion concentration : 50mM Na+<br><br>
 
results<br>
 
<<後ほど>>
 
 
 
 
</p>
 
</p>
  
<a name="Comparison of capture ability"></a><h2>Comparison of capture ability</h2>
+
<br clear="left">
<p>
 
One of constructional features of our structure ”Cell-Gate” is the use of new strand
 
displacement method.<br>
 
By comparing our selector strand and a toehold strand, the most popular method for<br>
 
strand displacement, we show the effectiveness our structure in terms of capture
 
ability.<br><br><br>
 
Model and Method<br>
 
According to the design of experiment section, we designed models as below of the<br>
 
selector strand and the toehold strand.<br>
 
<<モデル載せる>><br><br><br>
 
Hex-cylinder is represented as the assembly of electrically-charged mass points<br>
 
fixed on the field.<br>
 
<<モデル載せる>><br><br><br>
 
Simulation was carried out at the following condition.<br>
 
Temperature : 300K<br>
 
Ion concentration : Na+ 50mM<br>
 
Box size : 20nm×20nm×20nm (periodic boundary condition)<br>
 
Time-step size / simulation length : 0.01ps / 10ns<br>
 
Results<br>
 
<<後ほど>><br>
 
 
 
 
</p>
 
</p>
  
<a name="Reference"></a><h2>Reference</h2>
+
<h1>Application in future</h1>
 
<p>
 
<p>
1. Thomas A. Knotts et al. A coarse grain model of DNA , J.Chem.Phys
+
あんなことやこんなことに使えるというのを図入りで。
126,084901(2007)<br>
 
2. Carsten Svaneborg et al. DNA Self-Assembly and Computation Studied with a
 
Coarse-Grained Dynamic Bonded Model, DNA 18,LNCS 7433, pp.123-134,
 
2012<br>
 
3. Xhuysn Guo & D.Thirumalai, Kinetics of Protein Folding: Nucleation
 
Mechanism, Time Scales, and Pathways, Biopolymars, Vol.36, 83-102 (1995)<br>
 
4. GROMACS manual ()<br>
 
5. Cafemol manual ( http://www.cafemol.org/ )<br>
 
 
 
 
</p>
 
</p>
 
 
</div>
 
</div>
  
 
</body>
 
</body>
 
</html>
 
</html>

Revision as of 07:20, 24 October 2012

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<body> <div id="Container"> <!-- Menu --> <ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Home</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a> </li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Future Application">Future Application</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/Tohoku/Team Sendai/header"></a> </li>

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<body> <div id="Container">

<h1>Project</h1> <p> Our project is to create a new designable channel with a high selectivity and activity. We named the channel; Cell Gate. (Cell Gateが出てくるのが唐突だと思う) We make the Cell Gate of DNA. </p>

<h1>Why do we use DNA?</h1> <p> ・自然界にあるチャネルは(タンパク質でできていて?)人間の手で作り変えたりして自在に扱うということは難しい。だから、デザインが可能でsiRNAなどの生体分子と相互作用を持つDNAを使って、チャネルを作ることができれば、チャネル設計(?)の幅が広がるというようなことをまとめていただけると…。(タンパク質とDNAの対比表とか対比図があるとわかりやすい) </p>

<h1>How do we penetrate the Gate to membrane?</h1> <img src=" http://openwetware.org/images/e/e6/Format_gate_no_tukikata_project.jpg " alt="coreste&tutu " align="left" width="450px" height="290px" > <p> Lipidと親和性のあるコレステロールを使えばいいということを面白おかしく論理的に説明. どのように貫通するかなど。</br> (画像はプレゼン用のを拝借したので修正必要。特にHexagonalとかsmall tube とか。絵自体もまだまだ分かりやすくできそうな気が。数式みたいな絵じゃなく、もっと動きのあるものに(アニメーションにしろというわけではない)) <br clear="left"> </p>

<h1>穴開けただけでチャネル(細胞膜間輸送?)って呼べるの?</h1> <p> クーロン力があるから物質だだ漏れにはならない。Gateの内部にDNAの一本鎖並べて、DNAの特異性を利用することで、狙いの分子だけを、一本鎖DNAとの結合エネルギーポテンシャルの坂道に乗せることができる。その一本鎖DNAの列をPoaterと呼ぶことにする。PorterがCellGateのエンジン。みたいなことをうまくまとめる。ここでPorterの説明を終えるつもりで。画像に関してはとりあえず津沢のポテンシャルエネルギーのグラフは必須。 </p>

<h1>クーロン力があるならGateに近づけないんじゃない?</h1> <p> Porterの一番目を伸ばせばいいみたいなことをキャッチ―な図とともに。筒井さんのシミュレーション映像を貼る。 </p>

<h1>私たちが実験で目指したもの</h1> <img src=" http://openwetware.org/images/c/c8/Format_cell_gate.jpg " alt="hybrid graph" align="left" width="465px" height="315px" > <p> ここで初めてMembrane登場? 細胞のモデルとして使っただけ?本物の細胞どうして使わなかったのかという疑問が生まれそう。何かいい理由はないものか。画像はプレゼン用のやつそのままなので改善の余地あり </p>

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<h1>Application in future</h1> <p> あんなことやこんなことに使えるというのを図入りで。 </p> </div>

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