Archive for the ‘biomimicry’ Category

Beautiful flowers in small packages

20 May, 2013 2 comments
The latest addition to my collection...

The latest addition to my collection…

Anyone who has seen my home knows that I have a bit of a… hmm… obsession with orchids. To control my orchid intake, I meter my purchases to buying more plants only after I have either mastered or killed my latest orchid purchase. This has resulted in nearly 20 pots of these gorgeous plants with orchid “spa treatment days” (i.e., deep watering days) lasting hours at a time. So you can probably imagine the enthusiasm with which I embraced a recent article from the journal Science, in which Harvard researchers Wim L Noorduin and colleagues proclaim that they have discovered how to create predictable complex nano- and microstructures via biomineralization techniques, and then demonstrate this by creating micro-flowers!

Self-assembly of complex forms occur regularly in nature as a result of dynamic interactions with the surrounding environment. Many of these structures have a stunning beauty to them, with snowflakes being one of the most well-known examples of this phenomenon. The claim that no two snowflakes are alike is based on the understanding that the basic shape of a snowflake is guided by a combination of atmospheric temperature and humidity. However, its individuality is “crafted” as it falls through the atmosphere, tracing unique paths and being exposed to different air patterns as its shape shifts with each tumble, spin, pitch and glide, and twirl.

"Diatom Circle" by Graham P. Matthews (

“Diatom Circle” by Graham P. Matthews (

Another, perhaps lesser-known example is the shells of diatoms, a type of algae that is characterized as being encased in a shell formed of silica. These silica shells often exhibit a remarkable level of complexity, being extremely porous to permit gas and nutrient exchange with the surrounding environment.

What makes them of particular interest to physicists and materials scientists is their ability to repeatedly produce these intricate and complex shells through self-assembly with such accuracy that the identification and classification of these creatures can be guided by the patterns and placements of their pores.

Until recently, the study of how these patterns emerge has focused on looking at the chemical compositions and material properties of complex microsystems, or has worked on defining the initial conditions required to generate these forms. While the understanding that complex structures are usually created as a result of dynamic interactions with the surrounding environment is well-accepted, how these complex structures form through self-assembly had never yet reached the point of being something scientists could predict.

So Noorduin and co-authors set off undaunted to discover how dynamic environmental interactions can be used to generate predictable, patterned precipitation in synthetic systems, to create self-assembled complex structures… repeatedly (i.e., in a predictable manner).

Micro flowers grown in a beaker!

Micro flowers grown in a beaker! (Image by W.L. Noorduin)

It turns out that the secret to growing complex structures is to subject the solution to a dynamically-changing environment, one that responds to its growing shape. The images to the left are scanning electron micrographs that have been artificially colored, but aren’t they beautiful?

It’s important to realize that while Noorduin and colleagues did produce these flowers as a beautiful demonstration of their technique, that all of this isn’t purely just for fun and games. Rather, if we can harness the basic principles guiding self-assembly, especially that of biomineralization, this will change the face of how nano- and micromaterials are made.

As of now, our go-to method for creating nanomaterials is by using lithography techniques, through which 3D structures are laboriously etched. Not only is this slow, it is also very, very expensive. Using the methods this group is developing, it will soon become possible to mass-manufacture complex materials for drug delivery, development of catalysts for chemical production, micro-circuitry, etc., by mechanisms of self-assembly.

The possibilities are truly… endless.

What is Innovation?

15 February, 2013 Leave a comment


OK, so I just stole the title of this post from NSF”s first episode of a series they produced in collaboration with the U.S. Patent and Trademark Office and NBC Learn, to explore innovations… and their innovators, around the US. In a fantastic collection of eleven videos, they cover everything from prosthetic exoskeletons (bionic limbs) and 3-D printing,  through smart materials, security, and automation. Ready to learn how these innovators came up with their inventions? Are you ready to be inspired? If so, check out the videos here.

STEM-STEAM is it time? Are we ready?

