Related papers: Stacks in canonical RNA pseudoknot structures
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…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Stall cells are spanwise-periodic flow structures that spontaneously form on airfoils operating near stall, fundamentally altering the aerodynamic loading distribution. Despite decades of experimental observations, a complete theoretical…
This paper presents a set of Stata commands and Mata functions to evaluate different distributional quantities of the multivariate normal distribution, and a particular type of non-central multivariate t distribution. Specifically, their…
In this paper we consider the Shigesada-Kawasaki-Teramoto (SKT) model to account for stable inhomogeneous steady states exhibiting spatial segregation, which describe a situation of coexistence of two competing species. We provide a deeper…
We have examined extended structures, bridges and arches, in computer generated, non-sequentially stabilized, hard sphere deposits. The bridges and arches have well defined distributions of sizes and shapes. The distribution functions…
Learning hierarchical structures in sequential data -- from simple algorithmic patterns to natural language -- in a reliable, generalizable way remains a challenging problem for neural language models. Past work has shown that recurrent…
This is my PhD Thesis, part of it has published in Acta Mathematica Sinica. In this paper, a class of morphisms which have a kind of singularity weaker than normal crossing is considered. We construct the obstruction such that the so-called…
A (t,s)-rack is a rack structure defined on a module over the ring $\ddot\Lambda=\mathbb{Z}[t^{\pm 1},s]/(s^2-(1-t)s)$. We identify necessary and sufficient conditions for two $(t,s)$-racks to be isomorphic. We define enhancements of the…
We analytically explore the scaling properties of a general class of nested subgraphs in complex networks, which includes the $K$-core and the $K$-scaffold, among others. We name such class of subgraphs $K$-nested subgraphs due to the fact…
We explore the limiting empirical eigenvalue distributions arising from matrices of the form \[A_{n+1} = \begin{bmatrix} A_n & I\\ I & A_n \end{bmatrix} , \]where $A_0$ is the adjacency matrix of a $k$-regular graph. We find that for…
We investigate exponential families of random graph distributions as a framework for systematic quantification of structure in networks. In this paper we restrict ourselves to undirected unlabeled graphs. For these graphs, the counts of…
In this paper, we address several intersection problems for $r$-cross $t$-intersecting families of partitions. A $k$-partition of an $n$-set $X$ is a set of $k$ pairwise disjoint non-empty subsets whose union is $X$. For $1\leq i\leq r$,…
In this paper we enumerate $k$-noncrossing tangled-diagrams. A tangled-diagram is a labeled graph whose vertices are $1,...,n$ have degree $\le 2$, and are arranged in increasing order in a horizontal line. Its arcs are drawn in the upper…
We derive a formula for the expected number of blocks of a given size from a non-crossing partition chosen uniformly at random. Moreover, we refine this result subject to the restriction of having a number of blocks given. Furthermore, we…
The stack sort algorithm has been the subject of extensive study over the years. In this paper we explore a generalized version of this algorithm where instead of avoiding a single decrease, the stack avoids a set $T$ of permutations. We…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
We study the structural constraint of random scale-free networks that determines possible combinations of the degree exponent $\gamma$ and the upper cutoff $k_c$ in the thermodynamic limit. We employ the framework of graphicality…
The tensor network, as a facterization of tensors, aims at performing the operations that are common for normal tensors, such as addition, contraction and stacking. However, due to its non-unique network structure, only the tensor network…
Using methods from Analytic Combinatorics, we study the families of perfect matchings, partitions, chord diagrams, and hyperchord diagrams on a disk with a prescribed number of crossings. For each family, we express the generating function…