Diary of the 2003 Summer School on Theoretical and Computational Biophysics

Wednesday, June 4 -- Elif Ozkirimli

Today we went over steered molecular dynamics, in which I am very interested since I'm using a similar method to study my system. I was especially happy to learn more about how AFM works and about the comparison of forces in AFM and SMD; sometimes I need to be reminded that most of this computational work is motivated by experiments. The section on Jarzynski and umbrella sampling was exciting and new stuff, I should definitely read the paper. Elif Ozkirimli

The sun came out from behind the clouds for the first time since the summer school started and we had a very nice picnic lunch on the Quad; UIUC is pretty and lively after all!!
"UIUC is pretty and lively after all!"

I was very excited about the IMD hands on session. SMD really works! Learning how to calculate the PMF was very useful, but I didn't have a lot of time to think about what I was doing while I was doing it. It would be very good if there were a few more questions to make us think through the process rather than just follow the directions. The questions that were there were pretty beneficial, though.

After a nice coffee and dessert break, we went to the evening session and worked some more. These evening sessions are very useful for me. They also give me a chance to check my jobs that are running back home. Then, the usual: going out with friends and enjoying the fun Champaign night life.

I really enjoyed all of my time here and learned many things not only from the lectures and hands-on sessions but also from all the other people. Thank you summer school team, you did a fabulous job.

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