相关论文: Enumeration of symmetric arc diagrams
In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
We study associative multiplications in semi-simple associative algebras over C compatible with the usual one or, in other words, linear deformations of semi-simple associative algebras over C. It turns out that these deformations are in…
Labeled infinite trees provide combinatorial interpretations for many integer sequences generated by nested recurrence relations. Typically, such sequences are monotone increasing. Several of these sequences also have straightforward…
An avoidance pattern where the letters within an occurrence of which are required to be adjacent is referred to as a subword. In this paper, we enumerate members of the set NC_n of non-crossing partitions of length n according to the number…
We identify a structural pattern in the construction of known infinite families of trees whose independence polynomials are not log-concave. Using this pattern and properties of polynomial ring ideals, we derive linear recurrences for these…
In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…
We study an explicit description of semibricks and 2-term simple-minded collections over preprojective algebras of type $A$ via arc diagrams. We provide a bijection between the set of noncrossoing arc diagrams (resp. the set of double arc…
In this paper we compute the generating function of modular, $k$-noncrossing diagrams. A $k$-noncrossing diagram is called modular if it does not contains any isolated arcs and any arc has length at least four. Modular diagrams represent…
Many topological data analysis (TDA) pipelines compute large collections of persistence diagrams, yet vectorizations and kernel methods discard the rank-induced implication relations among persistence intervals that are essential for…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
We consider two problems that appear at first sight to be unrelated. The first problem is to count certain diagrams consisting of noncrossing arcs in the plane. The second problem concerns the weak order on the symmetric group. Each…
Given a surface with boundary and some points on its boundary, a polygon diagram is a way to connect those points as vertices of non-overlapping polygons on the surface. Such polygon diagrams represent non-crossing permutations on a surface…
We give a parity reversing involution on noncrossing trees that leads to a combinatorial interpretation of a formula on noncrossing trees and symmetric ternary trees in answer to a problem proposed by Hough. We use the representation of…
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…
We use the fact that certain cosets of the stabilizer of points are pairwise conjugate in a symmetric group $S_n$ in order to construct recurrence relations for enumerating certain subsets of $S_n$. Occasionally one can find `closed form'…