Related papers: Modular, $k$-noncrossing diagrams
In this paper we study abstract shapes of $k$-noncrossing, $\sigma$-canonical RNA pseudoknot structures. We consider ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes, which represent a generalization of the abstract $\pi'$- and…
A multigraph drawn in the plane is non-homotopic if no two edges connecting the same pair of vertices can be continuously deformed into each other without passing through a vertex, and is $k$-crossing if every pair of edges…
The number $Z(n):=\lfloor n/2\rfloor\lfloor (n-1)/2\rfloor$ is the smallest number of crossings in a simple planar drawing of $K_{2,n}$ in which both vertices on the 2-side have the same clockwise rotation. For two vertices $u,v$ on the…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
In this paper, we study the structure of the permutability graphs of subgroups, and the permutability graphs of non-normal subgroups of the following groups: the dihedral groups $D_n$, the generalized quaternion groups $Q_n$, the…
Scheinerman and Wilf (1994) assert that `an important open problem in the study of graph embeddings is to determine the rectilinear crossing number of the complete graph K_n.' A rectilinear drawing of K_n is an arrangement of n vertices in…
A connected graph of order $n$ admitting a semiregular automorphism of order $n/k$ is called a $k$-multicirculant. Highly symmetric multicirculants of small valency have been extensively studied, and several classification results exist for…
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…
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…
This paper investigates the relations between modular graph forms, which are generalizations of the modular graph functions that were introduced in earlier papers motivated by the structure of the low energy expansion of genus-one Type II…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
We prove that for all natural numbers $m$ and $k$ where $k$ is odd, there exists a natural number $N(k)$ such that any 3-connected cubic graph with at least $N(k)$ vertices contains a cycle of length $m$ modulo $k$. We also construct a…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
Instead of $k$-Dyck paths we consider the equivalent concept of $k$-non-crossing trees. This is our preferred approach relative to down-step statistics modulo $k$ (first studied by Heuberger, Selkirk, and Wagner by different methods). One…
We prove the non-planarity of a family of 3-regular graphs constructed from the solutions to the Markoff equation $x^2+y^2+z^2=xyz$ modulo prime numbers greater than 7. The proof uses Euler characteristic and an enumeration of the short…
Gerstenhaber showed in 1961 that any commuting pair of n x n matrices over a field k generates a k-algebra A of k-dimension \leq n. A well-known example shows that the corresponding statement for 4 matrices is false. The question for 3…
A graph $G$ is a non-separating planar graph if there is a drawing $D$ of $G$ on the plane such that (1) no two edges cross each other in $D$ and (2) for any cycle $C$ in $D$, any two vertices not in $C$ are on the same side of $C$ in $D$.…
Let $ K / k $ be a purely inseparable extension of characteristic $ p> 0 $ and of finite size. We recall that $K/k$ is modular if for every $n \in \mathbb{N}$,$K^{p^n}$ and $k$ are $k\cap K^{p^ n}$-linearly disjoint. A natural…
I present an algorithm that, given a number $n \geq 1$, computes a compact representation of the set of all noncrossing acyclic digraphs with $n$ nodes. This compact representation can be used as the basis for a wide range of dynamic…
A graph construction that produces a k-regular graph on n vertices for any choice of k >= 3 and n = m(k+1) for integer m >= 2 is described. The number of Hamiltonian cycles in such graphs can be explicitly determined as a function of n and…