Ankur Week 2 Post 2

As with any lab, there are problems. Many many problems. For project 2, described in my previous post (Week 1 Post 2). The objective was to take the underground gas, pass it through the Zeolite filled tank, and fill a small chamber with the filtered gas.

 Zeolite is a type of molecular sieve which traps mostly Argon and Nitrogen molecules and allows other gases to pass through it. It just looks like a bunch of small beads, for more information: http://en.wikipedia.org/wiki/Zeolite.  In this case, in order to increase the concentration of the Helium in the underground gas sample we wanted to remove as much of the other gases in the underground gas so it would be easier for the scientists in Harvard to analyse the Helium.

So the process began; we cut our own copper wire, attached our own fittings, fit our valves, tied strings to support the plumbing, and used nothing more than wrenches. Of course, we did not want to contaminate any part of the copper tubing or fittings so we had to carefully think about how we would go through with the plumbing. Unfortunately, (you'll see why it is unfortunate later) a part of the plumbing had been started earlier by Geoffrey and Dr. Calaprice. We added on to this hoping it would make the process faster.

So we completed the plumbing for the underground gas to pass through the Zeolite bottle, trigger a pressure gauge, then enter the small chamber which we would send off to Harvard. However, in order to increase the purity of the system we wanted to purge the whole system with a gas previous to allowing our precious underground pass through it. So originally we decided to purge the whole system with Argon gas. The idea was to use an inert gas to purge the Zeolite bottle and copper tubing via pushing all the other unwanted gases out of the system. Then after purging it we would have to pump down to pull all of the argon out of the system so we could pass the underground gas.

The Zeolite bottle was pretty large, probably like a 20-30 liter bottle. When we purged the whole system we passed Argon through the Zeolite and then vented it out to air to let it out. We knew that Argon would become trapped in the Zeolite and we hoped we could saturate the Zeolite and then push out everything else. What we didn't realize was how hard it would be to pump down the whole system with so much Argon trapped in the Zeolite. The turbo pump wasn't even able to reach its maximum RPM without overloading with power because it was having such a hard time pumping out the Argon from the tubing and Zeolite. We realized that the sheer amount of Zeolite made it very hard to pump down all of the Argon trapped in it.

Further, because we had added onto plumbing that was already there, the system became very large and relatively complex. It becomes much harder to pump down a large bottle when there is so much copper tubing it has to pass through before being pumped out. We spoke to the lab technician Allen who suggested we connect the Turbo pump much closer to the Zeolite bottle so that it wouldn't have to pump it down through so much copper wire. We disconnected a valve close to the Zeolite bottle and connected the Turbo pump there. Although the Turbo pump was eventually able to pump down the enormous pressure inside of the  Zeolite bottle it took almost 2 days to get this done.

Normally, atmospheric Helium is used to purge the Zeolite bottle, however we avoided using it because we didn't want atmospheric Helium to contaminate the underground gas sample. This is because Helium does not get trapped in the Zeolite and it is a very light gas making it fairly easy to pump down on. Since Argon was such a hassle, we decided to use Helium despite this.

In order to make sure we were actually pushing air out we connected a capillary to the tubing which lead back to a Residual Gas Analyzer (RGA) which is a mass spectrometer for gasses. Eventually we saw that after passing the Helium through the Zeolite bottle the Argon level drastically dropped suggesting that all the Argon trapped in the Zeolite was now mostly gone. Eventually through much trial and tribulation we were able to purge the system with Helium and then pump it down.

As I said before, the purging and pumping was done with the Turbo Pump connected close to the Zeolite bottle, however in order for us to pass the underground gas through the Zeolite bottle and into the small chamber we had to resort to the more complex tubing. So we reconnected all the tubing and leak checked it which took a full day on its own because we found that there were many many problems with the tubing and fittings. Punctured copper wire is never a good thing.

We were finally ready, so we pumped the whole system down and used  a pressure gauge to fill the small chamber with 20psi of Zeolite filtered underground gas (which was 99.9% Helium after passing through the Zeolite). It was relieving to finally finish a project that should have taken us 4-5 days but instead took almost 2 weeks. On Monday we will figure out how to ship it to Harvard.

In the meantime we had received a new sample of underground gas from a well in New Mexico which we will hopefully analyze with the RGA next week. Dr. Calaprice also outlined a new project for us which I will describe in the next post.

Ankur Week 2 Post 1

In the last 3 days we completed the first project and are now working on the second project. The first project was very simple, and all we had to do was connect the charcoal trap and storage bottle with stainless steel wires and fittings which is a little challenging because stainless steel is not bendable and flexible like copper wire is. However, stainless steel pieces are cleaner, stronger, more leak-tight, and more durable. Geoffrey introduced me to a new piece of equipment called a "Leak-checker" (at least that's what we call it). 

It is a pretty neat piece of equipment which is used to test the leak-tightness of a system to avoid any contamination. First it pumps down the steel wires and fittings ("pump down" is a common term for "sucks out all the air out of") hence creating a vacuum. Of course, high pressure moves to low pressure. As a result any air that is outside (high pressure) will try its hardest to enter the system (low pressure) through any loose fittings and possible punctures in the system. However, the Leak-checker detects specifically helium down to tiny tiny values. So, we pump down the system to about 10^-3 mbar then use a helium bottle and blow helium on to all the fittings and wire and watch for the Leak-checker to detect hints of helium. Because it's almost instant, we have to pay close attention to see where we were blowing helium in correspondence to the time the Leak-checker detected helium. This was a relatively small system so it only took about 20 minutes. 

We didn't find any substantial leaks so then we pumped down the system with a turbo pump to about 10^-7 mbar. The Leak-checker has a pump as well, but it is not as strong as the Turbo pump so we used the Turbo pump before we passed the gas through the lines. The Turbo pump takes a while, so it must be left for a large amount of time (60-80 minutes) and plus it cannot be touched for 30 minutes after it has finished pumping while it is cooling down. Once there was a good vacuum inside the wires we closed the valves to air so that we would avoid any air contamination.

