Week 1

I did read papers as introduction to the project to get first a general and then a more detailed idea about the whole protein folding simulation project and what will be my part to it. In particular I did read:

A Motion Planning Approach to Protein Folding. Guang Song, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2003.

Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment. Payel Das, Corey J. Wilson, Giovanni Fossati, Pernilla Wittung-Stafshede, Kathleen S. matthews, and Cecilia Clementi. Proc. Natl. Acad. Sci. USA, vol. 102, no. 41, pp. 14569-14574, Oct. 2005

I also started reading the code of the protein folding simulation program and started getting an idea of how it works in some details. I run the program a few times to get familiar with it.

Further questions about the project were answered during meetings with my Mentors

I wrote the pseudocode for the part I am adding. After checking with Lydia Tapia (one of my graduate Student Mentors), and finding out that my pseudocode represented exactly the code she already wrote a while ago, I included Lydia's code into the program. On Friday, it run the first time. Well, I don't know yet if it really does what it supposed to do.

At the end of the first week I was tired, but happy, and knew that I really like this project. It was an exciting week. Many thanks go to my Mentors. The introduction to the project could not have been better.