Title: RNA DBPAbstract: The RNA DBP focuses on the folding and dynamics of RNA, particularly the tetrahymena group I intron. In this review of progress, we will touch upon the details of year 1 accomplishments, and suggest the DBP trajectory for the next year, including new problems. The areas of progress include:
1. Analysis of experimental data to extract kinetic pathway information for RNA
2. Coarse grain simulations to understand the structural features of kinetic intermediates
3. Experimental-computational correlation of ion atmosphere studies.
4. Improving coarse grain sampling power with replica exchange methods
Areas for focus in the coming year:
1. Test utility of normal mode analysis for RNA dynamics
2. Test parameterization of coarse-grain potentials, by their ability to generate plausible RNA structures with limited data
3. Distribute ion atmosphere code as hardened, downloadable application
4. Distribute coarse-grain RNA modeling code
5. Create and distribute RNA morphing application at "physics level 0-1"