1. RNA world hypothesis (Gilbert) and diverse roles of RNA in cell biology
2. Review of thermodynamics for ab initio secondary structure modeling
3. Energy parameters via optical melting
4. Dynamic programming thermodynamics-based algorithms for structure prediction a) Minimum free energy structure, and variants thereof b) Partition function, sampling low energy structures for biological applications c) Saturated and locally optimal structures, expected 5'-3' distance
5. Coarse-grained kinetics via basins of attraction a) Gillespie's algorithm b) Kinfold, KFOLD, and related algorithms
6. Markov state models for secondary structure kinetics
7. Rational design of RNA structures a) Inverse folding problem b) Ribozyme and riboswitch design Appendix: Review of linear algebra and Markov processes for applications in kinetics