Artist’s Dye Fading Part 3: July 1st – July 25th

Science can be a fickle mistress; sometimes I feel like i’m blasting through experiments and making good progress while at other times I feel as if I haven’t made much progress. For a while I thought that the dye Alizarin had contamination in it which was changing the fluorescence spectra. While I got past that debacle it did suck up alot of my time which could have otherwise been more gainfully employed. ¬†With the summer more than halfway over I can start to feel the attrition set in. Up to this point the vast majority of my time has been spent on the fluorimeter trying to understand the photophysical behaviour of these molecules. However at this point there is not much more information that can be interpreted from any more spectrographic scans. This means that it is time for me to start transitioning from the experimental portion of this research to the theoretical part. The theoretical half of our research involves using matlab to simulate single molecule blinking data. Basically we have a set of rate constants that we put into the matlab program which then spits out data. Our goal is to set the parameters such that the simulated data matches up with the experimental data. These rate constants describe the photophysical behaviour of the dyes which can ultimately lead us to understand the physical mechanism by which the dyes fade. Besides this simulation, there are some other loose ends which need to be tied up such as confirming the chemical identity of Purpurin lake– the dye that we had to synthesize ourselves. Usually we would use techniques more familiar to us (fluorescence/absorbance) to determine the identity of the molecule– however purpurin lake has an annoying tendency to not dissolve in anything. This makes it hard to analyze chemically using solution state spectroscopy. Some techniques that we are considering using are x-ray crystallography, FT-IR spectroscopy, and NMR; all of which I have no idea how to do.