Week Eight
This week Laura and I worked on a creating a context-free grammar which would
generate all possible RNA strands with a secondary structure. If we could
obtain a grammar to generate all the possible RNA strands with secondary
structure and the grammar was context-free, then we could use formal language
theory to prove many things about the set of strands with secondary structure.
We determined that it probably was not possible to create such a grammar. However,
our reasoning was based solely on intuition and multiple guesses. We could not prove that
such a grammar does not exist. At this point, we decided to modify the grammar that
we were going to generate. We decided to generate the set of all strand that have RNA
secondary structure where the internal, bulge, and hairpin loops were limited to a length
"short" where "short" would be defined in terms of the word length. For a word length of
l, the length short would equal 2l-1. After several tries, we determined that this also was
probably not possible. We decided to modify again what we were generating. The final
grammar that we created generates all RNA strands which have a stable secondary structure where
all substructures have positive energy. This grammar is available in pdf form
here .
This weekend I decided to spend the day shopping. I took a cab to the store that was the furthest away,
and then shopped my way back to my apartment. I didn't get anything great, but I did buy myself a pocket
knife. You might be thinking that I would not need a pocket knife since I am
a city girl, but you would be wrong. I never realized how useful they are.
I also picked up a few things my mom had asked for that she either couldn't find in the
States or that were signifigantly cheaper in Canada. Gotta love that exchange rate.
All in all it was a relaxing week, as opposed to last week.