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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.

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