Category: Jared H.

Thoughts and Reflections

Before I entered the lab for the first time, I expected a more typical experience as a researcher. I go to lab, set up my procedure, and then test to get results. It sounded new and interesting to me so I couldn’t wait, but I afraid that I would not be able to work with the high level researchers in the lab. When I first arrived I could see I wasn’t going to be doing such a thing. My first day in the lab wasn’t expected. Instead of immediately beginning tests, I got to see and involve myself in the entire process building a fully functioning research facility. We put together optical tables, built optics systems, and developed techniques to be used in the lab. Nothing was black and white. Every aspect of the process took thought, innovation, and flexibility because not everything worked how we needed it to from the start. My day was never the same. I didn’t just repeat the same process to try and get slightly different results and complete my personal research. I worked in a team of highly intelligent people who were working together to create a place where their research could be done. We tested different ideas to make our procedures and equipment function as they should and built a foundation that would strongly support the development of optical resonator biosensors. I found myself finding new challenges everyday working with extremely amiable colleagues who were always willing to answer my questions and explain set ups unfamiliar to me. I couldn’t have enjoyed my time there anymore. I learned so much and never felt belittled or ignored.  None of my initial fears were of any worry. I was reminded of processes used in a startup while working in the facility. I would love to be part of the same process in the future, and hope to find a chance to work in another optical lab in college.

I would to thank Erol and Jaden for helping me in the lab as well as Dr. Su and Dr. Masud Mansuripur  letting me work in the lab and learn about high level optical physics for my Senior Research Project.


How we Fabricate the Microsensors

We spent every day in the lab perfecting using lasers and flame to produce high quality sensors for our research. Each sensor consists of an optical resonator which in our situation was an optical microsphere and a waveguide or tapered fiber to let light enter the microsphere. Both components affect the overall quality of the sensor system. I will first describe the process of creating the microsphere through a reflow technique.


The base of each microsphere is created by removing the protective coating of an optical fiber, cleaning the newly exposed fiber, and cleaving the end so that the end of the fiber is flat and unshattered. This prevents any outside material from melting into the sphere and unshattered glass will melt into a smoother surface during the reflow process. With this base finished, we have to align the center of the laser so that it is a few hundred micrometers above the bottom of the fiber where we exposed the end. This is to introduce more material into the sphere when the reflow begins. The reflow begins when we turn on the laser. By shooting a beam of about five watts at the sphere for 20 seconds we are able to create a sphere of about 150 micrometers. The sphere develops because the glass is instantaneously melted when it is hit by the focused laser. Surface tension then causes the glass to pull upwards creating a droplet like structure. As heating is allowed continue, the glass has more time to set into a stable smoother form; however, if the glass is melted for too long, the sphere will become more ovalic as glass is vaporized by the laser. We found that about 20 seconds, the sphere has had enough time to set while also not taking an oval shape.

Fiber taper

The next process is fiber tapering. It’s a process that sounds easy, but is actually very difficult requiring more skill than you would expect. It involves cleaning the center of a strand of fiber by removing the protective coating, and then placing the fiber over a flame while having it pulled my two motors so that the center begins to shrink in diameter as shown above. The motors move the fiber in increments of micrometers at a time pulling the fiber thinner. As the fiber thins, the light of a laser that is shown through the fiber can be seen to start blinking. This effect is caused as the fiber changing from multimode to single mode. The fiber will stop blinking once it is a single mode. A this time the diameter of the fiber at the taper is less than 5 micrometers in diameter. The fiber is able to transmit light into optical resonators at close distances(less than a micrometer) at this size, but the fiber is also very fragile at this size. Too much vibration could tear the fiber and the process would have to begin again. The flame during this process can also affect the results. If the flame is too high or too low the taper will be incorrect or nonexistent. If you taper for too long the fiber will break on its own as well. All of these factors make producing and implementing the waveguides difficult throughout the tapering process.

With both pieces ready, we secure them into place under a microscope and attach the fiber to a sensor and a laser allowing for the sensor to be tested. Spheres need to be replaced with each experiment, but fibers last about a day while being used.

What are the Advantages of Microresonators?

Biosensors have become an important tool in health, safety, and scientific fields. The market for biosensors is highly competitive, but highly sensitive tests cost large amounts of time, money and training. The development of small and cheap devices would shake the market and create an accessible supply of technology to people in need. This is the potential microresonators have. They are extremely cheap to produce because they are made of miniscule amounts of glass. They can achieve results almost instantaneously, and would require no special training to operate. The devices could be the size of smartphones using disposable sensor chips to perform different sensings. Other less sensitive techniques have achieved devices of smartphone size, but microresonators can operate in real time while giving more sensitive results than any previous sensor for lower costs.Biosesnor device.png

Why are Biosensors Important?

