Biomod/2012/TeamSendai/Simulation - Revision history

Kazuki Hirahara at 03:06, 28 October 2012

Kazuki Hirahara — Sun, 28 Oct 2012 03:06:27 GMT

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	{{:Biomod/2012/Tohoku/Team_Sendai/header}}		{{:Biomod/2012/Tohoku/Team_Sendai/header}}

Daisuke Kandatsu at 03:02, 28 October 2012

Daisuke Kandatsu — Sun, 28 Oct 2012 03:02:26 GMT

←Older revision		Revision as of 03:02, 28 October 2012
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	In order to test the model, here we carried out a simulation of Toehold displacement between two strands.		In order to test the model, here we carried out a simulation of Toehold displacement between two strands.

-	Toehold strands are modeled according to designs in [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Comparison_of_Porter_and_Toehold the experiment section].	+	Toehold strands are modeled according to designs of [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Comparison_of_Porter_and_Toehold the experiment section].

Daisuke Kandatsu at 03:01, 28 October 2012

Daisuke Kandatsu — Sun, 28 Oct 2012 03:01:02 GMT

←Older revision		Revision as of 03:01, 28 October 2012
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	In order to test the model, here we carried out a simulation of Toehold displacement between two strands.		In order to test the model, here we carried out a simulation of Toehold displacement between two strands.

		+	Toehold strands are modeled according to designs in [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Comparison_of_Porter_and_Toehold the experiment section].


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	<h3> Model and Method</h3>		<h3> Model and Method</h3>
-	According to the design of the experiment section, we modeled the porter strand and the toehold strand as shown below. <br><br>	+	According to the design of [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Comparison_of_Porter_and_Toehold the experiment section], we modeled the porter strand and the toehold strand as shown below. <br><br>
	[[Image: Format_selector.jpg \|left\|680px]]		[[Image: Format_selector.jpg \|left\|680px]]
	{{-}}		{{-}}

Daisuke Kandatsu at 02:50, 28 October 2012

Daisuke Kandatsu — Sun, 28 Oct 2012 02:50:01 GMT

Kazuki Hirahara at 02:14, 28 October 2012

Kazuki Hirahara — Sun, 28 Oct 2012 02:14:56 GMT

←Older revision		Revision as of 02:14, 28 October 2012
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	{{-}}		{{-}}
-	[[Image: Gibbs.png \|center\|800px\| Gibbs energies by the Porters in the GATE ]]	+	[[Image: Gibbs kai.png \|center\|800px\| Gibbs energies by the Porters in the GATE ]]
	{{-}}		{{-}}
	{{-}}		{{-}}

Kazuki Hirahara at 01:26, 28 October 2012

Kazuki Hirahara — Sun, 28 Oct 2012 01:26:49 GMT

←Older revision		Revision as of 01:26, 28 October 2012
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	Molecular robots works in meso-scale (from nm to sub-micro meter). In the meso-scale, characters of each molecule and cooperative movement of molecules could not be ignored. Without calculation of potentials or molecular dynamics simulations, it is difficult to predict the behaviors of the molecules in this scale. Thus, we calculated potentials to confirm the GATE effect, and simulated molecular dynamics of DNAs to strength reliability of our design.		Molecular robots works in meso-scale (from nm to sub-micro meter). In the meso-scale, characters of each molecule and cooperative movement of molecules could not be ignored. Without calculation of potentials or molecular dynamics simulations, it is difficult to predict the behaviors of the molecules in this scale. Thus, we calculated potentials to confirm the GATE effect, and simulated molecular dynamics of DNAs to strength reliability of our design.

-	<h1>Potential ~~Calculation~~</h1>	+	<h1>Numerical Analysis of Electrostatic Potential</h1>
	Electric potential of the GATE was calculated inside and outside the GATE. {{-}}The phosphate groups in the backbone of DNA are negatively-charged. Because the GATE is made by DNA origami, the GATE has the Coulomb force.		Electric potential of the GATE was calculated inside and outside the GATE. {{-}}The phosphate groups in the backbone of DNA are negatively-charged. Because the GATE is made by DNA origami, the GATE has the Coulomb force.

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	{{-}}		{{-}}
	{{-}}		{{-}}
-	[[Image: Helix.gif \|left\|500px\|thumb~~\| Condition: Temperature 298[K], Na+ 50mM~~]]	+	[[Image: Helix.gif \|left\|500px\|thumb]]
	{{-}}		{{-}}

Kazuki Hirahara at 01:08, 28 October 2012

Kazuki Hirahara — Sun, 28 Oct 2012 01:08:05 GMT

←Older revision		Revision as of 01:08, 28 October 2012
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	The result of Gibbs energy of the fixed Porter were defined as the maximum length of each form of Porter. For examples, Porter 1 has three forms: Stretched form, 1 loop form, and 2 loop form. In this Porter 1 case, we defined Porter 1 has three Gibbs energy according to the hybridization state. Since the maximum lengths of each form were different, the minimum energy of possible length was selected.{{-}} Gibbs energies were calculated at the center of hole in the GATE.{{-}}		The result of Gibbs energy of the fixed Porter were defined as the maximum length of each form of Porter. For examples, Porter 1 has three forms: Stretched form, 1 loop form, and 2 loop form. In this Porter 1 case, we defined Porter 1 has three Gibbs energy according to the hybridization state. Since the maximum lengths of each form were different, the minimum energy of possible length was selected.{{-}} Gibbs energies were calculated at the center of hole in the GATE.{{-}}
	The following figure shows the calculated energy of Porters and Toehold DNA used as controls in our project.		The following figure shows the calculated energy of Porters and Toehold DNA used as controls in our project.
		+
		+	{{-}}
		+	[[Image: Porter1.png \|center\|500px\| Three different form ]]
		+	{{-}}

