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| =Results=
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| While the [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project|overall project]] is the sorting of cargos on origami, we expected verification of all of the mechanisms would take longer than one summer. Therefore, this summer was spent verifying two aspects of the project:
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| # Verifying that the proposed mechanisms work when the strands are free-floating in solution (i.e. not bound to origami).
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| # Verifying that the random walking mechanism works as intended on origami.
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| __TOC__
| | = Progress = |
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| ==Verification of Overall Mechanisms in Solution==
| | Our progress over summer can be divided up to three categories as below. |
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| ===Gel Verification=== | | =====1. System Design===== |
| :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification|Gel Verification]]'' | | :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design|System Design]]'' |
| All of the essential mechanisms in our system were verified in solution using
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| polyacrylamide gel electrophoresis. These mechanisms include:
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_1|walker-track binding]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_2|triggering the walker]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_2|walking from one track to another]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_3|picking up cargo]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_4|walking while carrying cargo]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_5|triggering the cargo goal]],
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_6|dropping off cargo]], and
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| [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_7|irreversibly walking from tracks to the walker goal]].
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| We are fairly confident that all of these mechanisms work as expected in solution, with a few mysteries that do not seem to
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| interfere with the overall behavior of the system (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification|Gel Verification]]).
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| ===SPEX Verification=== | | =====2. Theoretical Analysis===== |
| | | :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Theoretical Simulation|Theoretical Analysis]]'' |
| ==Verification of Random Walking Mechanism on Origami== | |
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| ===SPEX Verification===
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| :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SPEX Results]]'' | |
| 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.
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| ===AFM Verification===
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| | =====3. Experimental Results===== |
| | :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results|Experimental Results]]'' |
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