22 January, 2011 1 comment

STEM to STEAM Conference, hosted by the Rhode Island School of Design, 20-21 January 2011

I have just returned from a truly stimulating conference co-sponsored by RISD (Rhode Island School of Design) and NSF (National Science Foundation). The conference was entitled, “Bridging STEM to STEAM: Developing New Frameworks for Art/Science Pedagogy.” Attendees included everyone from artists and designers as far-flung as Japan, policy-makers and program officers from NSF, National Endowment of the Arts, and AAAS, accomplished academicians/designers from Brown, RISD, MIT… and then there was me… mesmerized, overwhelmed, and thrilled.

I realize this is not truly a direct discussion of biomimetics or bioinspiration, for that matter, but it is directly related. STEAM is simply a reimagining of STEM (Science, Technology, Engineering, and Mathematics) with Art added in, to signify a new initiative to push for direct collaboration and synergy of the STEM fields with the arts. It also creates a clever, catchy, new acronym. My concern is with the question of whether we, as professionals, academics, students, ready for this collaboration, or are we looking instead at the generation of exactly what the new name suggests: hot air? And if we are ready, what can we do to maximize the success of this wonderful collaboration?

My personal hope is that the combination of art with the sciences will inspire and catalyze progress in both fields. To me, the contribution that art/design can make to the sciences is limitless (and thus a motivation for this blog). In the most obvious connection, art can help with maximizing the visualization and communication of our science. In fact, ask Edward Tufte, and he will probably tell you that the best scientists also have an impeccable design flair combining aesthetics with efficient information communication. See, also, the Nature Methods Points of View column by the Broad Institute’s Bang Wong, for monthly commentary demonstrating how basic design principles facilitate data accessibility. I think all us scientists have a lot to learn from our artist counterparts.

Open source software such as Circos can be used to visualize genomic data in a visually pleasing way while simultaneously enhancing communication. Shown here are ChIP-Seq, chr 22 methylation, whole-genome methylation, multi-species comparison, human genome variation and self-similarity and MLL recombinome. (from Circos website)

A more challenging aspect justifying combining arts with the sciences is in identifying how art can actually accelerate scientific progress. An excellent example of this is the use of animation software such as Maya for pushing forward X-ray Reconstruction of Moving Morphology (XROMM) development, an increasingly valuable tool for biomechanical analyses. Art can also inspire new science, as shown in the PBS documentary “Between the Folds“, in which the ancient art of origami is inspiring mathematics, engineering, and product design.

I leave the challenge of identifying how science can help the arts, to the artists, who can speak more directly about why they would want us in their world… and not for the lack of having ideas about how we can help (think prosthetics and ergonomics, for starters!).

The challenge of the STEM to STEAM conference was to discuss how we can increase the collaborations, to identify the similarities and differences among artists and scientists, and to devise strategies on how to go about bridging the gap… priming the machine, so to speak, for a rather revolutionary change in the way we all think about and do our work.

If you are out there reading this, please weigh in. I would love to hear your thoughts about this matter.

And I now leave you with a video of a project co-produced by one of the conference attendees, Jonathan Harris, called, “I Want You To Want Me.” He is only 30 years old, and already very clearly quite a force to contend with.

Bionics in 1999

9 November, 2010 2 comments

The Fly-O-Rama created in the Dickinson Lab to study how flies maneuver during flight, by tethering fruit flies to a metal rod and giving them a virtual world to react to (see photo below for a tethered fly's eye view!).

I was rummaging through my electronic library today and came across a paper had I read over and over again in 1999 as a new graduate student with a nearly insatiable appetite. I am now realizing that it was right around the time this paper was published, that the seed of biomimetics was planted in my head. This article is written by a then faculty member at UC Berkeley (now at Cal Tech), by the name of Michael Dickinson. Even then, as a fairly new professor, it was clear that Dickinson was a rapidly rising star — one with amazing vision and a force to contend with. As the head of a fly neurobiology and flight lab, he was a pioneer in understanding the mechanisms of fly flight using self-created contraptions such as RoboFly and Fly-O-Rama, pictured above. I hope you enjoy and are inspired by this article as much as I was.

Photo courtesy of M Dickinson

The great stone house of Portugal

5 November, 2010 1 comment

Photo by Feliciano Guimarães

On the hillside of the Fafe Mountains in Portugal stands A Casa do Penedo, or “the House of Stone”. This amazing home is constructed among four large boulders with walls made of a concrete mix, created to melt the actual house into the flanking boulders. The windows overlook the mountains of Marão.

