Related papers: On the genus filtration of diagrams over two backb…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
In this paper we study canonical $\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\gamma$-structure is composed by specific building…
Two types of connected chord diagrams with chord endpoints lying in a collection of ordered and oriented real segments are considered here: the real segments may contain additional bivalent vertices in one model but not in the other. In the…
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
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…
In this paper we consider the enumeration of orientable and non-orientable chord diagrams. We show that this enumeration is encoded in appropriate expectation values of the $\beta$-deformed Gaussian and RNA matrix models. We evaluate these…
A chord diagram consists of a circle, called the backbone, with line segments, called chords, whose endpoints are attached to distinct points on the circle. The genus of a chord diagram is the genus of the orientable surface obtained by…
Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike…
A recursive method is given for finding generating functions which enumerate rooted hypermaps by number of vertices, edges and faces for any given number of darts. It makes use of matrix-integral expressions arising from the study of…
This paper addresses the enumeration of rooted and unrooted hypermaps of a given genus. For rooted hypermaps the enumeration method consists of considering the more general family of multirooted hypermaps, in which darts other than the root…
Matrix congruence can be used to mimic linear maps between homogeneous quadratic polynomials in $n$ variables. We introduce a generalization, called standard-form congruence, which mimics affine maps between non-homogeneous quadratic…
Closed-form generating functions for counting one-face rooted hypermaps with a known number of darts by number of vertices and edges is found, using matrix integral expressions relating to the reduced density operator of a bipartite quantum…
In this paper we present a combinatorial proof of a relation between the generating functions of unicellular and bicellular maps. This relation is a consequence of the Schwinger-Dyson equation of matrix theory. Alternatively it can be…
The concept and the construction of modular graph functions are generalized from genus-one to higher genus surfaces. The integrand of the four-graviton superstring amplitude at genus-two provides a generating function for a special class of…
Determining whether two graphs are isomorphic is a fundamental problem with practical applications in areas such as molecular chemistry or social network analysis, yet it remains a challenging task, with exact solutions often being…
In this article, the enumeration of partial chord diagrams is discussed via matrix model techniques. In addition to the basic data such as the number of backbones and chords, we also consider the Euler characteristic, the backbone spectrum,…
A topological mating is a map defined by gluing together the filled Julia sets of two quadratic polynomials. The identifications are visualized and understood by pinching ray-equivalence classes of the formal mating. For postcritically…