Smell, taste, sight, sound, and touch. Our bodies are natural biosensors and highly sensitive to chemicals and dangers we commonly encounter in the environment. Food tastes disgusting, rot smells bad hot things burn, yellow and black suggest danger, and unusual sounds create suspicion, so why should we need to develop biosensors that do these functions for us? The answer is simple. Our world has changed faster than our senses have adapted. In the last 300 years technology has reformed our environment. We now have high quantities of poisons we can’t taste, creatures we can’t see, and gases we can’t smell. Methane and carbon monoxide are odorless and clear and colorless. Our bodies are unable to recognize them. Micro-concentrations of dangerous chemicals even with odor or taste are undetectable without external biosensors. These biosensors have the potential to save lives by finding these threats before they make an impact. Diseases could be cured faster and countermeasures can be prepared to prevent disaster. Biosensors are needed to protect people from the consequences of a technologically advancing society.5-senses

How Dangerous are Lasers?

I spent everyday in the lab for the past few weeks shooting high power lasers at microscopic materials, but how much risk is actually involved. Well, there were two lasers in my lab, a CO2 Laser and a small tunable laser. The tunable laser is of almost no concern with worst possible case being struck in the eye and blinking, maybe shedding a few tears. The real danger is the class 4 CO2 laser which has a maximum laser power of 75 watts. That beam possesses the same power as 15000 laser pointers. They are commonly used for cutting welding and engraving wood and metal. CO2 lasers also produce unseeable beams of infrared light. While in the lab, I only used the laser at 5% of it’s maximum power, but these dangers were always present. Making sure the laser was always aligned, removing anything that could reflect the laser from the beam path, and wearing infrared resistant goggles were essential to staying safe while using lasers. With all of these precautions, lasers must be pretty dangerous, right? Well, only a little. No one has ever died from a laser beam in the lab. Serious burns and eyesight loss have occurred during the operation of class 4(highest class) lasers.Superlaser2.jpg

In The Lab

After finally turning 18, I was able to enter and work in the optics lab. The lab, however, was not completely set up. None of the optical tables were operational, and equipment still hadn’t arrived. Throughout the rest of that week, I continued my research on cyanotoxins and microspheres.

The monday of the next week, we decided we would float the optical table. The several hundred pound table would be lifted from it’s legs with pressures between 50 and 80 psi. Floating the optical table prevents external forces such as vibrations from machinery and walking from affecting the optical system. We set up a system of pressure controllers and air filters to lift the table. After adjusting the individual pressures of the legs, we were able to get the table flat relative to the ground.IMG_2420

Two days later, we began to build our CO2 laser system. We used 6 mirrors, three of which were coated with zinc selenide to efficiently reflect infrared light, 2 pinhole positioners to precisely position both the visible light and CO2 lasers, a lense to focus the beam, a beam splitter and a flat top laser beam shaper to evenly distribute the wave’s energy. We used uv sensitive paper to see the laser as we adjusted the mirrors and lenses. The process took two days of tedious and meticulous work to get the beams accurately through the system. We then focused the microscope by melting a glass slide with the CO2 laser and adjusting the microscopes position until we found the spot where the laser hit the glass.

Once the system was completed, we decided to test it by producing microspheres from optical an optical fiber’s core. After some trial and error, we ended up shooting the laser for 1 second at about 3 watts to produce a small microsphere. We currently cannot calculate the quality (Q) factor of the sphere, but it was not large enough to be useful as a biosensor.IMG_2424

Now you are probably wondering what a Q factor is and what it’s purpose is (or not it’s up to you). Well, a Q factor for microresonators is numerical value describing resonators’ ability to maintain light with minimal decay. The longer it takes for light to decay, the better the resonator is at storing the light, the higher the quality factor. Finding this value is surprisingly simple. By finding the resonance wavelength of the microsphere and gathering data regarding the transmission of wavelengths close to but not the same as the resonance wavelengths, we can generate a lorentzian curve. The function can is used to determine the Full Width at half Minimum (FWHM), and then calculate the Q factor.

Example graph


The lab is almost finished, but until we receive the flow controller to manage the hydrogen, we find Q factors and produce microspheres.


Example Graph:

Weeks 2 and 3 Update

Throughout both of these weeks, I learned more about the technology I am developing while continuing my research on  cyanobacteria and cyanotoxins. The microsensors I am building worked by creating an evanescent field around a microtoroid by coupling an electromag magnetic wave from an optical fiber. The basic structure of the system is show below.Microtorid structure

In the above image, the electromagnetic wave resonates around the microtoroid at a measurable wavelength, creating the evanescent field. In order to allow the optical fiber to couple light to the silica toroid, the cladding is removed so that total internal reflection no longer occurs. Below is a diagram of an optical fiber.Optical fiber diagram

When particles bind to the surface of the toroid, the resonant wavelength changes and the energy being coupled from the fiber changes as well. This effect is measurable and can produce data such as the graph below.Resonant shifting

Each singular shift in this graph is a particle binding. The units of the shift in wavelength are femtometers or a quadrillionth of a meter. Each of the shifts is miniscule because relative to the size of the microtoroid, the particles are tiny. Below is an image of a microtoroid.