	{{-}}		{{-}}

Kazuki Hirahara at 18:58, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 18:58:05 GMT

←Older revision		Revision as of 18:58, 27 October 2012
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	<h1>MD Simulation</h1>		<h1>MD Simulation</h1>
	To further strengthen feasibility of our design, we examined the capturing mechanism and		To further strengthen feasibility of our design, we examined the capturing mechanism and
-	the effectiveness of our structure “CELL GATE" by molecular dynamics simulation.	+	the effectiveness of our structure “CELL GATE" by molecular dynamics (MD) simulation.


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	Results obtained from this simulation show that the selector strand can catch the target strand exists outside of the Hex-cylinder and hybridize completely while the toehold strand never hybridize to the target strand in simulation time.		Results obtained from this simulation show that the selector strand can catch the target strand exists outside of the Hex-cylinder and hybridize completely while the toehold strand never hybridize to the target strand in simulation time.

-	We run 5 simulations for each capturing mechanism under the same conditions and results were ~~almost the same as we first~~ obtained.	+	We run additional 5 simulations for each capturing mechanism under the same conditions (NOTE: random seeds were different) and very similar results were obtained. Thus, the simulation results are very feasible under our model.

Kazuki Hirahara at 18:55, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 18:55:36 GMT

←Older revision		Revision as of 18:55, 27 October 2012
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	<h1>MD Simulation</h1>		<h1>MD Simulation</h1>
-	~~We carried out molecular dynamics simulation to examine~~ the capturing mechanism and	+	To further strengthen feasibility of our design, we examined the capturing mechanism and
-	the effectiveness of our structure “CELL GATE".	+	the effectiveness of our structure “CELL GATE" by molecular dynamics simulation.


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	By considering results of electrostatic potential calculation around the hex-cylinder and MD simulation, it is clear that the electrostatic field prevents the entrance of DNA strands into the Hex-cylinder and the selector strand helps it to get into the cylinder.		By considering results of electrostatic potential calculation around the hex-cylinder and MD simulation, it is clear that the electrostatic field prevents the entrance of DNA strands into the Hex-cylinder and the selector strand helps it to get into the cylinder.

-	Therefore, we concluded that our novel selector strand provides a high capture ability to our system ~~“Cell~~-~~Gate”~~.	+	Therefore, we concluded that our novel selector strand provides a high capture ability to our system “CELL-GATE”.

Kazuki Hirahara at 18:51, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 18:51:28 GMT

←Older revision		Revision as of 18:51, 27 October 2012
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-	Following ~~figure~~ shows the scheme of a point-charge model and potential calculations.	+	Following GIF animation shows the scheme of a point-charge model and potential calculations.{{-}}
		+	(It takes about 7 seconds to watch one cycle of the GIF animation){{-}}
	{{-}}		{{-}}
	{{-}}		{{-}}
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	Electric potential was calculated by using C language.{{-}}		Electric potential was calculated by using C language.{{-}}
	Under our conditions, the target DNA has 25 electric beads.{{-}}		Under our conditions, the target DNA has 25 electric beads.{{-}}
		+	All calculation were performed under these condition: Temperature 298[K], Na+ 50mM.{{-}}

	<h3>Electric potential from the top of view of the GATE</h3>		<h3>Electric potential from the top of view of the GATE</h3>
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	{{-}}		{{-}}

-	The first three terms are intramolecular interactions, bonds, bond angles, and dihedral angles. In order to express the “tether like structure”, only bond interactions are considered in our DNA model.	+	The first three terms are intramolecular interactions, bonds, bond angles, and dihedral angles. These terms are important for maintaining structure. In order to express the “tether like structure”, only bond interactions are considered in our DNA model.

-	And the latter two terms are non-bonded interactions. Coulomb interactions are taken into account using the Debye-Huckel approximation which enables to internalize ~~counterions~~ contribution.	+	And the latter two terms are non-bonded interactions. Coulomb interactions are taken into account using the Debye-Huckel approximation which enables to internalize counter-ions contribution.