Although the home is built to blend into its natural surroundings, it still has the basic characteristics of a traditional home, with windows, doors, and a shingled roof, as well as creature comforts such as a fireplace and swimming pool, carved out of the side of a boulder.

Photo by Feliciano Guimarães

Apparently, the home was built in 1974 as a family retreat. However, with the overwhelming interest it has attracted due to its unusual design, the current owner, Vitor Rodrigues, has had to move to seek greater privacy. Also, as a result of problems with frequent break-ins, the home is now reinforced with bullet-proof windows, steel doors, and window grates. However, it apparently still contains a rather cozy interior, as shown by this video.

What do fish and ears have in common?

20 October, 2010 Leave a comment

I’ve got this great undergraduate student in my lab who is (at least for now) exhibiting all the traits of the ideal student any professor would love to have around: he volunteers ~10+ hours per week here, if no one is around, he finds things to do to teach himself new skills, he reads journal articles on his own accord that are aligned with interests of the lab, AND he’s creative! Lately, he has been trying to tackle a rather substantial challenge I presented to the lab: designing a force plate that can measure forces under granular media.


OK. Here’s the context: I used force plates to measure how hard and in which directions an animal is pushing when it steps on the ground. By combining this with measured movements of the animal that I quantify by analyzing synchronized high-speed video, I can calculate how much power the muscles must produce around each joint in order for the animal to move the way it does. This technology has been commonly used since the mid-1980s or earlier, for locomotion on flat, homogeneously hard surfaces. While we know a lot about how animals move across these types of “lab environment” surfaces, we know far less about movement over natural surfaces that may shift or change squishiness, orientation, etc. with each step.

Granular media, such as sand, therefore, is a particularly interesting material to me, as it actually makes state changes as an animal moves. For example, when sand is sitting undisturbed, it resembles a solid. Yet, when an animal strikes the surface and strokes through it with its foot, the sand actually becomes a fluid for a short while. Any sand that is kicked up during the step is actually acting like a gas! With all this in mind, measuring forces on sand can be a rather challenging conundrum.

In a meeting with my undergraduate student last week, he presented a design to me that involved peppering a surface with a grid of lumps that each could sense fluid movement. Little did he know, what he was showing me was something holding remarkable resemblance to hair cells, sensory receptors that are found in our ears AND in the lateral line system of fishes!


A haddock with the lateral line highlighted (black line running the length of the fish).


Ever wonder how a school of hundreds of fish manages to… school with such regularity and neat, synchronized prowess? The next time you catch that rainbow trout, sunfish, sailfish, or whatever strikes your fancy, take a close look at the side of their body and  you’ll see a series of dashes and dots that run from the rear side of the gill margin all the down to the base of the tail. These little holes mark the external opening to the lateral line, the pressure-sensing secret for fishes.


Detail of a lateral lines (the dots/pores on the scales). Photo by P. Spaans.


Within these pores are receptors called neuromasts. Neuromasts look a little like a thimble placed open side down on a table top. Each neuromast is made up of a group of cells called hair cells, named because they (grossly) resemble a Leprocaun troll doll, with different length hair bundles mounted on top.


Note the uncanny resemblance between the Leprochaun troll doll's hair and neuromasts!


The entire neuromast is covered in a gelatinous glob, forming a cupula. Deflection of these hair bundles due to changes in fluid flow causes the production of a receptor potential. Deflection direction also stimulates the production of different types and magnitudes of potentials, enabling the fish to determine the direction of the flow. Changes in fluid flow direction or pressure can be due to an underwater obstacle, a neighboring fish, or even a predator, enabling a fish to respond seemingly magically while the approaching object is still far away.


Anatomy of the fish lateral line, with a neuromast pictured on the right.



It turns out that my student (I guess not so surprisingly) was not the first person to think of using the neuromast as a biomimetic sensor: a group of scientists at the University of Illinois, Northwestern University, and Institut fur Zoologie have developed nano hair cells they call ALL (for artificial lateral line) that can localize the position of a crayfish placed in a tank. Take a look at their paper, published recently in Bioinspiration and Biomimetics. Call it bias or whatever you want, I am still excited to see where (if anywhere) my student will take this biomimetic idea of his. Let me know if you have any input on how he can potentially use this to invent a new type of force plate technology, and I’ll put you in touch with my student to try to make this a reality!

