A new kinetic metric from spectral analysis of transition rates is applied to RNA energy landscapes, showing that ultrametricity depends on nucleotide order for fixed composition.
Ultrametricity of Energy Minimum Configurations of RNA Secondary Structures in the Nussinov Model
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abstract
We present a numerical study of the ultrametric properties of the set of RNA secondary structures with the maximum number of base pairs (energetically degenerate minima) within the maximum matching model (Nussinov algorithm). Using 18 natural small nuclear RNAs as examples, we show that the degree of nontrivial ultrametricity varies widely. We consider the optimization problem for the degree of nontrivial ultrametricity of RNA secondary structures with the maximum number of base pairs under a fixed nucleotide composition. It is found that permuting the nucleotide sequence can strongly change the degree of ultrametricity, indicating the key role of nucleotide order in shaping the hierarchical properties of RNA secondary structures.
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cond-mat.dis-nn 1years
2026 1verdicts
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Kinetic metric for basins of attraction of RNA secondary structures and analysis of the ultrametricity of the energy landscape
A new kinetic metric from spectral analysis of transition rates is applied to RNA energy landscapes, showing that ultrametricity depends on nucleotide order for fixed composition.