Optomechanics Are Rad - Part II

In my last installment, I described the construction of a dip-coating apparatus for applying thin films onto the tips of optical fibers.  With that out of the way, the next step involved the construction of an optics system for measuring the fluorescence produced by a thin film on the tip of an optical fiber.  And so that's what I set about doing today.  Similarly to the dip-coater, I started with a clean breadboard.  Because I am measuring fluorescence with this system, I wanted to minimize any stray light, so I enclosed the breadboard within a black box.  The box is hinged in such a way that the top and front can be opened.

Inside the box, I put my detector - a handheld spectrometer (left) - and my light source - a blue laser (right).  Not shown is the laser's power supply.  This unit is somewhat bulky and, since it doesn't necessarily need to be inside the box, I left it out.  By the way, I apologize for the blurriness of these images; this is the product of a mediocre phone camera combined with shaky hands brought on by a bit too much morning coffee.

I decided that I would take all of my measurements by submerging the fiber tip into a fluid sample, into which I could then inject the analyte that I'm trying to detect and thus monitor any change in the fluorescence output in real time.  I also wanted to illuminate the fiber tip with the laser transversely - or perpendicular to the direction of the fiber - by slicing the laser's coherent beam directly across the tip of the fiber to maximize my excitation intensity.  In order for all this to work correctly, I decided to use a cuvette to hold the sample, therefore minimizing scattering as the beam enters the liquid sample.  So I put a cuvette holder into the box and secured it in place using a few breadboard mounts.  Then I aligned the laser so that the beam was directed through the center of the cuvette holder and bolted it into place.

With the cuvette holder and laser aligned and anchored onto the breadboard, I then needed some way of holding the fiber in place.  In order to make sure that each fiber could be accurately positioned into the path of the laser, I bolted two micro-manipulators onto the breadboard to act as the base of the fiber holder while also allowing me to adjust the X and Y position of the fiber.

Onto the micro-manipulators I then added a fiber holder.  The fiber holder seen in this image came more-or-less preassembled.  The lower section has a turnscrew that clamps the fiber in place and I added the tube seen in the upper section to help keep the fiber straight as it enters the cuvette.  Astute observers might notice that the fiber holder I've used is manufactured by Newport, whereas pretty much every other optomechanic component I've used is manufactured by ThorLabs.  What can I say?  The Newport fiber holder was all I had on hand.  It was a bit of a pain in the ass getting it secured to the ThorLabs components because the dimensions and threading are different between the two manufacturers, but I got things worked out nonetheless.  And once the fiber holder was in place, the whole thing was finished.

To test the system out, I popped an empty cuvette into the cuvette holder and threaded a fiber through the fiber holder and down into the cuvette.  I attached the other fiber terminus - the one with the SMA connector - to the spectrometer and turned on the laser.  Then I used the micromanipulators to position the fiber tip directly into the beam of the laser.  You can see in the picture below that once the laser was incident onto the fiber, the blue laser light was scattered everywhere and fiber tip seemed to glow bright blue.

If there were a thin layer of my novel fluorescence sensor material on the tip of the optical fiber, which there is not because this was just a spare fiber that I found lying around, it would emit a bright green fluorescence when excited by the laser.  The fluorescence emission would be guided through the fiber and into the spectrometer.  The spectrometer is connected via USB to a laptop computer equipped with software that shows the real-time fluorescence spectrum being sent through the fiber.  And there you have it.  Pretty easy to set up and use.  By using a coherent light source along with a fluorescent sensor material coated directly onto an optical fiber, I've negated the need for lenses or other optics.  Once you start adding lenses, alignment becomes a major issue, and the components have to be aligned and adjusted precisely.  On the other hand, this system required only minimal alignment and went from a clean breadboard to a fully functional optical measurement system with about 2 hours of build time.

Now you can hopefully see why these optomechanics systems are so fun.  Once I finished building, part of me wanted to break the whole thing down and start over.  Just like I did with my LEGOs when I was a kid.