Finally, we opened the valve from the charcoal trap at about 405psi into the storage bottle which was evacuated (10^-6 mbar = 1.5 x 10^-8 psi). The pressure disparity of course made the argon gas diffuse through the system filling up the storage bottle until pressure equilibrium was reached. Once the two tanks reached equilibrium we closed the valves and disconnected the wires.

We also started some of the plumbing for the 2nd project, however it is much more complex compared to the first project, so I will discuss it in the next post.

Ankur

6th Week (Rotimi Opeke)

14 days left.

We'll its me, myself and I in the lab now, going lone ranger and finishing my project while most people are finishing their overseas project. I leave on August 6 so the time to buckle down is really here and my opportunity to completely finish has presented itself. I plan to get the morphology part of my experiment finished this Friday as I selfishly and expensively booked the AFM microscope for the whole day. On the other hand, I plan to finish the electrical characterization part of my experiment early next week (Monday or Tuesday). All I have to do is have the solar devices ready so that the guys in Electrical Engineering can thermally evaporate aluminum to act as my cell's second cathode.

This doesn't sound like much, but along with the 4 hour long SAT classes I'm attending in the morning, it seems like I have little time to do all that I need to do. It's been to bed early and up early for the past few days and I don't expect things to change until I leave for Nigeria.

However, I can see the light at the end of the tunnel.

Rotimi Opeke

End of Week 2- Alec Mitchell

Despite it being a Monday, today is actually the last day of my second week at Columbia. Over these two weeks a lot has changed, but some things have also stayed the same.

To start, the changes:

1. Now when Zak, my grad student, introduces me to people, I've gone from "the kid who actually chose to volunteer in one of the three most dangerous labs on campus" to simply being a "minion" as all volunteers/undergrads are now called.

2. I've been able to do a lot of experiments either by myself or with significantly less grad student supervision.

3. I've gotten better at my grad student's random pop quizzes

4. Zak has actually started telling me I should go home because I'm staying so late

5. The experiments have gotten cooler, but with that the waiting time also increases. As Zak says, "a good chemist will be able to time experiments so that they can run one while waiting for another."

As for whats been going on in the lab, having the new glove box set up is really helpful. I've gotten to spin even more CdSe films, and see the results of pumping a vaccum on them while heating. After spinning those dots, I also recovered them from aluminum foil and cleaned them (I'll test the results tomorrow). Today I saw Cadmium Myristate made (it's a reagent for making the CdSe nanocrystals) as well. Throughout the week I have been testing a large amount of films using the UV-Vis spectrometer, which allows us to see changes in absorbency in the dots before and after they are spun. After that, I tried redissolving some of the films in toluene to see if the absorbency shifted back. Even though the results weren't clean enough to publish, it was clear that they did make somewhat of a shift back.

Just to be clear, for the last two weeks my lab has been in "crisis mode." The PI is going to the biggest conference that he will ever go to in his life and having his tenure go on trial (or so I've been told). Because of this, the lab has been scrambling for figures to put on his poster, and I have gotten to see a lot of the processes that happen in the lab.

My specific project should now be considered to be "projects." I am going to experiment with different concentrations in both Cd to Se ratios and Quantum Dots in solution. Just talking with the PI and my grad student, we have come up with a variety of projects that I can try.

Throughout my lab experience so far, I have learned more Chemistry than ever before. Not only do I get to work in the lab and be mentored by Zak, but I also get to attend group meetings (which are like presentations about what people are doing in our lab) and even lectures from scientists visiting Columbia. It's like getting the best education possible for a high school student just for volunteering. It's hard to believe that I'm almost halfway done already.

- Alec

Ankur Week 1 Post 2

By the Friday this week we were able to begin some assembly of the copper plumbing. Here I will explain in detail what we are doing in lab. There are two projects we are working on:

1. Previously, Geoffrey trapped Argon gas in a charcoal trap. Charcoal has a strong affinity for Argon when it is cooled to cryogenic temperatures; about 77 degrees C. This is a useful method for filtering Argon gas from air and other such gases because the Charcoal will trap Argon within itself and allow the majority of the other gases pass through. In order to analyse and store this gas we have to now remove the argon from the charcoal. 
2. Geoffrey received a shipment of underground gas from a well in Colorado, which should theoretically have a high Argon-40: Argon-39 ratio. These underground gases are derived form the mantle but as an aside, it is curious to figure out where they originate from. Previously it was believed that it was Solar Nebula gases trapped on in the early years of Earth's creation. However, new findings suggest otherwise. Because the Argon-39 abundance is so minimal, we use different ratios of Argon isotopes to predict where a) the gas originates from, and b) whether it might be suitable for the detector. Many inert gases such as helium, neon, and krypton have similar patterns in isotopic ratios between underground gas and the atmospheric gas. We are sending off a sample of the underground gas to Harvard Graduates who have a mass spectrometer which is sensitive enough to measure Helium-4: Helium-3 ratios, letting us know where exactly the gas was derived from: the mantle or crust, and if from the mantle, than how did it reach the mantle originally?

For the first project, it is necessary to know a basic property of charcoal. When charcoal's ability to absorb Argon has an inverse relationship with temperature. So in order to release the argon from the charcoal, we had to heat the  1L steel cylinder with heating straps. The heating straps were wrapped around the cylinder and then using a transformer we were able to effectively manipulate the temperature of the charcoal inside the cylinder. In order to monitor just how much Argon gas was being removed from the charcoal we attached a pressure gauge that allowed us to monitor just how much Argon gas we had accumulated. The tricky part was  getting the Argon out of the cylinder and into an empty storage bottle so we could use the charcoal trap for future. In order to do this we had to rely strictly on physics and common sense. If we heated the charcoal trap far enough, we would get a high pressure in the charcoal trap and if the storage bottle was evacuated, we would expect a flow from the charcoal trap to the storage bottle. So first we heated the charcoal trap. Then we vacuumed all the tubing because we didn't want air contamination in the argon. Finally we leak checked the tubing. Once the charcoal trap was a little over 400 psi, we allowed opened the valve that connected the two bottles and allowed as much argon to diffuse from the charcoal trap to the storage bottle until equal pressure through the whole system was achieved.  Of course some argon was left over in the charcoal trap, but we got the majority of it out. Next week we will begin project 2.

