July 17 Thursday

These are the Big ideas:
1. Math is the key to science. Much research is done through Mathematical simulations. Students must understand the relative size of things in the Universe and the effect of adding another zero as a beginning to explain what scientists are doing.

2. Functions are everywhere. Students will understand how graphs/distributions are created by functions. Not only what the graphs represent, but how we can utilize the information once it is compiled.

3. Students will understand the importance of proteins and the reasons researchers are studying them. They will understand how math is used in research and the things that we can do with the information it provides us.

The main thing I am taking from the research is how exciting the things that are being done at ASU are. What kinds of things we are researching, how the research is accomplished, and what will be done with it.

I had no idea about how math was being used to simulate what cannot be seen. Even though the math and physics is way beyond my capabilites, and certainly my students, I feel I have a good general understanding of what is trying to be accomplished, some of the things that have come from the research, and what they are hoping to find. Each day the explanations by the researchers were creating analogy after analogy in my head. These are what I will share with my students to help them understand what I have to share with them.

My students have difficulty seeing a longterm purpose for their math. With the information analogies I have to share, I hope my enthusiasm for what I have seen will be contageous.

The activities I am initially envisioning for the students will include Arizona Math Standards, Strands 1, 2, 3, and 5! I believe I can use the experiences from the summer in nearly every unit that we cover this year.

The 3 Main activities to address the 3 Main ideas are:

Powers of 10 - Two different short videos and a book to get their minds into motion. There are some existing activities to start with, then some modeling ideas for the students to create from their new experiences are still forming.

Boltzmann Game - Students will play an adapted version of the game to gather, graph, and analyze data. All three aspects will be assessed for understanding. Students will see how the knowledge is applied by playing the "Marble Game", which helps to explain how scientists perform the simulations in their research.

Movie Making - Students will create short videos from shapshots so they will better understand how increments of time effect what scientists can observe in their simulations, and also what they might miss, if the do not use the correct resolution.

Protein Folding Simulations in PyMol - students will observe and hopefully personally manipulate the images they see in PyMol of the proteins and their movements.

After our discussions today, I thought of something new to take to the students that might really spike their interest; this research into protein folding is being used in pharmaceutical research and the treatment and maybe prevention of diseases and conditions. This protein folding research might help to identify ways we can cure or prevent learning disabilities or at least understand them a little better. Many of my students feel there is something wrong with them, that they need or want their self perceived defect to go away.

This has given me some ideas for some research into what other research is currently being done in this area.

July 16 Wednesday

Michael Thorpe's topic today was How do we get students to understand the relationship of size between quarks and the universe? He showed us the video "Powers of 10" and another presentation he had about quarks. He had some great ideas to assist our students to think about the differences.

July 15 Tuesday

Michael Thorpe shared one of his favorite movies with us today, "Life Story". It is based on the book "Double Helix" by James Watson. It is the account of his discovery of the double helix and the Noble Prize he received for his work. It was much better than it sounds, Jeff Goldblum played Watson.

July 14 Monday

Spent the morning working on our poster. Good collaboration.

July 11 Friday

Normal Mode Analysis was the topic for today. We found some protein videos in YouTube that we can share with our students. Nevin, the grad assistant went through the process where we can create our own movies using the protein database models opened into PyMol so we can show our students how the different proteins have different movements for the functions they provide. Researchers use this information to better understand the relationship between structure and function.

July 10 Thursday

Daniel Barr went over Normal Mode Analysis with us today. He reviewed the time steps involved in the simulation process. He went over some of the things that Arjan introduced the other day to make sure we got it. Daniel helped me with PyMol also.

David and I went over some more of the project, coming along nicely.

The tours in the afternoon were great. The Spiderlab was very interesting, have been looking forward to that. I hadn't realized we would be seeing the NMR. We have been talking about it in our protein research so was especially excited to see that and learn more about it.

Decision theatre was neat, wish we had time to see the brain.

July 9 Wednesday

This morning, Dr. Lindsay took the CBP group on a tour of the Bio Design Center. Wow! The things that they are doing they are amazing. The research alone is mindboggling. The facility is beautiful, and the layout that encourages interaction among disciplines and projects seems to be the only way to do things. What better way to inspire ideas than to have the interaction between these bright minds, bouncing ideas off of each other, questioning and explaining. I was watching two men drawing on a white board and discussing. Don't know what they were talking about, but it looked important.
Dr. Lindsay is so well versed in all of the topics being researched. He has a tremendous ability to explain what is going on in terms that are understandable. Many commented on how much we appreciated him taking time from his day to take us around.

David and I made very good progress on our poster today. We also had an opportunity to sit down with Banu to get a preview on what she would like us to focus on for our project. She will not be going over it with the class until Friday. We now have a good idea of what she would like, and have some time to develop some ideas. We believe it will fit in well with what we wanted to do with the Movie Maker.

July 8 Tuesday

Banu helped us to match up with PIs today. David and I will be working with both her and Arjan(Daniel Barr). She has a project in mind for us, but we will not be getting the lecture until Thursday that will explain it. Daniel will be assisting us in clarification on some of the background information we will be using to develop the other ideas we have at this point. I am a bit concerned that my students will not be able to execute her project at the level she is hoping. We will do our best.

July 7 Monday

Molecular Dynamics was the topic of Arjan's lecture this morning. The simulations compliment the traditional experimentation. Certain types of data cannot be measured by experiments:
- Very high spatial and time resolution data
- certain energies, correlation functions, etc.
- decomposition of energies
Simulations are expensive, but safer. They are used to guide experiments and give insight to potential behaviors.

July 3 Thursday

Michael Thorpe ran through some of the algebraic calculations for the Popsicle Stick Project. He used a process that we might use with our students to set up a formula that could be used with any 2D structure we might make with the sticks. After we went through the whole process, which was a bit time consuming, he showed us an extremely simple way to get to the same answer. Great problem solving activity for our students.

July 2 Wednesday

Dmitry this morning. We tried a new simulation today with CCP4 Molecular Graphics. This program will enable us to create graphics for our presentations. In the simulations, graphs of data are studied to find the optimum conditions of energy (heat) and polarity in which the cells function. In their optimum environment, the proteins fold and can function normally. When the conditions fall outside the parameters, the proteins want to unfold, and cannot function normally. Alzheimer’s is a condition that happens when some of the proteins strands unfold, or straighten.

July 1 Tuesday

Spent the morning with Dr. Thorpe going over the popsicle stick models for rigidity.

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.