It spilleth over

Juan got back into town last Monday. Wednesday we met to discuss my near-term research and I now find myself as busy as ever. Thankfully over the summer I've acquired the skills to successfully do those things he proposes. It's not easy; it never is. If it were, it would have already been done! As I like to say, grad school isn't for sissies and it isn't for you normal folks either. (I think I qualified because of my unbridled enthusiasm for science (nerdiness) and lack of business and social acumen.)

My current projects are these:

1) Determination of the effect on DNA sequence length on rate of hybridization and the reasons for said effect. Experimentally it has been observed that the rate of reaction decreases exponentially with sequence length. We are interested in determining the mechanism responsible for such behavior. I will use forward flux sampling to calculate the rate of reaction, together with the methods of Northrup et al.

2) Elucidation of the mechanism by which DNA strands linker to gold nanoparticles hybridize. This will build on the earlier efforts of Hoefert (in preparation) and Sambriski who have preceded me in the de Pablo group. I will use transition path sampling and a harmonic spring to represent the alkanethiol linking the DNA to the gold nanosphere

3) Development of a new DNA model without a Go-like interaction capable of capture the formation of hairpins that would easily be extensible to RNA. To do this I will incorporate methods and ideas from the excellent models of Morris-Andrews et al. and Dans et al.

I find my cup brimming with work to do and I would not have at any other way. If the stars align just right and if I work up to my potential, I may get a few publications out of this work. Believe you me, when I publish I'll make sure to tell the world!