Janine Benyus at TED conference

28 September, 2010 Leave a comment

OK, so I know that some of you are a bit irked by Janine Benyus because her idealism is sometimes a bit too much (e.g., contrary to Benyus, nature really does generate waste, it is not in reality completely waste-free!). However, this TED talk still has a beautiful message that I wanted to share with you all.

Geeky dreams of an obsessed biomechanist

28 September, 2010 2 comments

There are countless stories (legends?) about dedicated faculty who conjure brilliant theories while showering, solve a major molecular roadblock while folding laundry, or dream up innovative interpretations of  complex data. Every time I hear a story like this, I have felt… so envious. But then I  would brush it off with the thought of, “Well, at least I’m not that big of a geek!”

My research strives to understand how we navigate through our complex universe with seemingly barely a thought. After all, how many of us have stood at the edge of a sidewalk in deep contemplation about how much we must flex our ankle, simultaneously activate our gastrocnemius and tibialis anterior, and then absorb the shock with the thick pad of flesh (and fat) on our heels combined with perfectly choreographed knee flexion, as we step down to the asphalt below? Should we have to go through such deep lines of thought, we would undoubtedly all go the way of the indecisive squirrel that gets 3/4 of the way across the road, just to turn around and throw itself under a tire in an effort to return to safety, rather than continue forth to the opposite side of the road a mere couple leaps away. To return to the point, we regularly move across a myriad of different surface types and barely notice it. To top it off, not only do we do it, there are tons of other organisms out there who do it better than we do. What’s going on?

To quantify movement across surfaces, my workhorse is something called kinematic analysis. This basically boils down to marking up an animal with a bunch of points (traditionally drawn on with correction fluid and a fine-tip Sharpie marker), filming with a high speed video, and then going through the record frame-by-frame clicking on each individual point across sometimes as many as 600 frames with 10-15 points per frame. Since our motion analysis is done in 3D, this means we then continue on to repeat this on a second camera (and in some instances, a third). Needless to say, this is a very time-consuming way to collect data, even when it is slightly automated with custom-written tracking software (e.g., see Ty Hedrick’s DLTdataviewer MATLAB program).

We recently purchased a super-duper auto-tracking high speed system to film our animal of choice: lizards. The system consists of six cameras that we mount in a ring, which automatically track reflective markers as the lizard runs through a calibrated filming volume. The amazing part of this system is that it literally can track up to 400+ points so accurately and quickly that we have all our tracked data the second the animal is done running through the field of view. The drawback is that we require markers covered in reflective 3M tape, which gets expensive fast, at $0.40 per mostly non-reusable marker. We are currently marking our animals up with 35-40 points, so burn through points at a rather high rate.

Chinese water dragon

A water dragon with nearly $17 worth of markers, most of which will get soaked off and destroyed in its water dish later that day.

At least one reason for the high cost of these points is that they are literally individually hand-wrapped. Yet, for us “non-professionals” in the way of sticker-wrapping beads, this can be a risky endeavor as the point is useless if it does not effectively reflect light. Additionally, wrapping beads can be extremely time intensive and mentally dull for anyone — including one of our undergraduate helpers — to do. As a result,  I have been in the midst of mental conniptions as of late, trying to figure out an inexpensive, easy way to build markers… all the while watching the dollars fall away as the lizards soak in their water bowls after a hard day’s exercise, destroying the markers so that they are unusable in future studies.

Water dragon model: lateral view

A side view of a tracked model of the lizard shown above running bipedally.

I woke up early this morning — too early by anyone’s standards at 4.30AM — and my brain started whirring. Perhaps it was due to the various discussions we have had in this course, or possibly it was due to one of our recent chapters from Janine Benyus’s book on Biomimetics, but I started seeing bubbles in my half-dream, half-awake state, and gradually began to realize (to my growing horror) that I had become a bona fide geek. These “bubbles” were actually phospholipid balls that were oriented with hydrophobic tails facing inwards and hydrophillic heads facing outwards. It was as if I had returned to Intro Bio my freshman year, only this time, it had really gotten in my head.