Final Post- GR

On Wednesday of my last week, I was able to perform the first step of the synthesis.  I was not able to see this step when I first started because the first two-steps were already performed on the sample that we were working on, but it turned out that more starting material was needed so it worked out that I was able to see all of the steps but the second.  On Thursday and Friday, we continued synthesizing and purifying the final product. It was a productive and busy week.

I am definitely going to miss everything about my time at the lab (except the commute, of course).  I had a fantastic time and was able to meet some great people.  I feel that one of the best things about it was that I was able to be in a professional environment while still learning as much as I would be while in a classroom.  Thanks so much to everyone who was involved!  Participated in university level research  was definitely as great as, if not greater than, I thought it would be.  Plus, another added bonus was that I was able to confirm my love of UPenn :)

…

This past Monday, after my volunteer shift at the hospital, I visited the lab to see how things are going.  I learned that 3.5 out of the 5 grams of the final product have been created and that the synthesis should be completed within a couple of weeks.   I also saw a very early draft of the publication of the class of compounds that I was working on!

Thanks,

GabRoss

Week 2 Post 1 - Alec Mitchell

So I'll start with a summary of what's happened this week:

Monday- Tested some spun films for thickness, and saw a full solar cell (with a film I spun) tested. Saw the CdSe dots I helped make cleaned.
Tuesday- Helped another graduate student with some work (mostly taking UV-Vis spectrums) and went to a presentation by another graduate student and two undergraduates.
Today- Did some NMR testing with Zak and ran a reaction with an undergrad. The glove box was finally constructed today, so I will probably start my project by the end of the week.

When written out, it does not seem like I've done much over the last few days, but I've really done so much! A lot of the reactions take time, but as long as you have the patience, they can be really cool.

I'm still having a great time working in the Owen lab!
-Alec

Rahul Lakhanpal- Fifth Week 6/11-6/15

So the objective of this week was to successfully find a vector that would be suitable for our experiment. We started by using two different vectors: HSA and HSA 4C.  Along with trying to find the correct vector, we also wanted to see which restriction enzyme gave us the smoothest and clearest cut. We created six solutions and tested them by running them under a gel. We discovered that the best vector we would use is HSA and the best restriction enzyme would be Xho I. Finding the correct vector was an extremely tedious process which required many digestions. One aspect I truly dislike about working at the lab is all the waiting time. In all these processes such as Gel Electrophoresis and Digestions I have to wait about 45 minutes- 2 hours; I wish this process could be expedited. After using this gel, we extracted the best one using a Gel- Extraction Kit. I have used many kits this summer, either to purify or extract DNA, and I am fascinated how through reactions that the DNA can be cleaned and purified.  Along with this, we were still working to find the best sample of insert DNA. Although, we found the correct size of the fragments (thanks to gels) we are noticing that not enough DNA is showing up after the PCRs. We continued to try and find a solution to this problem. By the end of the week, the DNA was still not as strong as we hoped but we decided to continue with our project, because I don’t have a lot of time left!

Ankur Week 1 Post 1

Monday, July 18, 2011
Ankur Toshniwal
Peddie Student '12
Summer Research with Dr. Calaprice @ Princeton University

Over the course of the previous month Dr. Calaprice (my PI), Ms. Helen Ju (his secretary), and I discussed many many things prior to beginning lab. I endured a brutal 3 hour Lab Safety seminar, read papers that made Scarlet Letter seem like Dr. Suess' Green Eggs and Ham, and we conferred all the necessary things such as where I would park in Princeton, where to eat lunch, and what I would be doing in lab. The night previous to July 18, my start date, I realized Dr. Calaprice (my PI) and I had never agreed on a time for me to come in in the morning. This posed a slight problem. I erred on the side of punctuality and showed up at 7:30am to find that I was alone with a single custodian. I went to the second floor and waited outside Dr. Calaprice's office till about 8:30am till finally his Ms. Ju led me to meet one of the employed researchers so I wouldn't make sleeping arrangements in the hallway. I met Brooke filling out some paper work and she took me on a quick tour of the laboratories. I was surprised when we began talking in technical terms that I was actually able to keep up with the lingo. She showed me the project she was working on: the Borexino Neutrino Detector. Luckily I had originally began my research with this project so I knew the background, unfortunately it was 8:45am and normally my brain and speech powers were limited to choosing between Lucky Charms and Cinnamon Toast Crunch cereal and telling my mom to wake me up in 30 minutes in 30 minute increments. I held it together till Dr. Calaprice finally came in and he briefed me on some recent news in geochemistry and what I would specifically be working on. As a brief summary, I will be working with Geoffrey Lou Guray who graduated from Princeton in 2010 and is now a 2-year employed researcher at Princeton. He works mainly with the rare gasses such as Argon, Helium, and Neon. To explain the motivation for the Dark Matter Detector which is currently being developed by the team I'm working with I'll give an outline of the theory.

There are many ways that scientists know Dark Matter exists, but I find the easiest one to understand and comprehend is the Cluster Coma theory. When scientists look into outer space they are able to identify all the luminous matter in galaxies throughout the universe. Based on light signatures they are able to accurately predict the mass of all the luminous (matter giving off light) matter. Based on calculations, they found that the amount of mass the luminous matter makes up is nothing close to how much the galaxy would need for gravity to hold it together. This means that there is an unknown type of matter making up for all the mass needed for gravity to hold the galaxy together. This unknown matter is labeled Dark Matter primarily due to the fact that we cannot see it. In order to identify what this matter is, labs across the world strive to build detectors so that we may detect this unknown particle and unlock a new chapter of our universe.

