Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Results - Revision history

YAE LIM Lee at 19:44, 3 November 2011

2011-11-03T19:44:45Z

←Older revision		Revision as of 19:44, 3 November 2011
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	Our progress over summer can be divided up to three categories as below.		Our progress over summer can be divided up to three categories as below.

-	===1. System Design===	+	=====1. System Design=====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''

-	===2. Theoretical Analysis===	+	=====2. Theoretical Analysis=====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation\|Theoretical Analysis]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation\|Theoretical Analysis]]''

-	===3. Experimental Results===	+	=====3. Experimental Results=====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''

	{{Template:DeoxyriboNucleicAwesomeFooter}}		{{Template:DeoxyriboNucleicAwesomeFooter}}

YAE LIM Lee at 19:43, 3 November 2011

2011-11-03T19:43:21Z

←Older revision		Revision as of 19:43, 3 November 2011
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	{{Template:DeoxyriboNucleicAwesomeHeader}}		{{Template:DeoxyriboNucleicAwesomeHeader}}

-	== Progress ==	+	= Progress =

	Our progress over summer can be divided up to three categories as below.		Our progress over summer can be divided up to three categories as below.

-	1. System Design	+	===1. System Design===
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''
-	2. Theoretical Analysis	+
		+	===2. Theoretical Analysis===
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation\|Theoretical Analysis]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation\|Theoretical Analysis]]''
-	3. Experimental Results	+
		+	===3. Experimental Results===
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''

	{{Template:DeoxyriboNucleicAwesomeFooter}}		{{Template:DeoxyriboNucleicAwesomeFooter}}

YAE LIM Lee at 13:13, 3 November 2011

2011-11-03T13:13:38Z

←Older revision		Revision as of 13:13, 3 November 2011
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	== Progress ==		== Progress ==

-	~~Out~~ progress over summer can be divided up to three categories as below.	+	Our progress over summer can be divided up to three categories as below.

	1. System Design		1. System Design

YAE LIM Lee at 09:58, 3 November 2011

2011-11-03T09:58:30Z

←Older revision		Revision as of 09:58, 3 November 2011
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	{{Template:DeoxyriboNucleicAwesomeHeader}}		{{Template:DeoxyriboNucleicAwesomeHeader}}
		+
		+	== Progress ==
		+
		+	Out progress over summer can be divided up to three categories as below.

	1. System Design		1. System Design

YAE LIM Lee at 07:04, 3 November 2011

2011-11-03T07:04:23Z

←Older revision		Revision as of 07:04, 3 November 2011
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		+	{{Template:DeoxyriboNucleicAwesomeHeader}}
		+
	1. System Design		1. System Design
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''
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	3. Experimental Results		3. Experimental Results
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''
		+
		+	{{Template:DeoxyriboNucleicAwesomeFooter}}

YAE LIM Lee at 07:03, 3 November 2011

2011-11-03T07:03:54Z

←Older revision		Revision as of 07:03, 3 November 2011
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-	~~{{Template:DeoxyriboNucleicAwesomeHeader}}~~	+	1. System Design
-	~~==Verification of Overall Mechanisms in Solution==~~	+	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design\|System Design]]''
-		+	2. Theoretical Analysis
-	~~===Gel Verification===~~	+	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation\|Theoretical Analysis]]''
-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/~~Gel Verification~~\|~~Gel Verification~~]]''	+	3. Experimental Results
-	~~All of the essential mechanisms in our system were veriﬁed in solution using~~	+	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results\|Experimental Results]]''
-	~~polyacrylamide gel electrophoresis~~. ~~These mechanisms include:~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_1\|walker-track binding]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_2\|triggering the walker]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_2\|walking from one track to another]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_3\|picking up cargo]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_4\|walking while carrying cargo]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_5\|triggering the cargo goal]],~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_6\|dropping oﬀ cargo]], and~~	+
-	~~[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_7\|irreversibly walking from tracks to the walker goal]].~~	+
-	~~We are fairly confident that all of these mechanisms work as expected in solution, with a few mysteries that do not seem to~~	+
-	~~interfere with the overall behavior of the system (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]]).~~	+
-		+
-	~~===SPEX Verification===~~	+
-		+
-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/~~Kinetics Results~~\|~~Kinetics (SPEX) Results~~]]''	+
-	~~We used fluorescent spectroscopy (SPEX) to study the kinetics of our mechanisms in solution~~.	+
-		+
-	~~==Verification of Random Walking Mechanism on Origami==~~	+
-		+
-	~~===SPEX Verification===~~	+
-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/~~SPEX~~ Results\|~~SPEX~~ Results ~~for Random Walking~~]]''	+
-	We used fluorescent spectroscopy (SPEX) to verify the random walking mechanism on the origami. Goals were tagged with fluorophores whereas walkers were tagged with the corresponding quenchers. Fluorescent signals will decrease when walkers reach their goals. Unlike AFM, which studied individual origami, SPEX experiments studied the collective behavior of all the origami in solution. Hence, the SPEX results were analyzed using both Matlab simulation and mathematical formulae.	+
-		+
-	~~===AFM Verification===~~	+
-	~~:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments\|AFM Experiments]]''~~	+
-	We are in the process of using atomic force microscopy (AFM) to verify the random walking mechanism on origami. We plan to image individual origami rectangles (using the 1D random walking playground layout) with an inhibited, biotin/streptavidin-tagged walker at its start site, and verify that walkers begin at their intended start site at one end of the random-walking track. We will then trigger the walker, wait for some amount of time, and image the origami again to verify that walkers have left their start site and are tending to stop at their goal at the other end of the track. This research is still in progress.	+
-		+
-	~~{{Template:DeoxyriboNucleicAwesomeFooter}}~~	+

