Everybody in my lab knows me for training caterpillars to perform various sportive activities. Well, inducing caterpillars to crawl underwater was a true story. My motivation was to test the role of gravity and external pressure on a behaving animal. As it turned out, 5th instar caterpillars float in water and thus experienced a force negative to gravity, but none of the kinematics characteristics changed. See my video "Manduca underwater walk" on YouTube.
Looking closely, I found that bubbles could be seemed to come out of the spiracles as the animal compressed itself. This observation illustrated the potential change of body volume due to tracheal compression (see video). If caterpillars can squeeze air out under the influence of water pressure, they must perform quite a lot of gas exchange in the air. In other words, locomotion facilitates gas exchange by compressing and squeezing the air out of the trachea.
Finally, I would like to share a video I shot the other day when one big caterpillar was crawling on top of a smaller one. It's quite an pathetic scene because the smaller caterpillar was actually in the molting process and could not fight back. Nevertheless, as the big caterpillar crawled along, I observed appropriate deformation on the substrate (in this case another caterpillar) as illustrated by my new ground reaction forces paper (to appear in Journal of Experimental Biology).
Wednesday, December 16, 2009
Tuesday, December 8, 2009
The missing post released!!
Dear readers,
There has been one missing post about the DARPA meeting which I started back in October but never finished. The reason was quite simple: I wanted to wait for better graphics. In any case, since I was orchestrating the live robotic demos for Tufts, there was no way I could take photographs as I always do. It turned out that it was not allowed anyways. DARPA actually hired prefessional film crew and photographers for the event.
Two months has gone by since the event so it's not news anymore. Nevertheless I thought some of you might be interested in reading my story a few days before the meeting! Now, according to the non-disclosure document I signed, I am not supposed to share anything I saw at the meeting. So in this post, I simply described what happened the very last week before the meeting in the labs. The ME professor that I worked with on this project said: "(It was) the most stressful/intense academic experience that I've gone through". Indeed, for the last month we worked at least 15 hours everyday. To hear more, see October 11 post which is newly released.
There has been one missing post about the DARPA meeting which I started back in October but never finished. The reason was quite simple: I wanted to wait for better graphics. In any case, since I was orchestrating the live robotic demos for Tufts, there was no way I could take photographs as I always do. It turned out that it was not allowed anyways. DARPA actually hired prefessional film crew and photographers for the event.
Two months has gone by since the event so it's not news anymore. Nevertheless I thought some of you might be interested in reading my story a few days before the meeting! Now, according to the non-disclosure document I signed, I am not supposed to share anything I saw at the meeting. So in this post, I simply described what happened the very last week before the meeting in the labs. The ME professor that I worked with on this project said: "(It was) the most stressful/intense academic experience that I've gone through". Indeed, for the last month we worked at least 15 hours everyday. To hear more, see October 11 post which is newly released.
Sunday, November 29, 2009
Hydrostatic skeleton model for caterpillars
As my regular readers, you might have noticed my dual role as a biologist and a roboticist. Indeed, I currently have 6 projects running in parallel, three in locomotion and other three in robotics. Of course, there are also many more side projects. In any case, the posting about caterpillar prolegs configuration was the motivation of a locomotion project. Here let me present to you another locomotion project of mine with some literature review. This one concerns modeling hydrostatic skeleton in caterpillars. The following photos show how an anesthetized caterpillar can lose turgor and fail to "stay in shape".
