RNA Macrostates and Landscapes

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Abstract:  RNA folds are often described with a single secondary structure, or microstate, the most probable of which is the minimum free energy (MFE) microstate. But quantitative prediction of characteristic properties far beyond the MFE is possible.  In this talk I will describe: 

(1) how to define and visualize RNA macrostates, the groups of microstates separated by free energy barriers,

(2) the scaling of base-pair probabilities, and more efficient algorithms to compute the ensemble, 

(3) how to optimize RNA to increase the over-expression of proteins.