Final Presentation for REU

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Yesterday afternoon I gave my final presentation for the NSF REU. I’ve posted it on Slideshare for you all to see. It wasn’t real obvious, until I started working on the presentation, how much Anthony and I have done over the last several months. We’ve gotten a lot accomplished!

I have had such a great experience this year that I volunteered to continue coming to the lab this summer. Thankfully Anthony and Dr. Koch aren’t tired of me and agreed to let me stay involved this summer. I hope to be able to work in Koch Lab at least 4 hours a week. I’m interested to see how the e.coli in D2O progresses.

Also, Anthony is really moving and shaking in the Open Notebook Science community. This is really exciting to me.  I’ll be taking my ONS experience with me to my next opportunity…

I’ve been given another NSF internship opportunity, the STEM Talent Expansion Program (STEP), for the summer. [I think that is the right link… the NSF site is down for maintenance until tomorrow night. Let me know if the link isn’t correct]. I’ll be working part-time with Dr. Ramiro Jordan, who seemed open to me keeping an online notebook. Stay tuned for some information about VHDL and circuits.

I am indebted and full of gratitude for all the support and guidance that both Anthony and Dr. Koch gave me this past year. Thank you seems like not enough. Thank you both.



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Today I ran FTIR spectroscopy on three ages of DDW, two ages of D2O and the four types of DI that Anthony is using in his current DDW5 experiments.

Many thanks to Stephen Myers for training me on the use of the FTIR, and Dr. Sanjay Krishna for providing me with access to the lab and machine. Stephen was in the lab today and was graciously helpful, as always.

As always I started with a scan of the empty cuvette for the background. Today I kept getting a really strange scan image. Stephen took a look and said confirmed that the scan didn’t look quite right. He changed the Bench Set Gain option to autogain, Anthony cleaned the cuvette, and the next scan came out as we expected it should. After we got a correct background we did a comparison of the previous FTIR background (2/2/2012), today’s background with no autogain correction, and the corrected autogain background. We used today’s autogain corrected background scan for all of our scans today.


Comparison background scans

For each of the following scans we used the same set up as my previous scans from 2/2/2012, using a quartz cuvette and 3µL of the specified water sample.

My first set of scans were three samples of DDW, each opened on a different date (9/6/2011, 1/17/2012, and 2/16/2012). I expected to see a difference because of possible atmospheric absorption of D2O. What I found was they were all pretty much the same the first scan that I ran. Unfortunately, I messed up the save process and had to re-scan the September and January samples. That scan produced a different result for January as shown in the following figure.

DDW second scan

DDW second scan

DDW (second scan) zoomed image

Next I scanned the four types of DI water Anthony is currently using in his current DDW5 experiment (see link). The four types of DI water are:

  1. DI from the Easypure RoDI (Thermohe) machine in our lab (Ro_DI – purple)
  2. CHTM’s DI (CHTM_DI – Red)
  3. Sigma molecular biology grade water (SMol_DI – light blue)
  4. Sigma double purified water (SDP_DI – green)

The results are surprising. The Sigma double purified water’s scan was slightly different than the other three, which were almost identical. This is certainly something to take a look at.

Deionized water scan

Deionized water - zoomed image

Next I scanned two samples of D2O:

  • a bottle opened on 2/16/2012 (red in the scan image)
  • a bottle opened on 11/1/2011 (blue in the scan image)

This scan also produced differing results, possibly from atmospheric absorption (what we had expected to see with the different aged DDW).

D2O scan

D2O scan zoomed

Finally just for comparison, I opened a new window and opened the scan of the February DDW and D2O, the Sigma double processed, and the Sigma molecular biology grade water just to see how the results compared. Interesting that the DDW and Sigma double purified water are identical. Hmmm…

Comparison of DDW, D2O and both of the Sigma DI scans

I’ve uploaded all the raw data onto FigShare with all the images.

My next project is to read up on water frequency and figure out what all the numbers mean. I’ve found a few papers and a website that will probably help shed some light on my very pretty graphs. I’ve ordered two of the papers from the library and the other information is available online.

FTIR scan data from 2-2-2012 uploaded to FigShare


I’ve uploaded a JPG image of all the scans from yesterday to figshare. The raw data is also available for anyone interested. I’m wondering if this makes me half as cool as Anthony.

