Research Journal

21 June 2006

Mike, Stephanie and I have been at Stony Brook for about a week now so I guess its time to start our journals. So far we don't have any individual projects to work on. We have spent much of our time reveiwing optics and Dr. Noe has also given us many demonstrations with lenses, lasers and various optical toys. Dr. Metcalf has also given a few lectures on laser cooling which we and a few soon to be graduate students attended. I suppose the most basic, important idea is that atoms will absorb light of a correct frequancy, and this light will transfer momentum along with energy. The linear momentum will then slow the atom down, thereby cooling it. I think one of the most interesting aspects is that the atoms have to be cooled down to about 30 mili Kelvins before you can use the laser system to cool them down to micro Kelvins. Dr. Metcalf also told us that an important application of laser cooling is for atomic clocks.

Yesterday the REU program arranged a luncheon during which many heads of departments talked to us about grad school. They discussed the application process, GREs and what people look for in a grad student. It was a very informative meeting and everone picked up nice booklets on the various grad programs. I picked up physics, engineering, and biophysics, since I still don't know what exactly I am interested in. Later that day Reinhold Blumel from Weslyan University visited and gave us a short talk on his interests and experiments in physics. He reveiwed the Schrodinger equation for a partical in an infinite square well, and the wave nature of matter. He then explained that he was trying to link together classical and quantum mechanics using density of states.

Oh, and earlier that day Maaneli took us to where the phsyics department has liquid nitrogen on tap, and we played with that for a while.

29 June 2006

I am finally done with my presentation!! The highschool students started this week (victor, matt, hamsa and scott) and we undergrads had to give them presentations, hopefully catching them up in their knowledge of optics. Stephanie did a power point on complex numbers, i did mine on Fermat's principle and ray optics, and Mike is presenting today on interference and diffraction. We also went to David Cardoza's PhD defense yesterday, which was very interesting. He works with short pulse lasers, studying the controlled breaking of bonds in molecules (in extremely simple terms). Sooooo now i have to get back to thinking up a project. Also, Happy Birthday Anna :-) .

7 July 2006

This week was a short one due to the 4th of July holiday. Over the holiday weekend I went to Rumney, NH to go rock climbing with some friends from Uconn. There is pretty much no climbing on long island, so I am very out of shape. I will have to frequent the gym to maintain my upper arm and shoulder muscles, and run on the treadmill to get endurance for the hikes to the climbs. One of the approaches to the climbing area was ridiculous; very steep and hard to do carrying gear etc. I'm just very out of hiking shape.

During the three days of work this week I've been looking on line, hoping to find something interesting to base a project off of. I'm very interested in materials, but it would be a good idea for me to do something related to microscopy since that's what Dr. Gibson is working on (what I'll be doing for my senior honors thesis). I'm probably changing my major to Materials Engineering Physics, so maybe next year I'll do an REU in the material science field :-) .

10 July 2006

Lately I've been reading about various types of microscopy on line trying to think of a project idea. Marty Cohen had suggested doing something with confocal microscopy, at least maybe setting up a one of the microscopes objectives we have to simulate it. Usually flourescence is used where a focused point of light is scanned across a specimen and the flourescence is detected by a photomultiplier which creates the image on a computer. The flourescent light is sent through a pinhole before going to the photomultiplier, to clean it of secondary flourescence, creating a much clearer image. I also read about phase contrast and differential interference contrast microscopy which use the different indeces of refraction of the specimen to create an image. Total internal Reflection microscopy creates an area of total internal reflection in the microscope slide, so that only the evanescent waves cause the specimen to flouresce. Since the evanescent wave field is only about 100 nm "thick" compared to the 1000 nm that confocal microscopes usually penetrate into the specimen, there is less secondary flourescence, giving a better signal to noise ratio and a clearer image. However, I'm not sure if anyone has made a TIRM yet, the website I was at only gave the theory, and didn't mention any working microscopes or current research using one. I'll probably look into that tomorrow.

Dr. Noe juat mentioned the interesting topic of Moire magnification, so I'll probably also research that tomorrow. Stay tuned for that journal entry. Now I'm off to dinner.

12 July

So I looked into Moire magnification but couldnt find much explaning the actual concepts. There were a couple articles about using the technique to look at errupting molars, but nothing i could use for a project yet. I did come acroos a few nice sites that have fun applets about the Moire phenomenon (see link). Then Dr. Noe and I played with an optical fiber for a while. He notices that when you hold an optical fiber right up to a two dimensional diffraction grating like the 3-D glasses an interesting checkerboard pattern appears. He is not sure why this happens: Dr. Metcalf suggested reflections off the grating, so i that is an idea for a project or mini project for people if more information can be found. Dr. Noe later told me to look into phase contrast microscopy becaue he found a paper that might give an easy experimental setup. He also told me to lok into the Abbe theory of diffraction in a microscope and inverted optical tweezers, since they have previously worked on a normal optical twezers set up.

July 14 2006

Well i don't quite have a project yet, but i'm hoping I can find a way to make a phase contrast microscope. The Strong book on optics said they made a phase plate by scoring a normal plate of glass with some HF, so maybe I can look online and find more simple ways to make a phase plate. Dr. Cohen suggested that I could probably also find a coated peice of glass and remove the coating from the middle. I didn't get to look into simple phase plates today, so i'll probably do that monday or over the weekend if I get a chance.