Liposome and micelle

When exposed to water, phospholipids will orient the hydrophobic fatty acyl side chains (tails) inwards, away from water, and their hydrophilic heads outwards, forming globules, or balls. Image by Mariana Ruiz Villarreal

As I was lying there confused, disturbed, and exhausted but still determined to stay asleep enough to continue this thought process while awake enough to remember it, I realized that if there were some way to attach reflective glass beads to the hydrophobic heads, I could drop this solution into water to form balls that I could use as quick and easy, highly-reflective markers. Of course, I would also need to find a way to make them solidify so they maintain their shape in air… but that’s just my cynical, awake inner voice talking.

Wispy weeping willows

23 September, 2010 1 comment

I consider myself to be among the lucky few in Philadelphia that get to both live in the city and also live on a large plot of land. My home is built on a 0.6 acre lot that is flanked on three sides by dense “forests” (i.e., unmaintained growth). This forest consists of quite the diverse flora, including introduced maples, pines, black walnut, cherry, and sycamore, as well as an understory dominated by a nearly equal mix of matted wild rose briars and poison ivy.

A gorgeous weeping willow tree that holds very little resemblance to our skinny backyard companion.

The centerpiece of our yard, and Rob’s pride and joy, is a rather Sideshow Bob-like weeping willow tree. Last winter, the unusual amounts of heavy, wet snow broke one of its primary branches off the main trunk, such that what used to be the crown of the tree draped over our lawn for easily 5-6 months before we finally managed to remove it. The lanky trunk and wispy branches that make the willow “weep”, combined with the thin halo of leaves form a deceivingly delicate facade on an incredibly tenacious plant. This enormous, 2 foot diameter branch actually began to heal itself during the course of the 5-6 months it braced itself against the ground! By the time we chopped the branch off in the spring, as it threatened to take down the rest of the tree in its fight to survive, it was sending out new branches and had actually even tried to root a section of itself to the ground!

The aggressive roots of willows are one of their most simultaneously beloved and hated traits. Those who hate the willow tree roots complain about the nearly magical ability for the roots to detect the presence of water, even through metal pipes, and will gradually bore their way through, repeatedly clogging pipes. In fact, there is even a blog dedicated to one such incident of a swamp willow that clogged water intake pipes, and continued to clog them even after the trees were chopped down!

swamp willow roots in pipe

An intake pipe clogged full with swamp willow tree roots.

Those who love the root’s determined hydrophilic nature plant these trees close to rivers, streams, and lakes, to control erosion on embankments. The complex root system wraps the soil, holding it in place, while presenting a zen-like tree above ground for all to admire.

The properties of roots are highly complex. They are very weak resisting compressive and bending forces, excelling in their tensile strength. In other words, roots are strongest when you are trying to play tug-of-war with them, which is precisely why they can be hard to pull out of the ground!

It turns out that the way the roots hold the soil in, is through a process known as edaphoecotropism — quite the mouthful to simply say “stress-avoidance”. In effect, wherever there are particularly high resistive or sheer forces, roots will turn and move down the path of least resistance. In short, what this means is that wherever there is a sheer plane in soil (i.e., one layer of soil moving relative to another), when the root reaches this layer of sheer, it will turn and orient itself parallel to the direction of sheer. Interestingly, what this does is transfer the sheer forces of the soil to tension in the roots, by means of friction of the soil along the entire length of the root. This tension causes the root to lengthen and deform, further increasing the surface area exposed to friction and making the pull out even more difficult.

A potential fruitful area of continued study would be to examine the precise mechanisms of edaphoecotrophism. We already utilize ideas of tensile reinforcement in many familiar materials such as clothing and fibreglass plates. However, I suspect that if we can harness the means of edaphoecotrophism from its sensory or even mechanistic perspectives, we may have some potential innovations for the fields of robotics or artificial growth of stronger construction materials.

Want to read more on soil reinforcement? Check out Simon and Bennett. 2004. Riparian Vegetation and Fluvial Geomorphology. American Geophysical Union.

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