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

YAE LIM Lee at 19:57, 3 November 2011

2011-11-03T19:57:49Z

←Older revision		Revision as of 19:57, 3 November 2011
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	=== 1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution ===		=== 1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution ===
-	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|SPEX Results for kinetics]]	+	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification Results]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics 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.		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 ===		=== 2. Random walking robot was successfully built and demonstrated on a 2D surface ===
-	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results\|SPEX Results for Random Walking]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments\|AFM ~~Experiments~~]]	+	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results\|SPEX Results for Random Walking]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM_Experiments\|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.		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.

YAE LIM Lee at 19:33, 3 November 2011

2011-11-03T19:33:46Z

←Older revision		Revision as of 19:33, 3 November 2011
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	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|SPEX Results for kinetics]]		:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics 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 ~~(see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|see kinetics experiments]])~~. 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.	+	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 ===		=== 2. Random walking robot was successfully built and demonstrated on a 2D surface ===

Shayan Doroudi: /* Future Work and Conclusion */

2011-11-03T18:43:03Z

Future Work and Conclusion

←Older revision		Revision as of 18:43, 3 November 2011
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	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.

-	==Future Work and Conclusion==	+	===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.		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.

Shayan Doroudi: /* =Future Work and Conclusion */

2011-11-03T18:42:50Z

=Future Work and Conclusion

←Older revision		Revision as of 18:42, 3 November 2011
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	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.

-	===Future Work and Conclusion==	+	==Future Work and Conclusion==

-	~~Finally, 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.	+	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!		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!

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

Shayan Doroudi: /* Discussion */

2011-11-03T18:42:31Z

Discussion

←Older revision		Revision as of 18:42, 3 November 2011
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	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.
		+
		+	===Future Work and Conclusion==
		+
		+	Finally, 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!

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

Shayan Doroudi: /* 2. Random walking robot was successfully built and demonstrated on a 2D surface */

2011-11-03T18:42:05Z

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

←Older revision		Revision as of 18:42, 3 November 2011
Line 16:		Line 16:

	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.
-
-	Finally, 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!

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

Shayan Doroudi: /* 2. Random walking robot was successfully built and demonstrated on a 2D surface */

2011-11-03T18:41:37Z

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

←Older revision		Revision as of 18:41, 3 November 2011
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	Finally, 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.		Finally, 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!
-	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!	+

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

Shayan Doroudi: /* 2. Random walking robot was successfully built and demonstrated on a 2D surface */

2011-11-03T18:39:48Z

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

←Older revision		Revision as of 18:39, 3 November 2011
Line 17:		Line 17:
	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.

-	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.	+	Finally, 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.

Shayan Doroudi: /* 1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution */

2011-11-03T18:39:24Z

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

←Older revision		Revision as of 18:39, 3 November 2011
Line 8:		Line 8:
	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|SPEX Results for kinetics]]		:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics 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 (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.	+	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 (see [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|see kinetics experiments]]). 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 ===		=== 2. Random walking robot was successfully built and demonstrated on a 2D surface ===

Shayan Doroudi: /* 1. All mechanisms (Random walking, Cargo picking up, Cargo dropping off) work in solution */

2011-11-03T16:34:13Z

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

←Older revision		Revision as of 16:34, 3 November 2011
Line 8:		Line 8:
	:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics Results\|SPEX Results for kinetics]]		:''Evidences shown here: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification\|Gel Verification]], [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Kinetics 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 ~~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.	+	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 (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.

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