The Return!

Yesterday the RET family was given the opportunity to get together and share how our experience has changed our teaching. Though some of the stories were unexpected, I came away motivated to try even harder to incorporate what I learned this summer. After spending the evening looking through the curriculum for ideal spots, I think I will add a PBL project to my unit on intermolecular forces (late December) and then another later in the year when we talk about reactions (I may try to bring our automotive department in on this).

It was also nice to share ideas with my peers. I am already trying to plan a STEM breakfast with my department head (based on Jessica's story) and am looking into how to better utilize our LabQuest data acquisition systems. I am already looking forward to our next callback!

From a personal point of view, teaching at Newton North has been amazing. I am constantly challenged on an intellectual level and forced to bring my A-game. There are things that I miss about English High, but this is a very different learning environment and I enjoy the change.

I have updated my website with the presentation I gave yesterday, please feel free to take a look and drop me a line!

All Good Things...

We are closing in on our final days of RET. All experiments are finished and it is now time to communicate our data, which is a crucial component of science. I've seen great experimenters hindered by their inability to get across their amazing results. Over the next few days we will be giving a presentation and a poster, both will expose us to questions from BU professors and graduate students (as well as RET peers). While it can sometimes be intimidating, the questions help push you to new learning.

Reflecting back on the last 6 weeks, I realize how far we have come in such a short period of time. Our biggest accomplishment was being able to get a good, repeatable thiol SAM on our chips. We spent the first week getting our feet wet, the next 2 stumbling around with a method that was incomplete, and the tail end getting positive results. Our biggest hurdle in this time was the cleaning/purging step in our chip making process. It took multiple runs and analyses to determine that we needed a change in method. With help from our advisors (no work is done in a vacuum, use your colleagues for advice!), we were able to get the process moving.

In the end, we were able to make SAM's with reproducible results over a range of different thiol solution concentrations. This is valuable because the amount of material used can be dramatically reduced and costs can be saved. We also found that the chips only need to incubate (sit in the thiol solution) for 6 hours, down from the overnight process it used to be. This will save time and allow for faster throughput (a single chip, from beginning to antibody layer, can now be done in a single day). I'd like to think our work pushed the project forward in some small way.

RET has been a great program, and one I'd recommend for any science/engineering teachers. It would be especially useful for educators who haven't spent much time in the research environment. We tend to view the fundamental principles we teach as well-organized sets of data, whereas research is often a "2 steps for 1 step back" process. It can be frustrating when things don't work like they are "supposed to" but it is rewarding to work through the problems and get results. The insight this provides is invaluable. Plus, it forces the teacher out of her/his comfort zone, making us remember what it is like to be a student. It is easy to forget that sometimes...

SEM

"This is mission control, you are clear for landing."








The quote above is an approximation of the first thing that came out of my mouth when I saw the scanning electron microscope (SEM). I was sure I had seen this in old movies of Apollo space explorations, but it turns out that the machine is a lot more contemporary than I imagined (less than 20 years old). And even for having that much age, I was amazed at the power.

An SEM is used to take high resolution pictures of objects. They can typically study features that are 10's of nanometers (about 1/1000 the thickness of a human hair) with striking clarity. To the left is an SEM image of an "trojan particle" from a paper I co-authored about 10 years ago. In photo "b", each of the smaller particles are less than 50 nm, yet they you can see them with ease. (The SEM used to take this picture had a different interface than the one we used this week, which is why I was so surprised by the control panel).




Using the SEM, we looked at the finer features of a nickel, examined the topography of different types of paper, and got up-close and personal with a fly. Part of the reason I teach science is to help students discover how cool it can be. We can actually see what a fly's eye looks like! Show me a student who doesn't find that interesting...

Positive Results and Technology in the Classroom

After 3 weeks of moving in fits and starts, we hit our stride this week. We were able to build a surface monolayer of thiol on our gold substrate and test it using FTIR. The peaks showed up with the proper intensity and position, so we feel confident that we can move on (My takeaway lesson from this is to get a good set of instructions early on so you are not reinventing the wheel). Next week, our last week of experimenting, will involve creating a concentration curve to determine the concentration where the monolayer starts to show incomplete packing. This will be valuable for the research group because it will minimize the material required to do experiments and add to the overall understanding of the system.

Our seminar today was on implementing technology in the classroom. In my short time as an educator, I have gone through many similar discussions, all with the theme "USE TECHNOLOGY!" However, more often than not, the suggestions would be impractical or laughably low-tech (Powerpoint?). Today's seminar was a refreshing change of pace. Our presenter was well informed and took us beyond the normal Teachertube/blog entry points. The most interesting site she showed us was voicethread.com, a site that allows you to post interactive movies/lessons/etc. I have wanted to podcast lectures this year, and this site will allow me to do this with ease. Students will then have a chance to post replies directly to me and/or make their own video/photo response. Direct implications for my teaching = yeah!

50% Already?

It is hard to believe that tomorrow will mark the midpoint of the summer RET experience. Time flies when you are having fun!

I spent the morning at home today, combining video clips I had made about the experience into a single movie. I hope it gives a little feel to the research we are doing and what it is like to be an engineer. Sadly, my direction and editing doesn't do it justice: research is exciting.

http://www.youtube.com/watch?v=ZtYUjb9oPx4

Today was also special because my family came in to visit the Photonics center. Here is a picture of me with my son in our lab. It's never too early to start training the next generation!















