The boundary length and point spectrum enumeration of partial chord diagrams using cut and join recursion

We introduce the boundary length and point spectrum, as a joint generalization of the boundary length spectrum and boundary point spectrum in arXiv:1307.0967. We establish by cut-and-join methods that the number of partial chord diagrams filtered by the boundary length and point spectrum satisfies a recursion relation, which combined with an initial condition determines these numbers uniquely. This recursion relation is equivalent to a second order, non-linear, algebraic partial differential equation for the generating function of the numbers of partial chord diagrams filtered by the boundary length and point spectrum.Comment: 16 pages, 6 figure

Topology of RNA-RNA interaction structures

The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting RNAs, called interaction structures, there exist for fixed genus only finitely many irreducible shadows. This implies that for fixed genus there are only finitely many classes of interaction structures. In particular the simplest case of genus zero already provides the formalism for certain types of structures that occur in nature and are not covered by other filtrations. This case of genus zero interaction structures is already of practical interest, is studied here in detail and found to be expressed by a multiple context-free grammar extending the usual one for RNA secondary structures. We show that in $O(n^6)$ time and $O(n^4)$ space complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities.Comment: 40 pages 15 figure