Modeling mechanics of biological soft structures has been a long time endeavor for functional morphologists as well as theoretical biologists. In general, this field focuses on morphologies without any rigid skeleton (internal or external). They are usually soft tissues supported by some fluid which allows very large deformation. The notion of “hydrostatic skeleton” became well-known by the 50’s largely due to research on worms (cnidarians, annelids, and nematodes). Clark and Cowey established how soft-bodied animals achieved extreme extension with helical reinforcing fibers in the body wall (Clark and Cowey, 1958). The oblique fibers winding around the body allows very large longitudinal stretching. Soon this type of fiber reinforcement was found in many other cylindrical biological structures including those of plants. In 1980’s, a new wave of theoretical investigation of soft-bodied animal locomotion began. Keller and Falkovitz attempted a model of worm crawling using finite difference method which calculated the transverse traveling wave along the body and its associated contact friction (Keller and Falkovitz, 1983). A few years later, Dobrolyubov generalized this line of reasoning to traveling deformation (both transverse and longitudinal). He claimed that the transverse traveling wave can represent caterpillar locomotion while the longitudinal traveling wave resembles crawling worms. Then he gave an example on how this model could describe snake’s locomotion (Dobrolyubov, 1986). These models proposed credible mechanisms for locomotion, but did not explain how animals achieved those body deformations. In another Journal of Theoretical Biology paper, Wadepuhl presented probably the first comprehensive finite element hydrostatic skeleton model based on medical leech which had been well studied by then (Muller et al., 1981; Sawyer, 1986; Stern-Tomlinson et al., 1986; Wadepuhl and Beyn, 1989). This model included geometry, elastic properties of the body wall, internal volume, and body pressure. It revealed some principles of antagonism in worm-like structures as well as the pressure-volume interactions (265 Wadepuhl, M. 1989). At about the same time, Wainwright nicely summarized the mechanics of cylindrical biological structures in his famous little book “Axis and Circumference” (Wainwright, 1988).
Before the turn of the 21st century, Journal of Theoretical biology continued to host models of hydrostatic skeleton. However, experimental data gradually dominated the modeling efforts. Skierczynski et al constructed an updated leech model empirically based on dimensions of animals in limiting cases, passive properties of the tissues, muscle responses to activation, and the transform from motor-neurons to muscles. It assumes elliptical shapes for cross-sections, constant volume, and that the shape tends to minimize the potential energy. It simulates the vermiform elongation and predicts the pressure changes (Skierczynski et al., 1996). Similarly Alscher and Beyn simulated the motion of leech using Lagrangian mechanics and a large system of differential-algebraic equations (Alscher and Beyn, 1998).
While leech models seemed to develop with fast pace, earthworm studies were thriving as well. Dobrolyubov refined his mass transfer wave model and published another paper in JTB with Douchy on peristaltic transport. This general model attempted to explain the digestive transport as well as locomotion by caterpillars, earthworms, snake and snails (Dobrolyubov and Douchy, 2002). Accoto et al added to JTB another earthworm kinematics model, again based on constant volume and simple friction (Accoto et al., 2004). With these numerous hydrostatic skeleton models, it was thought that soft-bodied animal locomotion is more or less realized and what we learned from worms can be applied to others such as caterpillars. Unfortunately, caterpillars are simply not worms in all biomechanical respects.
Caterpillar’s body differs from that of a worm in several essential features: 1) Extension in the longitudinal direction is accounted by numerous inter-segmental folds instead of body wall stretching. 2) Body pressure is highly variable and less predictable. 3) It contains more compressible volume in the body. 4) There is no segmental septum that compartmentalizes the animals. 5) Caterpillars are legged systems with discrete and on-off attachments. As the results, the helical fiber-reinforced cylinder model does not apply. The constant volume assumption does not hold, and real-time pressure recording lacks correlation to body movements. Frictional model based on mass transfer is useless in this system. What’s more, caterpillars don’t move with one single gait and/or body configurations. In this study, we seek an alternative approach to model this worm-like structure that is so much unlike worms.
References
Accoto, D., Castrataro, P. and Dario, P. (2004). Biomechanical Analysis of Oligochaeta Crawling. J. Theor. Biol. 230, 49-55.
Alscher, C. and Beyn, W. J. (1998). Simulating the Motion of the Leech: A Biomechanical Application of DAEs. Numerical Algorithms 19, 1-12.
Clark, R. B. and Cowey, J. B. (1958). Factors Controlling the Change of Shape of Certain Nemertean and Turbellarian Worms. J. Exp. Biol. 35, 731.
Dobrolyubov, A. I. (1986). The Mechanism of Locomotion of some Terrestrial Animals by Travelling Waves of Deformation. J. Theor. Biol. 119, 457-466.
Dobrolyubov, A. I. and Douchy, G. (2002). Peristaltic Transport as the Travelling Deformation Waves. J. Theor. Biol. 219, 55-61.
Keller, J. B. and Falkovitz, M. S. (1983). Crawling of Worms. J. Theor. Biol. 104, 417-442.