Let the Ft-IR scans begin


I was only in the lab for a few hours today. Enough time for Anthony and I to start our first round of water scans. Today was a repeat of the December scans of DDW, DI, and D2O. It was my first go at running the Ft-IR on my own.

Stephen Myers has given generously of his time to train me and help me with my first “solo flight.” Everything went really smoothly, and Dr. Sanjay Krishna has generously given us access to

I was able to follow my instructions from my training using my earlier post. Everything worked great. We obtained data that I will analyze next week when I’m back in the lab. The data looked like it matched Anthony’s original scans.

Next up will be weekly scans of DDW to determine how quickly it absorbs deuterium from the surrounding atmosphere.

Ft-IR scans

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I sent an email to Stephen last night requesting some (supervised) time on the Ft-IR. He responded right away and I have an appointment tomorrow around 2 to run the first of our scans.

For this run I’m going to repeat Anthony’s scans from December. I’m hoping that Stephen and I can get a few more sessions in next week so that I can get unsupervised use of the Ft-IR.

Anthony and I met this morning. There are a few things we are hoping to learn more about:

  • the absorption rate of D2O in DDW
  • what do varying amounts of D2O look like

I’ve started a table to track my work on these and any other questions that may pop up.

Project Update

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Some Background:  My long term goal is to complete a BS CompE and an MBA under the UNM 3+2 program, expected May 2015. I’ve got a ton of work experience in project management; I’m really good at it, and I love it.  I came back to school so I could eventually get into management.

Anthony and I have been talking quite a bit about the best fit for me here in the BioPhysics Lab. I really enjoy learning about everything, and it is all really interesting, and Anthony and I all work well together. One morning we were talking about all the projects we have going on and Anthony asked if I wanted to be the project manager for them. What a great fit for my goals and experience. We decided that I would work as a Research Assistant, focusing on the project management side of our work.

So, the semester is started, and I’ve finally gotten a regular lab schedule worked out. Anthony and I met today about all of our ongoing projects. The synopsis of current and upcoming happenings in our lab is posted on Google Docs.

P.S. I’ve had to shelve my R learning project for now. I’ve gotten a fair understanding of the language… enough to basically understand code already written and edit it if needed. I’ve also gotten the hang of the syntax. Had to put it down for a bit though, this semester I’ve got 4 classes with 4 languages to learn. I didn’t want to push my brain over the edge.

FTIR Training


Yesterday evening,  Stephen Myers from the NSMS department kindly gave me some basic Fourier transform infrared spectroscopy (FTIR) training. I learned what settings to use in the OMNIC software, how to position the cuvettes in the FTIR, and how to save the data to .csv files.

The training took about an hour, probably because I asked a  lot of questions about all the options in the Experiment Setup dialog of  OMNIC. For our purposes we will only need to set a few options as outlined below.

Collect Tab:

  • Number of Scans. The options are between 1 – 128. He suggested 32.
  • Data spacing. Select 4 or 8. The larger the spacing the smoother the curve (less points collected). Smaller spacing scans take longer.
  • Final Format. %transmittance.
  • Correction. None.
  • Under Background Handling, select Collect background after 100 minutes (more on this in a minute).

Bench Tab:

  • Select Min/Max option
  • Set Sample compartment to Main. The view should look similar to cross-hairs, not noise.
  • Set Recommended range max to 10,000 and min to 2,000. The range is  determined by dividing 10000 / the range limit. The resulting quotient is the wave length. Stephen figured our cuvettes would read best with a limit of 1 – 4 microns.

Click the OK button to accept the changes and exit out of the Experiment Setup dialog box. We are now ready to collect our background reading.

  • Set the empty cuvette in the scanner. Make sure the red beam is on the sample.
  • Close and lock the door.
  • Wait at least five minutes for atmosphere clearance.
  • Click the Collect Background button.
  • Save the file.

Once we’ve collected the background information, we want to change the Background Handling option in Experiment Setup to Use specified background file.

Now we can load samples and scan each of them. OMNIC will automatically remove the background information from each scan. When we are done we can save the file(s) in .csv format to use in any data analysis we need.

Stephen would like me to run a few scans with him present and then Anthony and I can schedule time on our own. I’m stoked!

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