In terms of our experiments, we have been gathering a lot of data, but it has been... inconclusive. Our monolayer thicknesses are low, but close to what is expected. Our FTIR analysis shows the peaks we are looking for, but not with the magnitudes we expect.

So what do we do?

Solving problems like this is where an engineer earns her or his salary.

We have decided to take a dual pronged approach. We are going to move forward with some of the chips that we have made and add the final layer. We can then test with the ellipsometer and FTIR to get an idea of how the bonding went. It MAY be that we have sufficient covering of the chip (despite our mediocre results). While doing this, we will also be testing different thiol solution concentrations. The thought being that if we soak the chips in a high molarity solution, we might get better bonding on the gold surface (and thus a better gold monolayer). We should have some preliminary results as soon as tomorrow and from there, we will analyze the data and make decisions about future experiments.

The Reality of Research

As you get farther away from life experiences, certain specifics tend to fade. The big lessons remain, but some of the details drop from the forefront. It has been 3 years since I have worked in a research lab and the idea of how to do research is still fresh (hammered home by an excellent lecture by Dr. Selim Unlu this week), but the ease with which projects can be delayed slipped from my memory. I often tell my students that science requires patience and my partner and I have had to exercise our own this week.

In our quest to create a multi-layered chip that can be used to detect viruses and proteins, we have hit a series of minor roadblocks. Our first thiol monolayer experiment appeared to go smoothly. Theoretically, it should look something like this (the red represents the sulfur group):












(image from http://www.personal.psu.edu/acs5112/ART101/art101ass5.html)

But the question is, how can we determine if this actually happened? The molecules are so small that we have no method to actually see them aligned as they are above, so we need to measure them indirectly. The first way we do this is using an ellipsometer. This apparatus measures the change in polarization of light after it is reflected off of a surface. This change, when coupled with a refractive index, can give you the thickness of the deposited layer. Our results came out to be a reasonable 1 nm (to give some perspective on the size, 1 nm is to the thickness of a human hair as 1 football field is to the distance between New York and Los Angeles). So we were confident that we could add layers 2 and 3. I will delve into more depth about these layers in future entries, but they will end up being used to bond the antibody of interest to our surface. The application process went smoothly, but when we went to check the new thickness of the ellipsometer, we ran into speedbump #1. The ellipsometer was down and the one person who could help us was out of the office. I had forgotten how frequently this happens in research, but instead of getting frustrated, we used the time to do more background reading on the topic. The delay allowed me to become more knowledgeable about my topic. With our short timeline, we feel rushed to move forward, but we forget that it is better to gather all information at each step in the process.

Speedbump #2 is getting trained on the FTIR (Fourier Transform - Infrared Spectrometer). While the ellipsometer tells you the thickness of the layer, it doesn't identify what is on the surface. We use the FTIR to tell use exactly what is on the surface (though it doesn't tell us the thickness, so we need both measurements to be sure). The FTIR is a complex machine, but in short, it emits a beam of infrared light onto the sample. The sample absorbs specific wavelengths depending on the bonds that it contains. The FTIR reads this absorbance pattern and can help us determine what we have. As is common with many analytical devices, it is tricky to use, so we need expert training (which we will get next week). Once this training is completed, we can test our chips to confirm that we have deposited the material correctly.

These 2 delays aside, the experimental plan is coming together nicely. Our first testable question is "Does our procedure provides consistent samples?. If we are successful, as judged by our ellipsometer and FTIR results, we will move on to "Can our chip be used to capture a specific protein?" This will involve a new set of tests, with a new set of vocabulary, but it is exciting to think of the possibilities!

Getting Work Done!

We made something yesterday.

In fact, we made 2 somethings!

We spent the morning in the clean room, a place where we have to wear layers of clothing, not to protect us, but to protect the equipment from our skin/hair/bodily dirt. Microchips are in all of our electronic devices, and this is the environment where they are made/researched.

Our first step in the clean room was to take a glass wafer (basically a piece of glass) and spin a chemical on it. The chemical is called photoresist and is made up of a material that is sensitive to certain light. After we put on the photoresist the chip was heated for about 1 minute (called the "soft bake") and placed in a machine to expose the photoresist. The machine contains a mask (which can be thought of as a stencil) and only the areas where light passes through are exposed. The light reacts with the photoresist to create a new substance with different chemical properties. This means that it cannow be put in a solvent that will selectively remove the area that was exposed (or, in some cases, the areas that weren't exposed). After removing the exposed areas in the solvent, we could see some of the features that were made. The chips were then stored for future use.

I went first, and made some mistakes... Below is my first chip where the photoresist was not spread equally (though it is hard to see the imperfections). This means that there are areas of different thickness, which can cause problems down the road. The second chip came out better, hopefully it will work as we move forward.












In the afternoon, my partner Valentina and I tried to make our first monolayer of thiol on gold (which is part of our main project). It started slowly (we needed to call Carlos, our post doc leader, to find out where the vials were... which is the absolute first step in the process). But from there we were pretty independent. We will analyze the chips today to determine if we did it correctly. Is it okay that I'm nervous?

Below is a picture of the chips as they were being cleaned.