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.