Muller, K. J., Nicholls, J. G. and Stent, G. S. (1981). Neurobiology of the Leech: Cold Spring Harbor Laboratory Pr.
Sawyer, R. T. (1986). Leech Biology and Behaviour: Clarendon Press Oxford.
Skierczynski, B. A., Wilson, R. J. A., Kristan Jr, W. B. and Skalak, R. (1996). A Model of the Hydrostatic Skeleton of the Leech. J. Theor. Biol. 181, 329-342.
Stern-Tomlinson, W., Nusbaum, M. P., Perez, L. E. and Kristan, W. B. (1986). A Kinematic Study of Crawling Behavior in the Leech, Hirudo Medicinalis. Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology 158, 593-603.
Wadepuhl, M. and Beyn, W. J. (1989). Computer Simulation of the Hydrostatic Skeleton. the Physical Equivalent, Mathematics and Application to Worm-Like Forms. J. Theor. Biol. 136, 379-402.
Wainwright, S. A. (1988). Axis and Circumference: The Cylindrical Shape of Plants and Animals. Cambridge: Harvard University Press.
Modeling mechanics of biological soft structures has been a long time endeavor for functional morphologists as well as theoretical biologists. In general, this field focuses on morphologies without any rigid skeleton (internal or external). They are usually soft tissues supported by some fluid which allows very large deformation. The notion of “hydrostatic skeleton” became well-known by the 50’s largely due to research on worms (cnidarians, annelids, and nematodes). Clark and Cowey established how soft-bodied animals achieved extreme extension with helical reinforcing fibers in the body wall (Clark and Cowey, 1958). The oblique fibers winding around the body allows very large longitudinal stretching. Soon this type of fiber reinforcement was found in many other cylindrical biological structures including those of plants. In 1980’s, a new wave of theoretical investigation of soft-bodied animal locomotion began. Keller and Falkovitz attempted a model of worm crawling using finite difference method which calculated the transverse traveling wave along the body and its associated contact friction (Keller and Falkovitz, 1983). A few years later, Dobrolyubov generalized this line of reasoning to traveling deformation (both transverse and longitudinal). He claimed that the transverse traveling wave can represent caterpillar locomotion while the longitudinal traveling wave resembles crawling worms. Then he gave an example on how this model could describe snake’s locomotion (Dobrolyubov, 1986). These models proposed credible mechanisms for locomotion, but did not explain how animals achieved those body deformations. In another Journal of Theoretical Biology paper, Wadepuhl presented probably the first comprehensive finite element hydrostatic skeleton model based on medical leech which had been well studied by then (Muller et al., 1981; Sawyer, 1986; Stern-Tomlinson et al., 1986; Wadepuhl and Beyn, 1989). This model included geometry, elastic properties of the body wall, internal volume, and body pressure. It revealed some principles of antagonism in worm-like structures as well as the pressure-volume interactions (265 Wadepuhl, M. 1989). At about the same time, Wainwright nicely summarized the mechanics of cylindrical biological structures in his famous little book “Axis and Circumference” (Wainwright, 1988).Before the turn of the 21st century, Journal of Theoretical biology continued to host models of hydrostatic skeleton. However, experimental data gradually dominated the modeling efforts. Skierczynski et al constructed an updated leech model empirically based on dimensions of animals in limiting cases, passive properties of the tissues, muscle responses to activation, and the transform from motor-neurons to muscles. It assumes elliptical shapes for cross-sections, constant volume, and that the shape tends to minimize the potential energy. It simulates the vermiform elongation and predicts the pressure changes (Skierczynski et al., 1996). Similarly Alscher and Beyn simulated the motion of leech using Lagrangian mechanics and a large system of differential-algebraic equations (Alscher and Beyn, 1998).
While leech models seemed to develop with fast pace, earthworm studies were thriving as well. Dobrolyubov refined his mass transfer wave model and published another paper in JTB with Douchy on peristaltic transport. This general model attempted to explain the digestive transport as well as locomotion by caterpillars, earthworms, snake and snails (Dobrolyubov and Douchy, 2002). Accoto et al added to JTB another earthworm kinematics model, again based on constant volume and simple friction (Accoto et al., 2004). With these numerous hydrostatic skeleton models, it was thought that soft-bodied animal locomotion is more or less realized and what we learned from worms can be applied to others such as caterpillars. Unfortunately, caterpillars are simply not worms in all biomechanical respects.
