June 30 Monday

Banu spoke with us today. She went into a little more detail about her specific research. She explained how the research is used to find possible drug treatments for diseases such as cancer. The drugs target certain characteristics that cells exhibit. The medications used for cancer, target cells that grow rapidly, any cells in the body that grow rapidly and doesn't distinguish between "good" or "bad" cells. Hair grows rapidly, so these cells are targetted by the cancer meds which is the reason cancer patients lose their hair during chemo treatments.

We began to play the game called "Fold It" today. It simulates protein folding. Online players change the folds on the protein using all of the "rules of folding". The players info is used to identify possible new proteins. The main demographic of these online players are 45 year old housewives. Supposedly they don't feel guilty spending hours on this game, because they are helping with scientific research.

June 27 Friday

Today's presenter was Daniel Barr, a Phd student working with Van der Vaart. He talked about Molecular Dynamic Simulations. He talked about "meaningful snapshots" and atomic resolution. We used a simulations applet that gave a graphic representation of the energy in the molecules. He said the simulations are not useful, unless they provide accurate results we can count on. The focus of his research is a specific lactose molecule that sits on the DNA.

We talked a little about how we might divide into groups.

June 26 Thursday

Fabulous morning session! Dr. Lindsay spoke on DNA sequencing. He covered a number of topics that we had intros to over the last week, reinforcing and elaborating on the concepts. He talked about some of the research they are doing and is going to try to set up a tour of the Biodesign Institute. He strongly encouraged us to read "Double Helix" by Jim Watson. Dr. Lindsay talked about the progress made on the study of the human genome. Epigenetic coding and X chromasome poisoning and how the methalation of DNA can prevent it was discussed.
He explained the process of how to get DNA from a crime scene using Polymerase Chain Reactions. The information on nanopores and carbon tubes was fascinating.

June 25 Wednesday

Dan Farrell one of the grad students was our presentor today. He gave a great explanation of the calculus and physics behind the simulations that we have and will be viewing. My biggest "aha!" moment was when he said that the derivative was the slope.

We downloaded Pymol today and watched a short demo. We will be doing things with it soon.

June 24 Tuesday

Presenter today was Kirill Speranskiy. we worked on http://flexweb.asu.edu
We were looking at rigidity anaylsis, rigid units, and flexibility of protein models. The Interactive Pebble game was interesting, but not quite sure what it was doing. The FRODA model showed a comparison of the crystalized models and the NMR models so we were able to see that the crystalized models, though not as acurate were pretty close to the NMR models. Daniel had told us yesterday that even though the NMR is available to rerun models, it is often not worth the effort if the crystalized models were run with a resolution of at no more than 3A.

June 23 Monday

Todays morning session was hosted by Daniel Barr - Phd student. He had great analygies of the protein chains and the bondings. Explained that Ucariotes have a nucleus, and procariots, do not. The nuclius protects the DNA which is good and bad. Good that is keep ucariotes, such as humans, in a stable form; not morphing all over the place. Bad, because if something undesireable gets into the nucleus and affect the DNA in a negative way, such as HIV, it is difficult to get possible antidotes or treatments into the nucleus to undo the affects.
Websites today: ftp://biophysics.asu.edu/drop-box looked under PDB. Other site http://trc.ucdaavis.edu/biosciv/bis10v/week2/2webimages/ch5-amino-acids.jpg Can recognize a backbone on the board now!

Brian brought us all 3-D glasses to view the models, very cool!!!

June 20

Today was with Dmitry. He had us go to a cool website www.rcsb.org/pdb/home/home.do where we could see virtual models of proteins. We used RASMOL and RASWIN to access and display the models. We were able to manipulate the models, highlighting various attributes and rotating to see the various parts at different angles.

June 19

"DNA, Inheritance, and the Struggle for Survival" was the title of the presentation given this morning by Adam de Groff, one of the grad students. The material was very interesting and very well presented. Better morning because I have better background information in this area. Good explanation of the polarity of molecules. Much more detail on the terms hydrophilic and hydrophobic. RNA, DNA, and cell differentiation which is tying in with some of the previous mornings info. Felt much better about what was covered this morning.

In the afternoon we got into the Wiki a bit. Some of the teachers at my school are starting to do things with Wikis, I can definitely see some possibilities. Also got some good ideas from the group work for both teaching possibilities and supply resources.

June 18

Brought old laptop today and was able to sign onto ASU wireless with a little help from Kirill. Also called helpdesk and got a generic sign on for the computers in the afternoon class.

Dmitry went over some more background information this morning. I can understand the pictures/diagrams on the board, but the formulas are full of symbols I do not know. Was feeling much like my own students, just lost. I am not even sure what questions to ask.
Dmitry showed us how to get on his and the other researcher's pages today, so will do that tonight.

John Morris helped me understand the size of Nano and Pico seconds today with a great analogy using Redwood trees, human hairs, and an inch on a ruler.
He said imagine holding a one inch piece of ruler up next to a redwood tree. Now the redwood tree is the size of a human hair, with the piece of ruler in a matching scale. About 3 Nanos would fit in that inch.
I can understand almost anything if I can make an analogy for it.

Looking forward to the "mini-workshops" in the afternoon. Can do most of the topics, but could do a lot more with them.

June 17

I managed to find both the a.m and p.m. locations without too much difficulty. Our mentor teachers gave a presentation on their experiences from last year, and shared some of their projects and how they were created. This was very helpful and encouraging after some of the concerns I was experiencing after yesterday. Dr. Matyushov gave us some background information this morning. This was extremely helpful. The math and physics pieces are much more advanced than my ability, however, getting some of the vocabulary that I am not familiar with gave me some idea of the outside reading I will need to do to be more comfortable. Two bonuses from this morning: I was able to understand some of the basic ideas, and being able to listen to him speak gave me a chance to understand his accent. The accent is going to be ok!

June 16

The first day of the project was interesting. Lots of locations to remember, when to be where. The researchers gave a short presentations on their research which was very interesting. Some concerns at this point: is the project I have been assigned to going to be “over my head.” The researchers that we will be working with are very interesting and I am excited that they are from parts of the world that I have never met anyone from. There is a little concern that being unfamiliar with their specific accents that it may take a few days to get “tuned into” the accents well enough to understand what they have to say.