Princeton happens to be working on one of these detectors. In order to avoid false signals, the liquid and gas Argon which the detector is filled with must be ultra pure. Argon is found in our atmosphere in small percentages, however atmospheric Argon has radioactive isotopes that would trigger false signals in the detector. However, Argon found underground has much larger amounts of the stable isotope Argon-40 and less amounts of the radioactive isotope Argon-39. I will be helping Geoffrey obtain some of this Argon gas through various filtering and purifying methods.

After discussion of what I will be doing in lab Geoffrey showed me his lab room. Filled with many gas tanks and several pieces of machinery later to be identified as a Turbo Pump and a Leak Checker, the lab was not too big nor too small. Geoffrey was at the time trying to store a small amount of underground natural gas from  a gas well in Colorado in a small chamber so he could send it to Harvard for mass spectrometry to analyze the Helium-3 to Helium-4 ratio which would help tell us where exactly the underground gas was extracted from. This is where much of the nuclear physics stopped, and the engineering began. In order to do this requires a simple, yet tedious and very very time consuming task. First copper wire had to be cut and bent to the specific shape that we needed our plumbing to go. Fittings had to be attached to each end of the copper wires to insure that air would not contaminate our sample of gas nor the main tank. Valves had to be screwed and tightened with wrenches so we could control the path of the gas through the plumbing. We haven't done it yet but we'll have to pump out all the air from the tubing with a vacuum pump because otherwise there is atmospheric air inside the plumbing. I will go into more detail with the next post of the procedure.

I got to leave at 5:00pm and from now on my start time is 9:00pm. So far all the people I have met are really encouraging and naturally wicked smart. After my first two days, I can tell there will be a pretty even mix of conceptual science and practical engineering physics.

Thanks,
Ankur Toshniwal

Long Overdue Part 2 (6th Week)---- Rotimi Opeke

But now, there is another problem that has come to the forefront. I cannot build the solar cells devices that I need because of a lack of proper foundation. Because we build these miniature solar cells on a glass substrate, the glass must be coated in one of the two necessary cathodes. The glass that we bought is completely covered in ITO instead of a strip that we need, so it seems we will manually have to erode the excess ITO from the surface of the glass. Using some fancy equipment and some UV staining, we should be able to erode away the ITO that we need, but nothing is certain. Wish me luck, because at this point this will decided whether I will have to come back in the fall to finish the experiment.

Long Overdue Part 1 (6th Week)---- Rotimi Opeke

My 1 1/2 week absence from the blog has been unexcusable, but things have been very busy in the past 2 weeks and I hope you can excuse my lack of journal entries.

After a weekend away from NJ with the Peddie Basketball team in Albright, PA, the push began to start recording my experimental data. I had met with Dr. Soboyejo on Friday of the previous week, right before he had left for Nigeria and he had asked me to take x-ray diffractions of the samples I was making. This was a bit of a surprise to me, but he claimed that recording chemical and structure composition were the two most "important" facets of my data. Unfortunately on Monday, July 11, the graduate students that were part of his research group informed me that I wouldn't be able to take X-Ray diffractions with the samples I was using.

Now what. My project had changed multiple times since I had come to the lab, and right when I was ready to begin, there was a problem. Dr. Soboyejo had long gone to Nigeria, and now it was up to me to draft a new project. With pressure to complete an actual project before I leave for home on August 6, I spent the next two days in Princeton Public Library writing and editing a new proposal that was as straightforward as possible.

Pat Quinn - Day 26

This is my final week in the lab so the work load has gone down. I no longer need to dissect eggs because I already have enough lungs to do my final staining. I am still in charge of maintaining the eggs and the incubators. This week I will be finishing off my last staining. Last week I finished staining smooth muscle actin and laminin. The smooth muscle staining of the lungs over a few days basically shows the development of the blood vessels within the lungs. In order to do the laminin staining the lungs must first be embedded and sectioned. Embedding the lungs means putting the lungs into an agarose gel that will hold the lungs in place. The sectioning means that you will cut the lungs horizontally at thicknesses measured in microns. Since I am not old enough to use the sectioning machince this part of the project has been done by an undergraduate. The process is much quicker for staining sections so it only takes about two days to get results. Laminin is found in the basement membrane within tissues which is the layer that epithelial cells lay on. From the laminin staining I found that laminin is not found on the tips of buds. This suggests that the basement membrane is broken down on buds in order for branching morphogenesis to occur. The staining that i will be doing this week is Vimentin which plays a role in EMT. I have also been organizing pictures and data for the poster.

Alec Mitchell- End of 1st Week at Columbia

Well, I officially survived my first week at my lab. Since I haven't started my planned project yet, this week has been composed of learning what goes on in the lab.

On Wednesday I got to help synthesize zinc oxide nanocrystals with Alex, an engineer from the Kymissis lab (they partner with the Owen lab, and help with the engineering end of making solar cells). In case you didn't know, the lab I work in makes nanocrystal semiconductors to be used in solar cells. By making a transistor with the crystals, we can determine how well the semiconductors work.

After doing the less dangerous synthesis, I also got to help make CdSe quantum dots. Unlike the ZnO crystals, CdSe crystals actually change colors during the synthesis. It's pretty cool, and it looks like this: http://www.youtube.com/watch?v=6Xm4LABNYzo. During the wait I got a quantum mechanics lecture from Zak, which I actually understood to some extent. Unfortunately we made a larger amount of crystals than usual, so the solution had to be distilled. Everyone in the lab compared waiting for it to watching paint dry.