Microtorid image

The toroid has about the diameter of a human hair to put the image into perspective. Since the toroid is so small, bacteria will not bind to the structure effectively. Instead of focusing on the bacteria, I began to focus my research on the chemical outputs of cyanobacteria. In doing so, I found that there are several common cyanobacteria that produce a wide range of toxins of similar structure. The species is Microcystis which produces microcystin, a liver  toxin that may also be a carcinogen. There are approximately 80 know microcystins all of which have varying levels of toxicity. I also found a toxin called BMAA (beta-Methylamino-L-alanine) which is produced by a majority of cyanobacteria, but is more difficult to detect.

When I begin my lab work, I will be using the same concept of detection but instead of using microtoroids, I will be using optical spheres made by melting optical fiber with a laser. They bend light in the same fashion as the toroid but can be produced using the equipment at hand at the University of Arizona.

Want to Build a Microscope?

Do you have some extra time and are interested, or are you bored over rodeo break and need a project. Well, in response to a comment I received last week, I will explain how to build a simple microscope for under 15 dollars. It’s, as I said, simple. All it takes is three long quarter inch screws, 3 washers, 9 nuts, 2 winged nuts, a piece of wood, 2 pieces of plexiglass the same width and different lengths, a quarter inch drill bit, an led flashlight and a cheap laser. First we need to measure out where to drill on the wood and plexiglass. Place the two pieces of plexiglass on the wood laying flat where all three pieces share a lengthy side. On the side where the pieces line up measure 2 holes about an inch into the pieces from their edges. Then place a marking at the back and center of the two larger pieces forming a triangles. Now, you drill with the quarter inch bit through all of the pieces. Afterwards take the largest piece of plexiglass and drill a hole between the two holes that were just drilled on the same side. This is the hole for the lens, but currently, we do not have a lens. To get that lens, we will take apart the lens of the laser. If your laser is cheap enough, it should take nearly no effort to remove the lens. Once you have your lens, you have to make it fit into the hole you just drilled which seems easy, but definitely is not. If yours does not feel like fitting into your hole, you can spend some time shaving the edges of the hole you made with the drill. Before you put the lens in, you should try and figure out which side of the lens magnifies. If you are unable to figure that out, it doesn’t matter, you can flip the big piece of plexiglass around later to fix fix that issue. With that said, you should just stick that lens right in there. You can use a little force or a lot. I hit mine with a book. Once again as long as the lens is secured you did it right. The ends will justify the means. By now we have completed the only difficult part of this project. Now we put all three screws through the holes in the wood then put on the washers and secure them with a nut each. Then, we put on the winged nuts on the screws that share a side and the we place the smaller piece of plexiglass on top of those. The final step is to set the larger piece of plexiglass on three nuts that you elevate to about the top of  the screws and then secure them with the last three nuts. After checking to see if your lens the right way and nothing is slanted, gently place your phone on the plexiglass so that the camera aligns with the lens, place the flashlight under the lens on the wood pointing up, and you can safely say that you have a microscope. Mine ended up having a maximum magnification of about 35x magnification before it lost focus. You can measure yours by placing a ruler under the microscope and comparing the lengths of the millimeter markings. Hope you enjoy your new homemade microscope.

P.S. If you want to learn about Microscopy Staining to use your microscope more effectively, but also don’t want to spend lots of money on expensive dyes, the read this article.

Week 1 Update

My first week of my internship started at home with me researching where I could find cyanobacteria.  I concluded that I should be able to find some growing in sabino canyon and other parks in tucson. I hiked 3 miles into sabino canyon and collected two samples. After updating my advisor on my progress, she suggested I build a simple microscope to see what I found. After gather all the pieces and finding my drill, I quickly assembled my makeshift microscope.


I used it to view the samples of water I collected from sabino canyon, but was unable to find the cyanobacteria. I found mostly organic debri in the water.


Unfortunately, I was unable to go on hikes for the rest of the week due to an injury, so I decided I would look around my house to see if I could find any algae. Fortunately (or unfortunately because I may have to clean it), I found some algae in the fountain in my yard.



In this next week, I hope to find better samples to use when testing the sensors in the lab.

Label-Free Molecular Sensing

Label-free molecular detection is the detection of chemicals without the use of a label.  The Judith Su Little Sensor Lab specializes in developing methods and technology for analyzing nanoparticles without the use of labels. The goal is to remove expensive and complicated labels that pose the risk of changing the molecular properties of the unknown from the process of nanoparticle identification in order to decrease the expenditure of time and money in molecular detection. This decrease will allow for more research to be done in fields involving nanoparticles such as medicine and chemistry.

During my internship, I will be involved in the fabrication and testing of the label-free sensors. More specifically, I will help produce the optical resonators used for detecting nanoparticles. I will also be finding samples of water sources that contain cyanobacteria and preforming tests using both the new sensors and traditionally proven ELISA, a label technique for identifying substances using antibodies, to determine water quality and assessing accuracy.