Lawson Gillespie and Ross Silver
The prerequisites of theoretical quantum biophysics research.
In this last week my work has been almost exclusively on learning the basics of using different research quality open source softwares, while simultaneously adapting to life without the comfort of a Windows operating system. I decided to make the switch to using the freely available operating system Linux Mint, one of many options for a UNIX environment. This environment is a perfect blend of daily usability and research tool feel and experience.
Figure I: The tools of the trade are still largely text command based.
As with every new skill, it takes time to practice and learn. In my experience, combining a slowly evolving intuition and good googling skills has been essential to making the transition possible. In the future our research will be conducted on a large box computer in a specially cooled room in Masters Hall. As such, my daily research has been to familiarize myself with these tools ahead of the computers construction.
Figure II: The powerful protein visualization tool, PyMol.
Over the course of my physics major here at Gettysburg I have not had to take any computer science courses, so the learning curve has been very steep over the last couple of weeks. My daily tasks over the last couple of weeks have alternated between studying quantum mechanics, photosynthesis, and what I will describe as “advanced computer literacy”.
Figure III: LaTeX typesetting software is the standard for research articles in physics and many other disciplines.
Being able to use all these different softwares will not only give me exposure to the programs I will use to do research in, but also has inspired me to explore the computer and its role as the “research apparatus” of theoretical physics.
Figure IV: A basic version of the research code, which is based on the Quasiasiadiabatic Propagator Path Integral Method.
Overall, the work that I am doing today will enable me to run conduct our research during next semester where we hope to study the quantum mechanical nature of the energy transfer process between different photosynthetic pigments.
My story is not going to be about my research experiences on campus this summer. Instead I will explain my week of June 23rd to June 30th in Arizona.
I went with one of the Physics professors, Dr. Milingo, and two students who are working for Dr. Johnson this summer, Mikayla Cleaver and Sabrina Marell. Gettysburg College is part of a Consortium called NURO, or National Undergraduate Research Observatory. NURO operates a 31” telescope at the Lowell Observatory in Flagstaff, Arizona.
We arrived in Phoenix on the 23rd and then drove up through Sedona (Figure 1) to Flagstaff. We worked Friday, Saturday, and Sunday night.
Figure 1 (Sedona)
We were supposed to work Monday night too, but it was too cloudy. Our typical work night means arriving at the observatory (Figure 2) around 6:15 pm.
Figure 2 (NURO)
We would then turn on all the computers in the warm room (Figure 3) and sign in.
Figure 3 (Warm Room)
Then we took bias shots (taking a picture with 0 second exposure) and flats (taking a picture of a blank, evenly colored part of the sky) with the telescope. Both are used to subtract any noise or other false data from our images. Then once the sun set and the sky got dark enough, we started taking images of NGC 6811 (Figure 4), a star cluster in the constellation Cygnus.
Figure 4 (NGC 6811)
We took six images at a time, which took 30 minutes. During this time we would play card games or watch Netflix. Sometimes we even watched make up tutorials… I was real thrilled about that part (not really). After the images were done, we would check the focus and adjust it if we decided it need to be. If not, we would start another six images. We did this until about 4 am. Then we would shut down the telescope and leave for the night around 4:30 am. This trip was focused on learning how to operate the telescope, but we did many other cool things too.
We toured through Sedona, visited the Northern Arizona Museum, and my favorite, saw the Grand Canyon (Figure 5). This was a truly unforgettable experience and I am very #blessed to have had the opportunity to go.
Figure 5 (Grand Canyon)