In 2016 I was accepted into the ARC/ORNL Summer Math-Science-Technology Institute put on by the Appalachian Regional Commission and Oak Ridge National Laboratory. I would be spending two weeks conducting research with other teachers in one of the top research labs in the country!

Link to our lesson plan

The Research

‘Crystal Structure of the Protein Lysozyme followed by a Molecular Dynamics Simulation’.

Preparing the samples

What does this all mean? Our goal was to determine the molecular structure of this particular protein. It was by no means difficult or ground-breaking (it was mapped decades ago). Our purpose was to show that this is something that students in area classrooms could do. The first week was spent trying to crystallize the lysozyme. Lysozyme is a protein abundant in organic materials such as egg whites, mucus, saliva, and tears. It is part of the immune system and a deficiency in lysozyme can lead to an increased incidence of disease. Our mentor chose this protein to use for our experiment because it is easy to see results and it is easily accessible.

My team!

We conducted several trials of different concentrations of the protein solution to see what would work best. Once that was done it was time to wait and see if the crystals would grow. Some samples produced many crystals that had many facets (and wouldn’t be useful) while other samples produced only one crystal that was perfect (very useful).

  • My beautiful crystal
  • Alaina’s crystals through a polarized lens

Once the crystals were grown we would have to try to scoop them up with these tiny scooping tools. Since they are so small we would have to try to scoop them up while looking through a microscope. To make things more difficult, they have the consistency of jello. Once we had the samples we needed we took some joy in crushing the extra crystals.

  • This is the scooping tool we used compared to a ball-point pen
  • Scooping tools

Once I scooped up the crystal I would have to slide a capillary tube over it to keep it hydrated. The tube had a diameter of less than 1-mm and if I didn’t get it just right, I would destroy the crystal. The tube would then be placed in an x-ray diffractometer. This tool would fire a beam of x-rays at the crystal. As the photons reach the crystal they will diffract around its crystal matrix. The diffracted x-rays will strike a screen which collects the data and sends it to a computer.

  • Analyzing the diffraction data
  • X-ray diffraction pattern

Our week at the Spallation Neutron Source was coming to an end. For the second week we would be at the main campus working on creating a molecular dynamics simulation of the data. Before we left for the week we got to enjoy Reuben Day.

Only my team, who was working at the Spallation Neutron Source, got to enjoy Reuben Day

Molecular Dynamics Simulation

The other groups were done with their research and spent the second week putting together their presentations, posters, and lesson plans. We had a second week of work to do. Our work was now moved to the Center for Molecular Biophysics. We would be using computer simulations to model the dynamic structure of the protein lysozyme. We weren’t really sure what we were doing as we just followed the instructions that were provided. We did come up with something though. After several days of work we ere able to produce the static structure of the protein. The software allowed us to represent it in several ways.

  • Structure of the protein lysozyme
  • Structure of the protein lysozyme showing secondary structures
  • Only the lysines and glysines
  • Protein in a 20-angstrom cube of water

Our final task was to produce a molecular dynamics simulation of this protein. That is, we were to create simulation to show the movements of the protein. After about two hours of compiling our simulation was complete! We had a simulation that was bout 10 picoseconds long. To put that in perspective, light will travel about 300,000,000 meters every second. That is fast enough for light to circle the Earth about 7.5 times each second. In 10 picoseconds light will only travel about 3 millimeters! If I were to try to use the computer to get enough data for it to be meaningful it would probably take at least a year. This is one of many reasons why supercomputers are beneficial.

Fun fact: Ten picoseconds after the Big Bang, electromagnetism separated from the other fundamental forces!

Side Trips

It wasn’t all work, the program provided us with numerous opportunities to experience the things Eastern Tennessee had to offer.

  • Rainforest Adventures
  • Feeding time
  • Tilted bedrock
  • A metamorphic rock with fossils!
  • Generator that produced the first electricity from fission
  • X-10 graphite reactor
  • 3-D printed Shelby 😍