Arrhenius Lifetimes of RNA Structures from Free Energy Landscapes
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- Sauerwine, B. & Widom, M. J Stat Phys (2011) 142: 1337. doi:10.1007/s10955-011-0174-2
We develop a novel method to define an effective free energy barrier between various conformations available to an RNA sequence. Our approach utilizes the energy landscape computed using the ViennaRNA package. Replacing the energies with configurational free energies yields improved agreement with the Arrhenius law provided we account for the entropies of both the basin states and the barrier states. This improved agreement comes without altering the computational complexity class of the algorithm. We discuss the combinatorial explosion of high-energy states available to RNA, and the properties of Kawasaki and Metropolis transition models that affect the applicability our method.