The next morning I spent with Alex in the Kymissis lab. I learned the process of spinning ZnO films on  ITO glass. In basic terms, it is comparable to spin art with a science twist. Later that day I got to see Zak spin a CdSe film and test a transistor that he made.

Starting tomorrow I will be synthesizing CdSe crystals with different Cd to Se ratios. Once the new glove box is installed on Wednesday I'll start on my planned project.

I've learned more than I could have imagined so far thanks to everyone, and it has only been my first week. I'm really looking forward to my next four weeks working in the Owen lab.

-Alec

Sixth week last week at Yale

So I'm finally done with all the work at Yale. This last week I basically didn't do much, just to wrap up everything and transfer all the data on my laptop to my PI's laptop. I didn't go to the office on Monday because I was returning from Boston. On Tuesday I went there and finished up my third project, making an Excel spreadsheet for the two groups of butterflies: these Bicyclus anynana does not have injection; they are just bred in west season and dry season as controls. And on Wednesday I transferred all these data to my PI's database and then she took me out for lunch. We talked for an hour and she also told me that Yale is opening a new liberal arts college in Singapore, she might be applying to go to Singapore if possible, time to get to know some tropical butterflies haha. And that was it, my last day at Yale and I flew back to Asia on Friday.

I really loved the five weeks at Yale, and I even told my professor that if possible I would still spend a few weeks at Yale next year. So lucky that I had such a great PI! :D

Santooooooooooooooooooo

End of Week 5 - Kate Wang

This is my last post ever to this blog. I can't believe it's already been 5 weeks!

On Thursday, Vince went over how to use an HPLC (high performance liquid chromatography) with me and I think I understood most of it. Then I started the usual trials and Rob also gave me polymers to sieve and wash while I was waiting. I think on Wednesday Tom went over how to use the GC (gas chromatography) with me and he used this great analogy with zoo animals breaking out and something. Then, after I finished everything I had to do, I went around and took photos of most of the people that I worked with but I missed a couple since they'd already left by the time I was done. I'd also brought in the cookiebrownie which everyone really liked. 

On Friday, my last day, I started out with the usual trial and I also sieved a polymer. Later, Dr. Chan walked me through how to use an ELISA machine (enzyme-linked immunosorbent assay). After that, they surprised me with an oreo ice cream cake and everyone came and it was like a small farewell party! We all sat and talked and ate delicious ice cream. After that, Humayra walked me through the Luminex machine which is almost like a fancy ELISA machine. Then, at the end of the day I hung out with Rob and Simon for a while before saying all my goodbyes and going home.

Over all, I think this has been a great experience and I met some very interesting and fun people. I really hope that I can visit them again sometime and I invited almost all of them to the dinner in November :)

Half of Week 5 - Kate Wang

I can't believe it's already the last week. I only have two more days!! This is absurd. So what happened in the past three days. On Monday I re-ran one of the trials that seemed funky only to come up with an even funkier result. After that, I had a chat with Dr. Chan that went on for about an hour and a half. It was a mix between a crash course biology, chemistry, organic chemistry, polymers, and medical terms. It was really productive though and I learnt a lot. We went over what I'd done so far and about the trials and controls and possibilities for my poster and presentation.

And then on Tuesday (yesterday) I re-ran another polymer that I'd messed up on (twice) and I think my final numbers were okay but a little low. Oh well, and then at the end of the day, I didn't know if I was supposed to present to Dr. Chan again so I ended up hanging out with Rob instead. 

Today, I ran another new polymer and got negative numbers :( I think for a little while in the middle of my work, I kept getting negative numbers but then after a while I started getting positive numbers which was really good only to ruin my streak and go back to negative numbers. Hopefully my numbers tomorrow will be positive. 

Tomorrow I'm bringing the cookiebrownie that I finally got around to making and I'm also bringing in my camera to get pictures for presentation and poster etc. and I believe that is it.

First Day at Columbia

After waking up at 5:30 in the morning to take the train into New York, I was a lot more nervous than excited for my first day. Before I even met with my grad student, he had me go to a different lab since he finally got some equipment fixed. When I got there, we cut and cleaned Silicon wafers for transistors. Of course the fire alarm sounds halfway through that, and we had to leave the building. Luckily it was just a drill.

Once we got back to the main lab I got a tour and a safety tutorial. My grad student gave me my own desk, and we went and got supplies. This is where the work started. Now that we had everything, I had to research how to synthesize metal oxide nanocrystals and decide which one I wanted to make. By the time I finished the first article on my desk, 7 more had appeared. I basically spent the rest of the day reading and meeting people in the lab.

Almost everybody in the lab asked me what colleges I was applying to by the time I decided on Copper Oxide. The lab is pretty small, so it's great that everyone is very friendly (They must have told me a million times that I can ask any of them a question at any time about anything). It's a lot of work, but everybody makes the most of it.

So what did I learn today? 1. I volunteered at one of the 3 most dangerous labs on campus 2. Half of everything in my lab is either toxic or liable to explode, and 3. If you add enough Nitrogens to anything, it will explode.

After working for 12 hours, I think I'm ready for some sleep.
-Alec

Santo fifth week and part of sixth week

Sorry for not posting for a long time..
Just a summary since the start of my first week till now: finished the project my PI gave me in the first three weeks, then she assigned me the second project to help someone else in the lab to collect analyze data of another species Junonia Coenia, and I finished that project within a week, so the professor gave me the third project which goes back to Bicyclus Anynana and collect some basic information of the butterflies bred in normal environment without injection of any hormone. And fifth week passed, I am almost done with this project as well. Since I am here for another week I still go help out in the lab and the inesectary.
Tomorrow I am going to the lab again to help out and need to teach another post graduate to use a software called Image J. I've been using this software in the past few weeks to measure the pupil area on the butterfly wings so I am becoming familiar with it. Besides helping the post graduate I still need to finish the third project, the data collecting and analyzing is done, all I need to do is to put them into a table. I do not think my PI will give me another project after this one since I will only stay there for another 2 days and it's my sixth week already. I might just write some instructions for the software I used since my PI usually found it hard to teach me how to use those, they don't have instructions or user guides online either.
So that's all I have for my fifth week and sixth week plan. Actually if possible I might still wannt to come back next year, this lab is pretty fun.

