Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Discussion

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=Discussion=
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==Start of page==
 
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Fill this in TODAY!
 
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While our high level goal was to have walkers sort molecules (see Project), we realized this was ambitious for a summer, so this summer we focused on two tasks.  (1) Verifying that all of the mechanisms we hope to implement on origami actually work when the strands are free-floating, and (2) verifying that our random walking mechanism works when the walker is on origami.  We were successful in achieving both of these goals.  Moreover, both successes imply that our overall project can be completed, as we shall explain. 
 
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Our gel results our sufficient to show that all of our mechanism work as desired in solution.  However, our gel results do not tell us anything about the speed of our mechanisms, which is why we used fluorescence spectroscopy experiments to measure the kinetics of our reactions.  While certain reactions (e.g. the walker moving to the walker goal) were deemed to be slow, the kinetics were deemed to be reasonable, since for example, our walker could reach the goal when on origami in reasonable time (see SPEX results)Thus, we are fairly convinced that we can continue working with the strands we currently have to show that our mechanisms work on origami.
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While our high level goal was to have walkers sort molecules (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project#Project_Overview:_Ultimate_goal|Project]]), we realized this was ambitious for a summer, so this summer we focused on two tasks.  (1) Verifying that all of the mechanisms we hope to implement on origami actually work when the strands are free-floating, and (2) verifying that our random walking mechanism works when the walker is on origami.  We were successful in achieving both of these goalsMoreover, both successes imply that our overall project can be completed in the future, as we shall explain.
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The most interesting results we obtained this summer were in showing that our walker does in fact walk on origami.  We saw that our walker reached its goal if and only if there were tracks present and we released the trigger, which is exactly how we expect it to behave. Furthermore, we saw that the speed at which the walker reached its goal was in fact dependent on track length, such that shorter tracks were completed faster than longer ones.  Even more impressive, the estimated time per step that we obtained complies very well with both our simulation results and theoretical work, which can be seen in the tables below.
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=== 1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution ===
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:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification|Gel Verification Results]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results|SPEX Results for kinetics]]
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Our gel results are sufficient to show that all of our mechanism work as desired in solution.  However, our gel results do not tell us anything about the speed of our mechanisms, which is why we used fluorescence spectroscopy experiments to measure the kinetics of our reactions.  While certain reactions (e.g. the walker moving to the walker goal) were deemed to be slow, the kinetics were still reasonable, since for example, our walker could reach the goal when on origami in reasonable time.  Thus, we are fairly convinced that we can continue working with the strands we currently have to show that all of our mechanisms work on origami.
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=== 2. Random walking robot was successfully built and demonstrated on a 2D surface ===
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:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SPEX Results for Random Walking]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments|AFM Experiment Results]]
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The most interesting results we obtained this summer were in showing that our walker does in fact walk on origami.  We saw that our walker reached its goal if and only if there were tracks present and we released the trigger, which is exactly how we expect it to behave. Furthermore, we saw that the speed at which the walker reached its goal was in fact dependent on track length, such that shorter tracks were completed faster than longer ones.
Furthermore, despite not being able to see our walker via AFM for a long time, we have finally developed a reliable method for seeing the walker, which means we can soon verify visually that the walker only walks when we release the trigger, it ends up on various positions along its way to the goal, and that it does in fact reach the goal after a sufficiently long period of time when we release the trigger, which will give us an additional level of confidence that our random walking mechanism works as intended.
Furthermore, despite not being able to see our walker via AFM for a long time, we have finally developed a reliable method for seeing the walker, which means we can soon verify visually that the walker only walks when we release the trigger, it ends up on various positions along its way to the goal, and that it does in fact reach the goal after a sufficiently long period of time when we release the trigger, which will give us an additional level of confidence that our random walking mechanism works as intended.
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Finally, since we have had success seeing that our walker reaches the goal using SPEX experiments, we are hopeful that we can have similar success showing that cargos reach their goals, when testing out the sorting mechanism.  Of course, the sorting mechanism will have an additional level of complexity, but many of the problems we will face are probably ones we have already dealt with, such as space walking, or perhaps "space sorting."  To counteract these problems, we will need to test out various purification protocols, because we truly need our walker to only walk and sort on the surface to claim our mechanisms work completely as expected.  Furthermore, the protocol we have developed for visualizing the walker on AFM can also be used to see the cargo on AFM!  While, we do expect to run into many new problems on the way, we feel confident that we can verify the sorting mechanism works as expected on origami in the near future. 
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===Future Work and Conclusion===
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By demonstrating a very simple random walker that can be modified to perform various tasks, only one of which is sorting cargos, we have already significantly added to the literature on molecular robotics.  Furthermore, we have a long-term goal that we anticipate accomplishing in the near future, which could potentially result in the most complex DNA robot built as of yet!  This is incredibly exciting for an undergraduate project.
+
Since we have had success showing that our walker reaches the goal using SPEX experiments, we are hopeful that we can have similar success showing that cargos reach their goals, when testing out the sorting mechanism.  Of course, the sorting mechanism will have an additional level of complexity, but many of the problems we will face are probably ones we have already dealt with, such as space walking, or perhaps "space sorting."  To counteract these problems, we will need to test out various purification protocols, because we truly need our walker to only walk and sort on the surface to claim our mechanisms work completely as expected.  Furthermore, the protocol we have developed for visualizing the walker on AFM can also be used to see the cargo on AFM!  While, we do expect to run into many new problems on the way, we feel confident that we can verify the sorting mechanism works as expected on origami in the near future. 
 +
 
