End of the Summer

Hello,

This summer has been so productive and fun at the same time! For  a quick summary, my research is related to solar energy cells and understanding electron transfer between organic dyes and the semiconductor TiO2. The end goal was to find a probability distribution function that best fit the data to represent the system and kinetics behind electron transfer.  I collected data of Rhodamine B on glass, Rhodamine B on TiO2 and Rhodamine 6G on TiO2. After working up the data to test if the Power Law is a goof probability function, I rewrote a code to test the Weibull function. Interestingly enough, the power law best fit both RB on Tio2 and R6G on TiO2 on times, while Weibull best fit all of the off time data sets. Unfortunately, there might still be some glitches in the code for a Weibull function, but I am working on hammering out these problems by the end of the week. Despite this, these results are very interesting, and next I will be working towards re-writing a code to test a stretched exponential function. I have learned so much about statistics and probability and have put my math skills to the test, but decided that I really enjoy math and am happy this summer was another way to confirm that.

Does Anyone Know How to Use ‘R’?

It is already July! I find it hard to believe that we are halfway done with the summer research session, however I am super pleased with the progress I have made so far. I have finished collecting data of Rhodamine B, understand the MATLAB analysis and coding, and have applied this analysis to the data. I am now trying to finish up collecting data on Rhodamine 6 G, a dye of similar structure to Rhodamine that we are testing for comparison. As for additional analysis and coding, I have quite a challenge ahead of me.

MATLAB Clauset Codes

After spending a week staring at a computer screen filled with numbers and strange codes, I have gotten a good handle on the MATLAB Clauset codes we are using to analyze blinking traces. Aaron Clauset created 3 MATLAB programs to fit blinking data with a probability distribution function and then asses the accuracy of this fitting. A power law distribution has commonly been seen across literature as potential probability distribution function for blinking traces. Because of this, the Clauset codes focus on the power law.

ABC easy as 123, what about CDF?

Hello,

So after one week I have completed my data collection by 102 blinking traces of Rhodamine B on TiO2 single molecules. I have been analyzing the blinking data with a MATLAB using a CPD code. Just as reminder, blinking is the when a molecule jumps between fluorescent and non fluorescent states. This code uses a change point detection logarithm, and determines the number of significantly different intensity states, what the intensity states are and whether or not they are ‘on’ or ‘off’. A state is on/off if it is above/below a threshold, which is also determined by the program. After working up the data, 102 molecules has resulted in 1002 on segments and 246 off segments. Now how do we analyze this?

100 molecules to go

Hello,

I have just completed my first week of summer research and have set a few short term goals for the following week. I am currently focusing on two things: data collection and literature research. I am continuing my work from the school year of collecting blinking traces of Rhodamine B (RB) dye on TiO2. To quickly recap, the RB dye is diluted with water and TiO2 to 1e-9M. This solution is then spin-coated onto a blank slide and analyzed under a confocal microscope. A laser is then used to hit the slide, resulting in fluorescent molecules, a photon detector and scanning acquisition program then produces an image, in which molecules show up as bright spots. Once the molecules are located, each one is hit with the laser and blinking are traces are collected as the molecule switches from on (fluorescent) states to dark states(Fig.1).  Once in a permanent dark state, the molecule is photo-bleached. Data collected on a photo-bleached molecule provides no useful information, so I am experimenting with different factors to increase the molecules stability for longer data collection time. Currently, molecules are put in a Nitrogen atmosphere for increased stability. The power of the laser also effects how long the molecule may fluoresce until being photo-bleached, and currently the best power has been a wave plate length of 20nm. Half of the times blinking traces are collected, however the other times the molecules are already photo-bleached. There are some cases where the molecules begin to fluoresce after certain periods of times, making it difficult to know if a molecule is truly photo bleached.  As more data is collected this week, I hope to better understand patterns and time duration of the blinking traces. The goal is to collect useable data from 100 molecules! Currently I have 28, I guess I have a ways to go.