Santoooooooooo

Jack

Sorry for not posting, but my week's been kind of crazy. Basically, we finally ran full simulations of my system, and while they went well, the program that I had learned to use proved far to inefficient. Even with 64 cores working, I was only getting about 1ps a day, and I need 100ps, give or take, to have any sort of reasonable certainty that my system is stabilized. Since I don't want to be here till November, we've decided to switch to a new, more efficient program called NAMD. The bad news is that most of my old simulations are now fairly useless. The good news is that NAMD is fairly similar in terms of usage to amber, and most of the preparatory work I did is still valid. Since I am also going to be using Calhoun (our supercomputer) for all the simulations, this time around should be much quicker. At the moment I'm working on a ion bunching problem which we had encountered early with amber and which we had fixed. Unfortunately, that fix, for convoluted reasons, didn't carry over the NAMD, so no I have to re-fix it. Luckily, this time I know how.
Jack

Week ???-PK

Yeah... It's been along time since I've "talked" to you guys. A lot has happened in the past few weeks. First off, Dr. Peretz and Ms. Rodrigue came to visit my lab. I took a day off for July 4th (yay!) and am currently on a week vacation. I actually started the week vacation the day before I was supposed to give a talk with Teuta, my supervisor, and Steven, the senior undergraduate. Most people would say that good, but in reality, it's very bad. Firstly because I have to give my presentation without any help from Steven (I probably would have looked better with him presenting before or after me). Secondly  because when I come back and give the presentation, I'll forget most of what I did these past few weeks.

I have done a lot of things these past few weeks. I'm almost done with the program, I just need to edit a few lines. I've read a lot more literature simply because I am actually planning my experiment now. Based upon what I read and what I expect, that's what I am probably going to be studying. I also get to make my own primer with the help of Teuta; however, I'm not done yet. I'm really excited to start on that part of the project! Also, there's been some pretty interesting things with the results. I'd love to attach it here, but right now I can't since I need to be connected to Princeton's network.

Since my last post, I've been much better with the tricky procedure. I'm actually doing the whole procedure by myself. Teuta just does her thing and only randomly peeks in to make sure I'm not messing up any lab procedures. The only thing I don't know how to fix is the really big, complex, and expensive optical trap. It's basically an inverted light microscope that focuses light to "trap" and control small particles (less than 1 um!). It can even be used to play tetris! Too bad I don't have time for that :(

Another thing I need to do when I get back is making growth curves because I have been working with different strains and each strain has a different incubation time. It's very annoying to find out that after 4 hours of work, you can't continue because you waiting too long. So I have plenty to do in the next few weeks. I can't believe summer is almost 1/2 over!~

Peace~

-PK 

End of Week 4 - Kate Wang

I kind of had a bad day yesterday. I kept dropping things, spilling things, and then having to redo them, etc. And then the worst of all was when I forgot to save each of the samples after I put them through the UV spec so my entire day’s work basically went to waster. At the end of the day I had two full hours where I had nothing to do so for the last hour of so I just hung out with Simon and Anthony and later Rob. And Simon wanted me to tell his famous turtle joke on here so here goes:

Why did the turtle cross the free way??

Take the “F” out of Free and the “F” out of way.

Punch line: there is no “F” in way! (There is no effing way..)

Also Simon was trying to teach me how to spin the pen around my thumb and the two times that I did manage to do it, none of them were watching so they didn’t believe me.

Today, I re-ran the trial that I forgot to save yesterday, only to find out that I’d made the stock solution wrong. Sometimes I make 250mL and sometimes only 200mL and I’d accidentally put the wrong amount of the solute into the 250mL volumetric flask. Other than that, I broke something again today, it was only one of the small flasks I use for the assays but this means that I am up to five broken things in four weeks. Which really isn’t that bad compared to Rob’s record but still. It makes me feel really clumsy.

Pat Quinn - Day 20

Today my time was spent listening in on the group meeting and organizing some of the photos I have taken. Today's meeting went over some lab maintenance and then two graduate students presented what they are currently working on. One graduate student is working on to see if tumors proliferate in certain areas of the mammary gland and if so, what in the micro-environment causes this. The other student is working on the cell signaling involved in Epithelial-Mesenchymal Transition, a process in which epithelial cells lose cell adhesion and have increased cell motility. After the meeting I started my anti-alpha smooth muscle actin staining which will help show some developmental features of the lungs during day 6 and day 7. After that I started to collect some pictures from the microscope computer and moved them to my own. It took me some time to figure out that I had to convert the images into the jpg format in order for my computer to be able to open the document. Eventually I was able to get the pictures into photoshop where I played with the lighting in order to get the best pictures. I then arranged the pictures on PowerPoint and then saved the whole slide as a new picture. I now have one picture for my new poster.

Pat Quinn - Day 20

Today my time was spent listening in on the group meeting and organizing some of the photos I have taken. Today's meeting went over some lab maintenance and then two graduate students presented what they are currently working on. One graduate student is working on to see if tumors proliferate in certain areas of the mammary gland and if so, what in the micro-environment causes this. The other student is working on the cell signaling involved in Epithelial-Mesenchymal Transition, a process in which epithelial cells lose cell adhesion and have increased cell motility. After the meeting I started my anti-alpha smooth muscle actin staining which will help show some developmental features of the lungs during day 6 and day 7. After that I started to collect some pictures from the microscope computer and moved them to my own. It took me some time to figure out that I had to convert the images into the jpg format in order for my computer to be able to open the document. Eventually I was able to get the pictures into photoshop where I played with the lighting in order to get the best pictures. I then arranged the pictures on PowerPoint and then saved the whole slide as a new picture. I now have one picture for my new poster.