Zibo Chen: /* SPEX Verification */

2011-11-03T07:01:29Z

SPEX Verification

←Older revision		Revision as of 07:01, 3 November 2011
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	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|Kinetics (SPEX) Results]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|Kinetics (SPEX) Results]]''
-	We used fluorescent spectroscopy (SPEX) to ~~verify~~ the kinetics of our mechanisms.	+	We used fluorescent spectroscopy (SPEX) to study the kinetics of our mechanisms in solution.
-		+

	==Verification of Random Walking Mechanism on Origami==		==Verification of Random Walking Mechanism on Origami==

Zibo Chen: /* SPEX Verification */

2011-11-03T07:00:12Z

SPEX Verification

←Older revision		Revision as of 07:00, 3 November 2011
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	===SPEX Verification===		===SPEX Verification===
-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results\|SPEX Results]]''	+	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results\|SPEX Results for Random Walking]]''
-	We used fluorescent spectroscopy (SPEX) to verify the random walking mechanism on the origami. Goals were tagged with fluorophores whereas walkers were tagged with the corresponding quenchers. Fluorescent signals will decrease when walkers reach their goals. Unlike AFM, which studied individual origami, SPEX experiments studied the collective behavior of all the origami in solution. Hence, the SPEX results were analyzed using both Matlab simulation and mathematical formulae.	+	We used fluorescent spectroscopy (SPEX) to verify the random walking mechanism on the origami. Goals were tagged with fluorophores whereas walkers were tagged with the corresponding quenchers. Fluorescent signals will decrease when walkers reach their goals. Unlike AFM, which studied individual origami, SPEX experiments studied the collective behavior of all the origami in solution. Hence, the SPEX results were analyzed using both Matlab simulation and mathematical formulae.

	===AFM Verification===		===AFM Verification===

YAE LIM Lee at 06:50, 3 November 2011

2011-11-03T06:50:19Z

←Older revision		Revision as of 06:50, 3 November 2011
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	interfere with the overall behavior of the system (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]]).		interfere with the overall behavior of the system (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]]).

-	==Verification ~~of Random Walking Mechanism on Origami~~==	+	===SPEX Verification===
		+
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|Kinetics (SPEX) Results]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|Kinetics (SPEX) Results]]''
	We used fluorescent spectroscopy (SPEX) to verify the kinetics of our mechanisms.		We used fluorescent spectroscopy (SPEX) to verify the kinetics of our mechanisms.
		+
		+
		+	==Verification of Random Walking Mechanism on Origami==

	===SPEX Verification===		===SPEX Verification===

YAE LIM Lee at 06:49, 3 November 2011

2011-11-03T06:49:13Z

←Older revision		Revision as of 06:49, 3 November 2011
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	==Verification of Random Walking Mechanism on Origami==		==Verification of Random Walking Mechanism on Origami==
		+	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|Kinetics (SPEX) Results]]''
	We used fluorescent spectroscopy (SPEX) to verify the kinetics of our mechanisms.		We used fluorescent spectroscopy (SPEX) to verify the kinetics of our mechanisms.