Week 1 Update

The first order of business each morning in the lab this week has been to remove the previous day’s glassware from the base bath (an extremely strong solution of ethanol, potassium hyroxide, and ultrapure water), rinse it thoroughly in ultrapure water, and leave it to dry before storing it in our respective drawers. As a single-molecule spectroscopy lab, we want to be sure that no molecules besides the ones we’re studying show up on our scans, and this makes cleaning extra important. I’ve worked hard so far to start the summer off on the right foot by following this protocol and avoiding contamination.

Another crucial step to take before single molecule scanning is to take a bead scan. We use microscopic polystyrene beads that absorb a specific wavelength of light to align the laser and sensitive photodetector in a way that maximizes photon emission intensity from our dyes later on. Essentially, this ensures that we can actually see the molecules we’re looking for. A lot of work this week has gone into making sure our beads are good: they deteriorate over time, and we need them to be round and regularly distributed to work well. A good bead scan looks generally like this:


Most of our beads look okay shape- and packing-wise overall, but all of their “counts” (photon emissions) are (at least consistently!) lower than we’re used to seeing, so that’s definitely something to keep an eye on in the coming weeks.

Yesterday I finally got to the main event, the Eosin Y dye scan. But I learned the hard way that you have to walk before you can run: it’s important to work down to single-molecule concentrations with control experiments, and starting out at 1×10^-9 M, it was hard for me to find almost anything of value. This issue also could have come from the age of the stock solution I was using – the dye, like the beads, is only good for so long, and tends to aggregate eventually, making it hard to see molecules on their own as we want to do. Therefore, today I made a new one that I plan on taking a look at next week. In doing so, I’ll be stepping down in concentration and comparing each step to past data of EY on a glass substrate. At a given concentration, we should see about the same number of molecules in each scan, and that’s how I should know I’m ending up at the right concentration to see single molecules. I also got practice working up my raw dye and bead scan data into images like the one above today, so that was another learning experience that came from my missteps.

Overall, I learned a lot this week about the research process in general, and my path forward for the summer has become a little more clear. I’m excited to continue next week!