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| | 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:
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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===
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| :''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.
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| ==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 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.
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| ===AFM Verification===
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| :''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments|AFM Experiments]]''
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| 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.
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