Abstract:A method is proposed for testing the hypothesis of ultrametric organization of the energy landscape of RNA secondary structures, based on the analysis of transition kinetics between basins of attraction. The method relies on a kinetic metric constructed from the spectral decomposition of the symmetrized Kramers transition rate matrix and the Mahalanobis distance, which is not an ultrametric by construction. A complete computational framework is developed, including automatic filtering of noisy eigenmodes and a procedure for analyzing disconnected structure graphs arising from stochastic sampling. The method is demonstrated on a set of reference and random RNA sequences. It is shown that, for a fixed nucleotide composition, the degree of nontrivial ultrametricity of the energy landscape is determined by the order of nucleotides.
From: Alexander Zubarev [view email]
[v1]
Wed, 24 Jun 2026 13:41:09 UTC (37 KB)
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