Optomechanics Are Rad - Part I

There are a lot of fun things about my job.  And I'd like to devote a couple of posts to one of my favorite aspects of developing optical sensors.  One challenge that arises occasionally is when the optical or fluorescent analysis instruments that we have on hand in the lab are not sufficient for analysis of the optical sensor platforms that I've developed.  This is often the case when dealing with flat, planar substrates onto which a sensor architecture or layer has been applied or when we apply a sensing mechanism onto the tip of an optical fiber.  When this happens, I have to build a bench-top optics system using our inventory of detectors (PMTs and hand-held spectrometers), light sources (LEDs and lasers), and optomechanics components that we keep in the lab just for this type of situation.  And let me just say this:  building a bench-top optics platform is outrageously fun.  It's like playing with LEGOs.  But these LEGOs are bigger, studier, and able to achieve precise alignments.  They also cost thousands of dollars.

My research project is nearing a point at which we will begin applying our fluorescent sensing material onto optical fibers (I'll discuss the application of a sensing mechanism onto optical fibers another time).  This has left me with a couple of specific needs that must be addressed before the project can move forward:  1) the sensor material must be dip-coated onto the optical fiber tip and to do this, the rate of withdrawal of the fiber tip from the precursor solution must be kept constant at a particular rate, and 2) I have to have some way of accurately measuring the fluorescence emission from the layer coated onto the fiber tip.  In this post, I'm going to focus on the dip coating apparatus.  As it turns out, the optomechanics components that are used to build bench-top optics systems are also quite useful for constructing a home-built dip-coater.  Here's how I did it:

First, I started with a plain breadboard.

Next, I bolted one large post into the center of the breadboard.  The large post allowed me to align the entire system vertically.

Onto the post, I clamped a small system of rails.  The top and bottom of the rails are secured using filter/lens holders.  I used these because they have large holes cut out of their centers.  In between the two filter/lens holders is a modified filter/lens holder that has a small metal cylinder attached with epoxy.  The cylinder is just the right size to a hold a 4 ml vial - and this will hold the precursor fluid that is to be dip-coated onto the optical fibers.  While the top and bottom holders are clamped tightly to the rails, the vial holder in the center was left loose, allowing it to slide up and down the rails freely.

Above the rail system I added a small v-clamp.  The clamp will hold the optical fiber in place during the dip-coating process.

Last, I added a small actuator and the accompanying controller.  The actuator moves the vial holder up and down, like an elevator.

When I clamp an optical fiber into place, you can hopefully see how this apparatus works.  The fiber is submerged into the fluid to be dip-coated onto the exposed tip.  Then I just flip a switch on the actuator and the vial holder slowly descends, withdrawing the fiber tip from the liquid.  When the fiber tip has been completely removed from the fluid, it can be removed from the apparatus and the thin layer that has been deposited on the tip is allowed to crosslink and/or cure into a solid film.

Now this setup was pretty simple.  And because no light sources or detectors were involved, alignment of the entire apparatus was not a big deal.  I just needed the little elevator to withdraw the fiber from the fluid at a constant rate.  My next project - which I'll be working on over the next couple of days - will be to build a system for measuring the fluorescence of the thin film dip-coated onto the fiber tip.  This will be slightly more difficult, though using the fiber itself to gather the fluorescence emission does make things much easier.  But more on that to come.

Should I Stay or Should I Go? - Update Style

In regard to the question of whether to start a new blog, thereby leaving this one to a die a quick death, my abnormally beautiful and supremely intelligent wife offered to co-author a blog related to bicycles with me.  Having a co-author would allow me to worry less about posting regularly on the new blog.  This means that I might indeed have enough time to continue updating this blog, while also occasionally posting on another.  So as for now, I am going to keep this blog alive with semi-regular updates.  If it begins to look like I can't keep up with both blogs, I'll make an executive decision at that time.

So it looks like I'll be starting a new blog with my wife.  My wife will author posts focused on cycling fashion - particularly with respect to office-appropriate clothing that is feasible for a bicycling commute.  This is more or less the content of her current blog, which is very good.  She'll also include tidbits about her daily commute.  This is also a feature of her current blog, and most of the notable moments during her commute consist of encounters with asshole motorists.  My posts will likely also include information about my daily commute - dipshit motorists and all - but I plan to focus more on bicycle repair and restoration.

