Week+of+August+31st,+2009

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__September 1st, 2009__ I have not made it into lab (still), I'm going to try to go in Thursday afternoon for an hour or two, and on Friday. I think Fridays will be the best for me to go in because I won't have to stress about the homework due the next day.

Here are some images that I have been analyzing in my free time (I'm attempting to make a statistical analysis): These images, captured on the same day, are of DNA origami with sticky ends. In the bottom image, you can see that there are some offsets in the DNA trails at (1.50, .50 ). I am attempting to make a statistical analysis based on the offsets seen in DNA origami with sticky ends. I believe the offsets to be either 0 nm or around 35 nm (the width of a DNA origami is around 60-70 nm.

__September 03, 2009__ Today I went into lab and talked with Dr. Lieberman and Nan Kim (the graduate student I've been working under). We discussed scheduling during the fall semester and my project. I decided on going to lab every Thursday and Friday, it should work well with my schedule.

Dr. Lieberman gave me a few pointers on how to work on the current statistical analysis I have (the offsets of the DNA origami in chains). I'm working on that tonight as well. Tomorrow I'll be going into the lab to show Dr. Lieberman and Nan what data I have gathered regarding the statistical analysis. I will also be working on two other stat. analysis' tomorrow (the lengths of the chains and the average width of each chain).

When I complete the analysis' I will put them up on the wikispace.

Dr. Lieberman also said that if I was interested in learning about a new instrument or area of DNA tiling, that I could possibly become educated in that area. Probably later on in the semester I will began learning about something new, as of right now: I still have a lot to do for my current project.

__September 04, 2009__ I went into lab today to show Dr. Lieberman and Nan the data I've been collecting. I spent about 1 1/2 hours in lab today working on my stat. analysis. I discussed with Nan my project. After I finish collecting enough data, I will be assisting her in depositing DNA origami with sticky ends on an APTES trail pattern, which will possibly lead to my learning of the EBL (Electron Beam Laser) machine. Nan also said that I will probably have to learn to use the liquid cells with the AFM. I'm not sure exactly what this is, but I do know that it is imaging your sample under liquid rather than in air. Both Paul Rothemund (the developer of DNA origami) and Hao Yan (a significant figure in the DNA origami department) image their origami under liquid cells.



This image (sorry about not having a scale bar) has the slightest hint of the index pattern. Its in the origami closest to the top on the left (I wish I could draw a circle around it), its on the bottom left corner of thhe origami. The area is lighter in color than the rest, that suggests that there is a height difference which leads to the idea that it may be the index pattern.