Rahul Lakhanpal- Third Week

So I wrote this blog over Monday, but then as I went to submit it the internet went out and my whole blog was erased, thus I am forced to rewrite it today (about last week). I have also learned from my mistake and am writing this first on a word document. My third week was a very busy week in which I felt I started to truly move along with my procedure. As I stated in my last blog, my second week concluded with me creating my own primer which we ordered. On Tuesday we received these primers and I set up my first PCR (two containers of DNA). In order to save our DNA and effectively do the PCR we had to dilute our primer. Using the diluted primer I had to use a PCR kit, to get my sample ready for PCR. The PCR kit called for 1 ul of my primer (3-5), 1 ul of another primer (5-3), 1 ul of template DNA, 22 ul of autoclaved h2o and 25 ul of primestar (PCR mix). The PCR then did its cycling over night and the next day I came excited to see my DNA.

In order to confirm if the PCR worked, we had to do a gel electrophoresis. I again got a manual and had to follow steps to first make the gel for the GE, then my solution I was going to put in the wells, and then how to run and read it. The gel was supposed to be 2% agarose which meant I had to measure out 2g of agarose and add  100 ml solution of TAE buffer, and 5 ul of Ethidium Bromide (toxic). I then heated my solution in the microwave for a minute, let it sit, and then poured it into the container in which is solidified into a gel. I then created my two samples in which I was going to load into the wells, they were made of 7 ul of my PCR DNA, 2 ul of h2o and 1 ul of buffer. I loaded them in the wells, along with 2 samples of DNA marker. The loading was at first difficult, but after practice I got pretty good at it. I waited 45 minutes then looked at the gel under a UV light, and it looked pretty well.

But... In the research world a confirmation one time is apparently not good enough… So I had to do another GE on Thursday. I can honestly say, that Thursday was by far the worst day of my young researcher life. On Thursday, none of my GEs were working and I ended up doing 3 trials all fiascos. I left the lab on Thursday at 8pm and was exhausted. The only one more stressed out than me was probably my mother who called me every 20 minutes to make sure I was safe in the city.

After a long Thursday, Dr. Li decided that I should run another PCR so we get better results. So, basically I am pretty much an expert at running both PCR and GE. I set up the PCR reaction and put them in the machine. Next week I look forward to more GEs and along with this Dr. Li also put some cells in to culture and we will be transferring the DNA to them next week! 3 weeks done, onto the next one…

Rahul Lakhanpal

PS: I’m working a short week this week (Monday was July 4, and Tuesday he couldn’t make it back) so I will write my next blog at the end of the week  (hopefully NOT during next week)...

Half of Week 4 - Kate Wang

I know I wrote a post just yesterday but here’s another one for week 4. I can’t believe this is already my second to last week! Time is going by way too quickly. Today I finished tests for the data that I will be presenting as part of my research. Over the past three working days I tested three different sized polymers for their absorbance of a macromolecule. I got good results for all of them and found a visible trend which is really good.

Other than that, not much has happened since I last posted. I still haven’t brought in the cookie brownie since I don’t have a stick of butter lying around in the room. 

Oh, Dr. Peretz visited yesterday morning and I showed her around the lab. One of the guys who work in production, Simon, told me he thought Dr. Peretz was very pretty and asked me if she was married.  I told him that yes she was and I would pass on the message so if you are reading this now, Dr. Peretz, Simon (the Asian you met in the lab along with Rob) thinks you are very pretty. He actually reminded me about it again today at lunch and asked if Dr. Peretz had asked about him. I told him I hadn’t talked to Dr. Peretz since. I think you have an admirer, Dr. Peretz.

Right now, I’m just digging for stuff to do since I finished my assays and I have about one and a half hours left till I can leave. Although technically I could leave now but that means I’d have to work extra some other day to make sure I can fill the 200 hours required. So, instead I decided to write this post. Another thing I could be doing is working on the poster that we’ll be presenting in the fall but I already changed everything that I could on it other than the data. And I don’t particularly want to keep reading the books Tom and Rob gave me since I’m at the point where they don’t make much sense anymore so I guess I’ll just have to find something else to occupy my time with. In the end, Rob told me to start putting my data into charts and graphs.  

End of Week 3 - Kate Wang

I know I was supposed to post this at the end of last week but because of some password issues I didn’t get a chance to post it until today.

Anyway, not much has happened since I last posted. Today I started working on the project that I will actually be presenting in the fall since everything I’ve been doing up till now has really been practice and research for the company. Now I’m finally starting the project to determine the correlation between particle size and the absorbance of a macromolecule. The first polymer that they gave me to test was really small and particle sizing with the microscope was very difficult to do since the computer wouldn’t recognize the separate beads without me having to remove majority of the selections they made. Also, the polymer gave some ridiculously high adsorption rates which was very good since it helped Tom figure out what size is the most helpful in absorbing the macromolecule.

At the end of the day, Rob had to leave early and I didn’t know how to find something to occupy my time with so I asked Tom if he had anything I should work on and so he told me I should start working on my presentation (which I didn’t really want to do yet since I wasn’t 100% sure that I understood everything yet). Luckily, in the end Rob gave me some polymer to wash. Also, we ran out of one of the buffers that I use to make stock solution so I had to mix together all of the previous stock solution which was very tedious and irritating because of the shape of the volumetric flasks. In the end, I did look at the power point slightly while I was waiting between the washes. 

Week 4 and Beginning of Week 5- GR

I completely forgot to write any posts last week (sorry, Dr. Peretz), so this will summarize all of last week and also today...