With the holidays imminent, I'm not sure when we'll get the new blog up and running, but I'll post a link to it here when the time comes.  In the meantime, I'll try to keep the science-related updates coming as best I can.

Should I Stay or Should I Go?

I've become a regular reader of a motorcycle blog called Chin on the Tank.  Although the theme is cafe racers and similarly-styled vintage motorcycles, the content varies quite a lot.  The author has a workshop and is a skilled photographer, so he takes a lot of pictures of his shop and the bike projects that he works on.  He also includes information on the local cafe racer scene, promotes motorcycle events, and documents group rides.  It's a fun blog and it's made me yearn for a vintage motorcycle.

Why am I bringing this up, you ask?  Well, as I've mentioned before, I am a bicycle enthusiast of sorts.  In particular, I enjoy restoring older bikes and putting them back on the road.  In my garage I essentially have a fully functioning bicycle workshop and I spend a fair amount of time working on my personal restorations, as well as a pretty steady stream of projects for my friends.  And so I'm considering starting a bicycle blog.  On this blog I would document and detail the projects that I work on.  Posts would include a lot of photographs - particularly before-and-after images of full-on rebuilds.  And I would try to include a lot of information on the restoration process, costs involved, problems and challenges that I came across, etc.  I would probably also talk about group rides that I participate in, and discuss any notable events from my daily bicycle commute.

The reason I'm mentioning this here is because if I start a new blog, it is unlikely that I would be able to continue updating this one.  There are only so many hours in the day, and I'm unable to spend much of them writing blog entries.  I should note that there are a number of other good science blogs out there, whereas I have been unable to find a good bicycle restoration blog.  On the other hand, I sometimes go fairly long periods without having any bike-related projects, and the cold Missouri winter can really cripple my motivation to work out in the garage.  So updates might sometimes be sparse (though it's not like I'm doing a great job of updating this one consistently).  A few things I should note about this:  1) it's likely that a bicycle blog will motivate me to spend more time tinkering in the shop, 2) I can always ditch the new blog and pick this one back up if things aren't working out the way I had envisioned, and 3) I have a fairly substantial back-log of projects, so I could fill the gaps in current projects with old projects that I've worked on in the past.

Thoughts on which direction I should go?  Let me know...stay the course or try something new?

That. Was. Unexpected.

An article at ScienceInsider is reporting that the new spending bill proposed by the House of Representatives is a little more science-friendly than one would have expected.  Not only are the National Institutes of Health and the Department of Energy slated to receive modest budget increases in this bill, but Rick Shindell of SBIR Insider is also reporting that SBIR/STTR program funding has been reauthorized for another 6 years as part of the National Defense Authorization Act.

This is definitely a glimmer of light in what has been an otherwise dim season for scientific research and education funding - see here and here - but I'll definitely take the good news wherever I can find it.

The End of Movember - Update Style

As I mentioned in my previous post, I did indeed shave my moustache on December 1, signifying the end of Movember.  Now that the moustache is gone, I'll be working on my winter beard.  Here is a picture of me without the moustache - not totally clean-shaven, as I was sporting four days worth of growth when this picture was taken; but not looking particularly bearded, either.

I should note that this picture, along with the last one I posted in which I am sporting the moustache, were taken by my lovely wife and featured on her blog, CoMo Cycle Chic.  I should also note that her blog is a lot better than mine.

Anyways, subsequent to last week's post, I received a comment regarding an additional issue concerning beard wearers:  hygiene.  But not just any normal old pirate-on-the-hair-ship hygiene.  The journal article that was brought to my attention by my colleague and good friend KP is titled, 'Microbiological Laboratory Hazard of Bearded Men.'  This study examined the risk that a beard poses to exposing the wearers' friends and family to potentially dangerous microorganisms.  Of course, this only applies to microbiologists or other laboratory workers who often come into contact with such dangerous organisms.  I don't commonly deal with harmful species of bacteria, so this isn't much of a concern for me personally.  But for all of you bearded microbiologists out there:  beware!  You may be exposing your loved ones to more than just unfettered manliness!