I've also been reading about Abbe's theory and his resolution limit equations. Yesterday I found a very good pdf file about his theory and what is sometimes missing from college optics textbooks, so once I have that all read and understood I'll put a link to it on my links page. I also spent a while yesterday and a little today revising my links page. I have a template from Lidya's website, and I still have to get rid of her Talbot links and add a few more of the sites that I've found. From working on the page, however, and writing in this journal, I'm quickly getting the hang of using linux and html format. OH, and I read about numerical aperture, which is related to the size of the finest detail that a lens can resolve, and F number (focal length over diameter of the lens), which is used in photography a lot. The numerical aperature is related to the F number by the expression N.A = n/2F. So a large F number means a smaller numerical aperture (in photography you can take n as 1, since the light is just traveling through air into the lens.) Mike brought in his juggling balls for a little while one day, so I also learned how to juggle; that was fun.

19 July 2006

So we have finally decided that my project will be to work on inverted optical tweezers. Dr. Noe and I decided this about two days ago. I had been looking into phase contrast microscopy, but Dr. Noe returned from a visit to Kiko Galvez's lab at Colgate very excited about using optical votices with optical tweezers. Since anything dealing with microscopy would be beneficial to me for my senior thesis next year, making optical tweezers should be an interesting project. The idea right now is that I'll set up the microscope in a normal way to observe the Brownian motion of some particles, and basically get a refresher on using a high powered microscope with oil immersion. Hamsa is going to work with me on this project since she has (among many other things) been looking into optical vortices. We will then set up an inverted optical tweezers (the LTC has done optical tweezers before but with the infra red trapping light coming from above). Dr. Noe has plently of micron order polystirene spheres and yeast cells for us to look at. Possible we can crush some calcite crystal and cause the birefringent particles to spin by sending circularly polarized light through. Or, as Dr. Galvez is doing, we could use the orbital momentum of an optical vortex to make the dieletric spheres travel around in a circle. Today Hamsa and I just took apart what was left of the last tweezer set up and cleaned the whole area, including all the slides with dried samples on them (yuck).

21 July 2006

Today Hamsa and I got a light source and put together a normal microscope using a high intenscity fiber optic light source, microscope stage and objective, and a CCD camera to image a specimen. We spent a while putting this together, (clamping the fiber optic cable in place, positioning the camera, etc.) and then mounted different people's hair on a slide to observe them. Next we will make a yeast sample to look for brownian motion. Hopefully early next week we can set up the optical tweezers. I will work with Hamsa on designing this and then setting it up, we are not working in a very big space, so the direction and dimensions of the system will have to be planned.

27 July 2006

Well I havn't written in my journal for a while because I've been so busy, so this entry will span a few days. Hamsa and I calculated the total magnification in out optical system using the 100X lens. The focal length of the objective and camera lenses are 1.6 and 16 mm giving a magnification of 10 onto the CCD camera element. From the CCD element to the TV screen is 50 times magnification, so this gives an overall 500X from the microscope stage to the screen. The magnification of the image from the camera to the monitor was determined by placing a 1.4 mm slit directly in front of the CCD element (or as close as we could get it, about 1 cm away), illuminating it with a fiber optic cable at a distance of 4 m and measuring the size on the monitor. The 10X magnification from the stage to the element was checked experimentally by measuring the slit distance in the 3D glasses diffraction grating by looking at it under the 100X oil immersion objective, and by measuring the diffraction pattern from a laser pointer (532 nm), calculating the slit distance by d sin(theta) = m (lambda). On tuesday the rest of the REU physics student came for a tour of the LTC. Hamsa and I showed them Brownian motion in yeast, and the rest of the LTC people explained their projects. Yesterday, Dr. Metcalf said he had some random microscopes hanging around and he actually gave us a Nikon inverted microscope, taking out almost half of what we needed to build. Dr. Metcalf is AWESOME. Today Hamsa and I found the correct cylinder and spherical lenses and set them up on our optical table. None of the cylindrical lenses were labeled, and lots of the spherical ones aren't in their correct places, so we had to go out side and measure a lot of foci using the sun, to find the correct 2:1 ratios in our lenses. We are working on getting the laser up and running- YiYi has a goo explanation of how to work it, but the power source she used is now on Maaneli's table. Dr. Noe has two 24 volt power supplies that we will have to wire to the laser control box, and have someone also build in a plug. I have no idea how to do anything electrical, so getting the laser into operation might be slow going. I also can't find the pieces for the periscope people had been using in the tweezer setup, but if I can find that Hamsa and I can build the rest of the tweezer tomorrow. Then I will need to find the infra red veiwing card, which people remember seeing two weeks ago but is missing now, and align the laser- once we get the laser running.

28 July 2006

The two little 24 volt power supplies would take too much time to hook up, so we're just using the power source that was used before. Hamsa and I took a very long time toset up the fiber optic light source, but it diverges so quickly, it doesnt work very well. Luckily, Dr. Cohen took the light source that came with the microscope and hooked it up to a different power source using some wires, beacuse we didnt have the proper plug. The light source needed a 12 volt power supply and we just happened to have one nearby. The tweezer set up is complete, the cylinder lenses shrink the beam on the x axis, then spherical lenses expand the whole beam. the beam enters the microscope by reflecting off of a dichroic mirror.

31 July 2006

Today the REU students got a tour of BNL. We got to see the Phenix detector at RHIC, the light source, and technology division (or something like that. It was freakin sweet- shows us what kind of a place we could be working at in the future. When I got back from BNL I got a phone call from Hamsa telling me that they tested our infra red laser today and it was only producing 3 mW, where we should have 20. So I came in to the LTC and stayed until about 12 am fixing the set up. I tested all the other lasers in the lab and took the highest power HeNe i could find (Mike's). I created a new setup which disposed of the cylinder lenses since the beam from a HeNe is already circular. I also had to change the enlargment ratio from 2:1 to 4:1. The beam is now aligned, and we will hopefully get the illumination aligned tomorrow.

Karen Cydylo

karen.cydylo (a)
Laser Teaching Center