Caterpillar’s body differs from that of a worm in several essential features: 1) Extension in the longitudinal direction is accounted by numerous inter-segmental folds instead of body wall stretching. 2) Body pressure is highly variable and less predictable. 3) It contains more compressible volume in the body. 4) There is no segmental septum that compartmentalizes the animals. 5) Caterpillars are legged systems with discrete and on-off attachments. As the results, the helical fiber-reinforced cylinder model does not apply. The constant volume assumption does not hold, and real-time pressure recording lacks correlation to body movements. Frictional model based on mass transfer is useless in this system. What’s more, caterpillars don’t move with one single gait and/or body configurations. In this study, we seek an alternative approach to model this worm-like structure that is so much unlike worms.
References
Accoto, D., Castrataro, P. and Dario, P. (2004). Biomechanical Analysis of Oligochaeta Crawling. J. Theor. Biol. 230, 49-55.
Alscher, C. and Beyn, W. J. (1998). Simulating the Motion of the Leech: A Biomechanical Application of DAEs. Numerical Algorithms 19, 1-12.
Clark, R. B. and Cowey, J. B. (1958). Factors Controlling the Change of Shape of Certain Nemertean and Turbellarian Worms. J. Exp. Biol. 35, 731.
Dobrolyubov, A. I. (1986). The Mechanism of Locomotion of some Terrestrial Animals by Travelling Waves of Deformation. J. Theor. Biol. 119, 457-466.
Dobrolyubov, A. I. and Douchy, G. (2002). Peristaltic Transport as the Travelling Deformation Waves. J. Theor. Biol. 219, 55-61.
Keller, J. B. and Falkovitz, M. S. (1983). Crawling of Worms. J. Theor. Biol. 104, 417-442.
Muller, K. J., Nicholls, J. G. and Stent, G. S. (1981). Neurobiology of the Leech: Cold Spring Harbor Laboratory Pr.
Sawyer, R. T. (1986). Leech Biology and Behaviour: Clarendon Press Oxford.
Skierczynski, B. A., Wilson, R. J. A., Kristan Jr, W. B. and Skalak, R. (1996). A Model of the Hydrostatic Skeleton of the Leech. J. Theor. Biol. 181, 329-342.
Stern-Tomlinson, W., Nusbaum, M. P., Perez, L. E. and Kristan, W. B. (1986). A Kinematic Study of Crawling Behavior in the Leech, Hirudo Medicinalis. Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology 158, 593-603.
Wadepuhl, M. and Beyn, W. J. (1989). Computer Simulation of the Hydrostatic Skeleton. the Physical Equivalent, Mathematics and Application to Worm-Like Forms. J. Theor. Biol. 136, 379-402.
Wainwright, S. A. (1988). Axis and Circumference: The Cylindrical Shape of Plants and Animals. Cambridge: Harvard University Press.
Friday, November 20, 2009
Research odds and ends...
Sorry for the delayed posting again! I've been occupied with the end of the year academic madness: grants writing. One can tell how bad the economics is by looking at how people panic about funding. That's very much the case in academia. In any case, I didn't find these experiences extremely appealing to talk about so I blanked out last Sunday when I was supposed to update my blog.
Regarding the robot videos many people inquired about, I've done my best to push the school administration for video hosting. Unfortunately Tufts is still an university and all administrations eat time. Actually, that's the main reason why I started this blog. Our labs websites update never caught up with our research pace, because we researchers cannot access the webpages ourselves.
By the way, I do have a facebook account, but I don't use it very often. My colleague asked me about it a couple of weeks ago here is how I responded:
Regarding the robot videos many people inquired about, I've done my best to push the school administration for video hosting. Unfortunately Tufts is still an university and all administrations eat time. Actually, that's the main reason why I started this blog. Our labs websites update never caught up with our research pace, because we researchers cannot access the webpages ourselves.
