Biomod/2012/TeamSendai/Simulation: Difference between revisions

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<h2>Contents</h2>
<h2>Contents</h2>
<ol>
<ol>
<li><a href="#Calculation">Calculation</a></li>
<li><a href="#Numerical Calculation for Electric Potential">Electric Potential Numerical Calculation</a></li>
<li><a href="#Model&Fomula">Model&Fomula</a></li>
<ol>
<li><a href="#Electric Potential">Electric Potential</a></li>
<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>
</ol>
Line 340: Line 356:


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


Line 350: Line 366:
</p>
</p>


<a name="Model&Fomula"></a><h2>Model&Fomula</h2>
<a name="Model"></a><h2>Model</h2>
<p>
<p>
<br>
<br>
Line 369: Line 385:
</p>
</p>


<a name="Electric Potential"></a><h2>Electric Potential</h2>
<a name="Results"></a><h2>Results</h2>
<p>
<p>
<br>
<br>
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</p>
</p>


<a name="MD Simulation"></a><h2>MD Simulation</h2>
<p>
We carried out molecular dynamics simulation to examine the the mechanism and
the effectiveness of our structure “Cell Gate”.
</p>
<a name="DNA Model"></a><h2>DNA Model</h2>
<p>
For simplicity, course-grained DNA model is used in our simulation. One DNA
nucleotide is represented by one bead in the model and each bead can be
hybridized with complementary bead.
　　＜＜モデル載せる＞＞
The potential energy of the system includes 5 distinct contributions.
　　＜＜ポテンシャル載せる＞＞
The first three terms are intramolecular interactions , bonds , bond angles, and
dihedral angles. In order to express “tether like structure”, only bond interactions
are active in our DNA model.
And the latter two are non-bonded interactions. Coulomb interactions are taken into
account using the Debye-Huckel approximation which enables to internalize
counterions contribution.
Constants of these potentials are achieved from references.
The force on bead i is given by a Langevin equation
Langevin equation
http://openwetware.org/images/1/11/Langevin.pngより
」
http://openwetware.org/images/2/23/F%3D.pngより
The first term donates a conservative force derived from the potential U and the
second is a viscosity dependent friction.
The third term is a white Gaussian noise and effects of solvent molecules are
internalized in this term.
Langevin equation is integrated using a Velocity-Verlet method.
Toehold displacement of dsDNA
In order to test predictive capability of the model, here we carried out a simulation
of Toehold displacement between two strands.
Length of strands and simulation situation was as follows.
Target strand/Toehold A/Toehold B : 25nt / 9nt (+10nt spacer) / 13nt (+10nt
spacer)
Temperature : 300K
Time-step size / simulation length : 0.01ps / 100ns
Ion concentration : 50mM Na+
results
＜＜後ほど＞＞
</p>
<a name="Comparison of capture ability"></a><h2>Comparison of capture ability</h2>
<p>
One of constructional features of our structure ”Cell-Gate” is the use of new strand
displacement method.
By comparing our selector strand and a toehold strand, the most popular method for
strand displacement, we show the effectiveness our structure in terms of capture
ability.
Model and Method
According to the design of experiment section, we designed models as below of the
selector strand and the toehold strand.
＜＜モデル載せる＞＞
Hex-cylinder is represented as the assembly of electrically-charged mass points
fixed on the field.
＜＜モデル載せる＞＞
Simulation was carried out at the following condition.
Temperature : 300K
Ion concentration : Na+ 50mM
Box size : 20nm×20nm×20nm (periodic boundary condition)
Time-step size / simulation length : 0.01ps / 10ns
Results
＜＜後ほど＞＞
</p>
<a name="Reference"></a><h2>Reference</h2>
<p>
1. Thomas A. Knotts et al. A coarse grain model of DNA , J.Chem.Phys
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>


</div>
</div>

Revision as of 21:37, 20 October 2012

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<ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai">Top</a></li> <li> <a href="#">Project</a> <ul> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea">Idea</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> </ul> </li> <li> <a href="#">Experiment</a> <ul> <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><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Method">Method</a> </li> </ul> </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> </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> <br><br> 


</p>

<a name="Numerical Calculation"></a><h2>Numerical 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.

</p>

<a name="Model"></a><h2>Model</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>


</p>

<a name="Results"></a><h2>Results</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. </p>


<a name="MD Simulation"></a><h2>MD Simulation</h2> <p> We carried out molecular dynamics simulation to examine the the mechanism and the effectiveness of our structure “Cell Gate”.

</p>

<a name="DNA Model"></a><h2>DNA Model</h2> <p> For simplicity, course-grained DNA model is used in our simulation. One DNA nucleotide is represented by one bead in the model and each bead can be hybridized with complementary bead. 　　＜＜モデル載せる＞＞ The potential energy of the system includes 5 distinct contributions. 　　＜＜ポテンシャル載せる＞＞ The first three terms are intramolecular interactions , bonds , bond angles, and dihedral angles. In order to express “tether like structure”, only bond interactions are active in our DNA model. And the latter two are non-bonded interactions. Coulomb interactions are taken into account using the Debye-Huckel approximation which enables to internalize counterions contribution. Constants of these potentials are achieved from references. The force on bead i is given by a Langevin equation

Langevin equation

http://openwetware.org/images/1/11/Langevin.pngより 

」

http://openwetware.org/images/2/23/F%3D.pngより

The first term donates a conservative force derived from the potential U and the second is a viscosity dependent friction. The third term is a white Gaussian noise and effects of solvent molecules are internalized in this term. Langevin equation is integrated using a Velocity-Verlet method. Toehold displacement of dsDNA In order to test predictive capability of the model, here we carried out a simulation of Toehold displacement between two strands. Length of strands and simulation situation was as follows. Target strand/Toehold A/Toehold B : 25nt / 9nt (+10nt spacer) / 13nt (+10nt spacer) Temperature : 300K Time-step size / simulation length : 0.01ps / 100ns Ion concentration : 50mM Na+ results ＜＜後ほど＞＞

</p>

<a name="Comparison of capture ability"></a><h2>Comparison of capture ability</h2> <p> One of constructional features of our structure ”Cell-Gate” is the use of new strand displacement method. By comparing our selector strand and a toehold strand, the most popular method for strand displacement, we show the effectiveness our structure in terms of capture ability. Model and Method According to the design of experiment section, we designed models as below of the selector strand and the toehold strand. ＜＜モデル載せる＞＞ Hex-cylinder is represented as the assembly of electrically-charged mass points fixed on the field. ＜＜モデル載せる＞＞ Simulation was carried out at the following condition. Temperature : 300K Ion concentration : Na+ 50mM Box size : 20nm×20nm×20nm (periodic boundary condition) Time-step size / simulation length : 0.01ps / 10ns Results ＜＜後ほど＞＞

</p>

<a name="Reference"></a><h2>Reference</h2> <p> 1. Thomas A. Knotts et al. A coarse grain model of DNA , J.Chem.Phys 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>

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