On Monday and Tuesday of Week 4, I continued the characterization of GR-1 (whose real name is CNDR-51489) and also the synthesis of the main compound.  We were able to make about 600 mg of the final amine, purified and ready to go.  There was a blip in the purification process, but it ended up working out and we found a very efficient way to purify more samples in the future.  It was thought that this compound could only be purified by the expensive, time consuming HPLC method, so that's where we began, in the HPLC room.  We were disappointed to discover that the HPLC was not working as well as was needed. The product still contained impurities after.  This unfortunate circumstance led us to retry using silica gel column chromatography.  This ended up working fantastically.  The column was quick and easy to run (unlike some other ones that I had to struggle through), the final fractions were very clean, and we were able to put all of the compound into one column compared to the 10 that would be needed for HPLC purification.  It was basically an all around win.  Also, Dr. Peretz visited the lab on Tuesday, so Carlo and I showed her all of the cool stuff that I've been using.

For the rest of the week (up through today as well), I was at a biology lab in the Center for Neurodegenerative Disease Research.  It was a completely different experience.  In addition to the fact that I didn’t really do much work myself (I mainly watched people because I had no experience in the tasks that were being performed), it was a completely different atmosphere then in the chem lab.  The lab itself is much newer, so that was cool, but the type of work was completely different.  It was mainly micropipetting samples into wells.  Plus, the amounts are so miniscule that you can barely see what you're doing.  It's pretty tedious stuff.  The cool thing though, was that, based on the two assays that were analyzed (one was a ThT flourescence assay and the other a sedimentation assay), my compound is actually more active than the one we are making for in vivo testing.  There were a few discrepancies in the data though, so that might not be 100% true, but still, I was happy.  I also got to keep the gel of the protein that we ran as a souvenir :)

I really can't believe that it's already my last week in the lab…

Thanks,

GabRoss

Week 3 Part 2 (Rotimi Opeke)

Well the pressure is on.

I have a month left, and I still have much to do. The lab techniques for sample preparation are out of the way, I just need to learn how to analyze these samples. Although I have already taken a class in how to use the Scanning Electron Microscope, my PI still is asking for me to learn how to use the Atomic Force Microscope in order to analyze the active layers for my project.

 At the end of last week, I prepared dummy samples to run under the SEM microscope. They were created at 1/2 of the normal polymer concentration, specially meant for practice purposes only. In the hope that my project advisor was going to show up today, I ran these dummies under the SEM microscope, but to no success.

I was able to procure a clear picture,  but at a very low magnification, and it seems it was only a scratch mark and not anything special with the surface morphology. The microscopy specialist told me that I will have to learn how to coat my samples in ions so that the SEM machine works better. It's a shame that the next class is on July 25....

I have a lot of questions and doubts and not a lot of answers from anyone (but the microscopy expert Jerry). I hope to see my advisor in the lab, but no response from text messages in the morning seem like a clear sign that I won't get those questions answered today.

Ala Viva

Pat Quinn - Day 17

The lab has become over crowed now and I can no longer go into the office due to the amount of space. Myself and the undergraduates are now moved downstairs to an undergraduate lounge. When I spend my time there it is    to research the proteins I am working with and to start organizing my information so that it is presentable. Today I will finish up staining for the lCAM proteins which are proteins found on epithelial cells. I have already used the epifluorescent microscope to look at some of the lungs. Tomorrow I will be taking pictures of the lungs. Tomorrow I will also begin staining for alpha smooth muscle actin, which are the proteins used for contraction in smooth muscle. This staining will also give a better look at the structure of the lungs. I hope to have this finished this week. Then for the remainder of my time here I will be staining for proteins that were either found in other animals or other organs and see if they can be found in the lungs of chicken. 

Jack

The rest of the past week has been pretty slow. The PI and a good portion of the lab have been out of town for a meeting. As such, the lab has largely shut down. The results of my MD (molecular dynamics) simulation are in, though, and I'm glad to say nothing looks too messed up. I had time to do an initial analysis, which seemed to show that both simulations I had ran were moving towards the active conformation, which is very good news. The analysis also showed, however, that neither system was fully equilibrated. Because I need a fully equilibriated system to be able to draw real conclusions from the data, I ran the same simulations again, but this time for 2.5x longer. This should be long enough for the system to equilibrate completely.

Pat Quinn - Day 15

The last couple of days have been all about dissections. Everyday I have been dissecting at least 15 eggs. It takes me the whole morning to get through them all. But the good news is that I am getting better at it and faster. I found out that my dissections are better than the dissections in the senior thesis I read in preparation for the lab. I have to dissect many eggs because I will start staining them for different proteins. The more lungs I have the more staining I can accomplish and the more information I will have. The way the staining process works is that you take specific antibodies that target a certain protein within the tissue. You then add a second antibody that targets the original antibody.Then you add fluorescent tags to the tissue. The second antibody allows for more fluorescence to be seen from the one protein. I have already stained for an lCAM protein, a protein on the epithelial cells, which allows the lung branches to light up. Next week I will be staining for different proteins that will help show the structure of the lungs. 

Middle of Third Week - Kate Wang

So I'm still doing the exact same stuff. Although we did have a meeting today so now I finally understand what I am actually doing and all the numbers finally make sense. Also, I got really good numbers today. Turns out that the numbers today were very important since both Tom and Vince came and asked if I was done. Actually, yesterday I finished so early that I had two hours at the end where I just didn't know what to do. I was talking to Rob and apparently he didn't have much to do either. In the end, I asked Matt if he had anything for me to do so I spent the last hour or so washing dirty glassware. But that's okay with me.

Anyway. Also, Tom is already starting to help me prep for the presentation that isn't taking place until autumn but I am grateful since this helps me figure out if I have any questions I need to ask or if there is anything I need to do extra research on. Which there is a lot of actually, since all this stuff is organic chemistry which I haven't learned a lot about and when I was reading articles for the EXP class, it was mostly about the medical side, not so much about the research and development of it which is what I'm working in now. Either way, this can be my crash course in organic chem and hopefully it'll help me in the autumn when I take my actual organic chem class.