By the way, I do have a facebook account, but I don't use it very often. My colleague asked me about it a couple of weeks ago here is how I responded:
Sunday, November 1, 2009
Caterpillar prolegs diversity
While we are waiting for the caterpillar robot video links, let's come back to some morphological discussion of lepidoptera larvae. All my biomechanics studies so far are based on a well-known model system tobacco hornworm (Manduca sexta). It is a fair size macro-lepidopera species commonly found in the America. It has 4 pairs of abdominal prolegs plus 1 pair of anal prolegs (or terminal prolegs). This is thought to be the ancestral form.
However, we are perfectly aware of the diversity of lepidoptera species. Caterpillars really vary in numbers and arrangement of prolegs. They also adopt different gait patterns accordingly. So how do we generalize what we learned from Manduca? Or can we?
To find out why, I am planning a field study to compare body overall scaling across different species of caterpillar. Although much work has been done on comparing morphological changes in the evolutionary context of species interaction, little is known about the physical constraints during evolution. I believe that there is a link between locomotor biomechanics and the evolution of prolegs configuration.
However, we are perfectly aware of the diversity of lepidoptera species. Caterpillars really vary in numbers and arrangement of prolegs. They also adopt different gait patterns accordingly. So how do we generalize what we learned from Manduca? Or can we?
To find out why, I am planning a field study to compare body overall scaling across different species of caterpillar. Although much work has been done on comparing morphological changes in the evolutionary context of species interaction, little is known about the physical constraints during evolution. I believe that there is a link between locomotor biomechanics and the evolution of prolegs configuration.
Sunday, October 18, 2009
From InchBot to GoQBot - video links coming soon!
Dear readers,
If you see this message, then I must thank you for your loyalty to my blog. I apologized for missing out almost a month of blogging, but really I can't afford to get into trouble. In any case, welcome back to my rapid pace of locomotion research and biomimetics. Currently I have two robotic lineages: InchBot[7 generations] and GoQBot[4 generations]
Each robot generation has a very specific research aim and target performance. I think it's time for me to present them to you in a video format. While all the videos have been edited and annotated, I still need to link them from the Tufts Media Server. Please be patient! They are coming soon.
If you see this message, then I must thank you for your loyalty to my blog. I apologized for missing out almost a month of blogging, but really I can't afford to get into trouble. In any case, welcome back to my rapid pace of locomotion research and biomimetics. Currently I have two robotic lineages: InchBot[7 generations] and GoQBot[4 generations]
Each robot generation has a very specific research aim and target performance. I think it's time for me to present them to you in a video format. While all the videos have been edited and annotated, I still need to link them from the Tufts Media Server. Please be patient! They are coming soon.
Sunday, October 11, 2009
DARPA Review
It's peculiar how things evolve. I never meant to get into this DARPA project until I realized how far I've been sucked in. So here I am working on my robots in the second room of Biomimetic Devices Laboratory every minutes of my awareness.System engineering requires a lot of collaboration but creation really has to be solo. A roboticist has to be able to work with people as well as alone. I was fully aware of the importance of this final review, because a lot of people depend on this funding at Tufts, including many friends and colleagues. For me, that's enough at stack even if I had alternative funding source for my primary research. I simply had to do everything in my power to make this robotic demonstration rock solid and fail-proof. I was really up for the job!
In September, I produced a plan for preparing this robot demonstration. Following is a rough list of the issues we had to consider:
1. Transportation protection
2. Demonstration platforms
3. Displays cases and proper Logos
4. Portable power supply and charging units
5. The robots (obviously) and their doubles
6. The control system and a secondary backup
7. Primary robot operator, backup operator
8. Demonstration program and rehearsal
9. Robot specification data
10. Backup video shots in case some live demos fail
11. Tool boxes
This list just went on... My job was to coordinate the designs, search for the parts, arrange the purchases, find appropriate help, and do as much as possible to complete my robots and their accessories. In a typical day, I would spend 5+ hrs doing micro-soldering and bonding, 2+ hrs programming, 2+ hrs literature research, 3+ hrs robot testing, 2+ hrs casting/molding. On top of that, I had to purchased about $500 worth of components everyday on average. Actually, I found shopping the most stressful task among all. In order to get the right thing on time, I had to check the mechanical/electric compatibility, availability, pricing, shipping, and make payments. That's probably why R&D companies always have a person or a group of people specifically do purchasing. It's such a tough job.
Anyways, it's Sunday night now! We are up for the show in two days. I better get some sleep and hope for the best.
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