 +
By demonstrating a very simple random walker that can be modified to perform various tasks, only one of which is sorting cargos, we have already significantly added to the literature on molecular robotics.  Furthermore, we have a long-term goal that we anticipate accomplishing in the near future, which could potentially result in the most sophisticated DNA robot built as of yet!  This is incredibly exciting for an undergraduate project!
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Discussion

While our high level goal was to have walkers sort molecules (see Project), we realized this was ambitious for a summer, so this summer we focused on two tasks. (1) Verifying that all of the mechanisms we hope to implement on origami actually work when the strands are free-floating, and (2) verifying that our random walking mechanism works when the walker is on origami. We were successful in achieving both of these goals. Moreover, both successes imply that our overall project can be completed in the future, as we shall explain.

1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution

Evidences shown here: Gel Verification Results, SPEX Results for kinetics

Our gel results are sufficient to show that all of our mechanism work as desired in solution. However, our gel results do not tell us anything about the speed of our mechanisms, which is why we used fluorescence spectroscopy experiments to measure the kinetics of our reactions. While certain reactions (e.g. the walker moving to the walker goal) were deemed to be slow, the kinetics were still reasonable, since for example, our walker could reach the goal when on origami in reasonable time. Thus, we are fairly convinced that we can continue working with the strands we currently have to show that all of our mechanisms work on origami.

2. Random walking robot was successfully built and demonstrated on a 2D surface

Evidences shown here: SPEX Results for Random Walking, AFM Experiment Results

The most interesting results we obtained this summer were in showing that our walker does in fact walk on origami. We saw that our walker reached its goal if and only if there were tracks present and we released the trigger, which is exactly how we expect it to behave. Furthermore, we saw that the speed at which the walker reached its goal was in fact dependent on track length, such that shorter tracks were completed faster than longer ones.

Furthermore, despite not being able to see our walker via AFM for a long time, we have finally developed a reliable method for seeing the walker, which means we can soon verify visually that the walker only walks when we release the trigger, it ends up on various positions along its way to the goal, and that it does in fact reach the goal after a sufficiently long period of time when we release the trigger, which will give us an additional level of confidence that our random walking mechanism works as intended.

Future Work and Conclusion

Since we have had success showing that our walker reaches the goal using SPEX experiments, we are hopeful that we can have similar success showing that cargos reach their goals, when testing out the sorting mechanism. Of course, the sorting mechanism will have an additional level of complexity, but many of the problems we will face are probably ones we have already dealt with, such as space walking, or perhaps "space sorting." To counteract these problems, we will need to test out various purification protocols, because we truly need our walker to only walk and sort on the surface to claim our mechanisms work completely as expected. Furthermore, the protocol we have developed for visualizing the walker on AFM can also be used to see the cargo on AFM! While, we do expect to run into many new problems on the way, we feel confident that we can verify the sorting mechanism works as expected on origami in the near future.

By demonstrating a very simple random walker that can be modified to perform various tasks, only one of which is sorting cargos, we have already significantly added to the literature on molecular robotics. Furthermore, we have a long-term goal that we anticipate accomplishing in the near future, which could potentially result in the most sophisticated DNA robot built as of yet! This is incredibly exciting for an undergraduate project!


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