Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results

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= Progress 3: Experimental Results =  
= Progress 3: Experimental Results =  
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__TOC__
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==Verification of Overall Mechanisms in Solution==
==Verification of Overall Mechanisms in Solution==
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===Gel Verification===
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====Gel Verification====
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification|Gel Verification]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification|Gel Verification Results]]''
All of the essential mechanisms in our system were verified in solution using  
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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polyacrylamide gel electrophoresis.These mechanisms include:  
[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_1|walker-track binding]],  
[[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|triggering the walker]],  
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[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel_Verification#Gel_6|dropping off cargo]], and  
[[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]].  
[[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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====SPEX Verification====
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results|Kinetics (SPEX) Results]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results|SPEX Results for Kinetics]]''
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We used fluorescent spectroscopy (SPEX) to study the kinetics of our mechanisms in solution.
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All of the essential mechanisms were verified using fluorescent spectroscopy.  We also analyzed the kinetics of our mechanisms in solution.
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==Verification of Random Walking Mechanism on Origami==
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==Demonstration of Random Walking Robot on Origami==
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===SPEX Verification===
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====SPEX Verification====
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SPEX Results for Random Walking]]''
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SPEX Results for Random Walking]]''
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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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Random walking robot on origami was successfully demonstrated by fluorescent spectroscopy (SPEX). The results show that walking completion time dependent on the track length, and the random walking curve fits well with the theoretical equation. 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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====AFM Verification====
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments|AFM Experiments]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments|AFM Experiment Results]]''
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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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Atomic force microscopy (AFM)was used to verify the random walking mechanism on origami. We imaged individual origami rectangles (using the 1D random walking playground layout) with an inhibited, biotin/streptavidin-tagged walker at its start site, and observed that the 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.  
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Progress 3: Experimental Results

Contents


Verification of Overall Mechanisms in Solution

Gel Verification

Main article: Gel Verification Results

All of the essential mechanisms in our system were verified in solution using polyacrylamide gel electrophoresis.These mechanisms include: walker-track binding, triggering the walker, walking from one track to another, picking up cargo, walking while carrying cargo, triggering the cargo goal, dropping off cargo, and irreversibly walking from tracks to the walker goal.

SPEX Verification

Main article: SPEX Results for Kinetics

All of the essential mechanisms were verified using fluorescent spectroscopy. We also analyzed the kinetics of our mechanisms in solution.



Demonstration of Random Walking Robot on Origami

SPEX Verification

Main article: SPEX Results for Random Walking

Random walking robot on origami was successfully demonstrated by fluorescent spectroscopy (SPEX). The results show that walking completion time dependent on the track length, and the random walking curve fits well with the theoretical equation. 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: AFM Experiment Results

Atomic force microscopy (AFM)was used to verify the random walking mechanism on origami. We imaged individual origami rectangles (using the 1D random walking playground layout) with an inhibited, biotin/streptavidin-tagged walker at its start site, and observed that the 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.


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