	Parameters of these potentials were fit to the reference literature ; Thomas A. Knotts ''et al''. A coarse grain model of DNA .		Parameters of these potentials were fit to the reference literature ; Thomas A. Knotts ''et al''. A coarse grain model of DNA .
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-	<h2> Toehold displacement of dsDNA</h2>	+	<h2> Verification of the Coarse-grained model: Toehold displacement of dsDNA</h2>
	[[Image: Format_toea_toeb.jpg \|right\|400px]]		[[Image: Format_toea_toeb.jpg \|right\|400px]]
	In order to test the model, here we carried out a simulation of Toehold displacement between two strands.		In order to test the model, here we carried out a simulation of Toehold displacement between two strands.
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-	Movie 1 shows the trajectory of each strand from the simulation. The target strand moves from Toehold A strand to Toehold B strand which are fixed on the field. This result agrees with the energy gradient.	+	Movie 1 shows the trajectory of each strand from the simulation. The target strand moves from Toehold A strand to Toehold B strand which are fixed on the field. This result agrees with the energy gradient. The result supported our coarse-grained DNA model is feasible.


	<h2> Comparison of capture ability</h2>		<h2> Comparison of capture ability</h2>
-	One of constructional features of our structure ~~”Cell~~-~~Gate” is~~ the use of a novel strand displacement method.	+	One of constructional features of our structure ”CELL-GATE”is the use of a novel strand displacement method.

	By comparing our selector strand to toehold strand, the most popular method for strand displacement, we looked at the effectiveness of our structure in terms of it's strand capturing ability.		By comparing our selector strand to toehold strand, the most popular method for strand displacement, we looked at the effectiveness of our structure in terms of it's strand capturing ability.

←Older revision		Revision as of 02:50, 28 October 2012
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	<h2> Comparison of capture ability</h2>		<h2> Comparison of capture ability</h2>
-	One of constructional features of our structure ”CELL-GATE”is the use of a novel strand displacement method.	+	One of constructional features of our structure ”CELL-GATE”is the use of a novel strand displacement method, called porter system.

-	By comparing our ~~selector~~ strand to toehold strand, the most popular method for strand displacement, we looked at the effectiveness of our structure in terms of it's strand capturing ability.	+	By comparing our porter strand to toehold strand, the most popular method for strand displacement, we looked at the effectiveness of our structure in terms of it's strand capturing ability.

	<h3> Model and Method</h3>		<h3> Model and Method</h3>
-	According to the design of the experiment section, we modeled the ~~selector~~ strand and the toehold strand as shown below. <br><br>	+	According to the design of the experiment section, we modeled the porter strand and the toehold strand as shown below. <br><br>
	[[Image: Format_selector.jpg \|left\|680px]]		[[Image: Format_selector.jpg \|left\|680px]]
	{{-}}		{{-}}
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	Hex-cylinder is represented as the assembly of fixed electrically-charged mass points.<br><br>		Hex-cylinder is represented as the assembly of fixed electrically-charged mass points.<br><br>
-	[[Image: Format_Hexagon.jpg \|left\|~~265px~~]]	+	[[Image: Format_Hexagon.jpg \|left\|750px]]

	<html><div style="clear:both;"></div></html>		<html><div style="clear:both;"></div></html>
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-	Movie2 and 3 shows the result of each simulation, ~~selector~~-target and toehold-target.	+	Movie2 and 3 shows the result of each simulation, porter-target and toehold-target.

	We note that this simulation was carried out under a periodic boundary condition, where the size of the simulation box is 20nm×20nm×20nm. Then, the distance between the target strand and the Hex-cylinder is maintained virtually constant.		We note that this simulation was carried out under a periodic boundary condition, where the size of the simulation box is 20nm×20nm×20nm. Then, the distance between the target strand and the Hex-cylinder is maintained virtually constant.

-	One of the advantages of the ~~selector~~ strand is shrinking ability. The ~~selector~~ strand hybridizes to the target making a loop which makes it possible to extend the strand length without changing the final structure's length.	+	One of the advantages of the porter strand is shrinking ability. The porter strand hybridizes to the target making a loop which makes it possible to extend the strand length without changing the final structure's length.


-	Results obtained from this simulation show that the ~~selector~~ strand can catch the target strand exists outside of the Hex-cylinder and hybridize completely while the toehold strand never hybridize to the target strand in simulation time.	+	Results obtained from this simulation show that the porter strand can catch the target strand exists outside of the Hex-cylinder and hybridize completely while the toehold strand never hybridize to the target strand in simulation time.

	We run additional 5 simulations for each capturing mechanism under the same conditions (NOTE: random seeds were different) and very similar results were obtained. Thus, the simulation results are very feasible under our model.		We run additional 5 simulations for each capturing mechanism under the same conditions (NOTE: random seeds were different) and very similar results were obtained. Thus, the simulation results are very feasible under our model.


-	By considering results of electrostatic potential calculation around the hex-cylinder and MD simulation, it is clear that the electrostatic field prevents the entrance of DNA strands into the Hex-cylinder and the ~~selector~~ strand helps it to get into the cylinder.	+	By considering results of electrostatic potential calculation around the hex-cylinder and MD simulation, it is clear that the electrostatic field prevents the entrance of DNA strands into the Hex-cylinder and the porter strand helps it to get into the cylinder.

-	Therefore, we concluded that our novel ~~selector~~ strand provides a high capture ability to our system “CELL-GATE”.	+	Therefore, we concluded that '''our novel porter strand provides a high capture ability to our system “CELL-GATE”.'''