Related papers: $k$-noncrossing RNA structures with arc-length $\g…
Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The transient number of a knot K, denoted tr(K), is the minimal number of simple arcs that have to be attached to K, in order that K can be homotoped to a trivial knot in a regular neighborhood of the union of K and the arcs. We give a…
Let $\mathrm{PG}(k-1,q)$ be the $(k-1)$-dimensional projective space over the finite field $\mathbb{F}_q$. An arc in $\mathrm{PG}(k-1,q)$ is a set of points with the property that any $k$ of them span the entire space. The notion of…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
Twisting a given knot $K$ about an unknotted circle $c$ a full $n \in \mathbb{N}$ times, we obtain a "twist family" of knots $\{ K_n \}$. Work of Kouno-Motegi-Shibuya implies that for a non-trivial twist family the crossing numbers…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
We are giving tables of quasi-alternating knots with $8\le n \le 12$ crossings. As the obstructions for a knot to be quasialternating we used homology thickness with regards to Khovanov homology, odd homology, and Heegaard-Floer homology…
Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. The longest arc-preserving common subsequence problem has been introduced as a framework for studying the similarity of…
The current state of knowledge of genus g orientable crossing numbers of complete graphs through K11 is reviewed. It is shown that cr3(K10)=3, cr3(K11)<=14, and cr4(K11)=4. It is established with the aid of an algorithm that there are…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
Tur\'{a}n number $T(n,5,3)$ is the minimum size of a system of triples out of a base set $X$ of $n$ elements such that every quintuple in $X$ contains a triple from the system. The exact values of $T(n,5,3)$ are known for $n \leq 17$.…
For a nontrivial knot $K$, Negami found an upper bound on the stick number $s(K)$ in terms of its crossing number $c(K)$ which is $s(K) \leq 2 c(K)$. Later, Huh and Oh utilized the arc index $\alpha(K)$ to present a more precise upper bound…
For a knot or link K, let L(K) be the ropelength of K and Cr(K) be the crossing number of K. In this paper, we show that there exists a constant a>0 such that L(K) is bounded above by a Cr(K) ln^5 (Cr(K)) for any knot K. This result shows…
An equilateral stick number $s_{=}(K)$ of a knot $K$ is defined to be the minimal number of sticks required to construct a polygonal knot of $K$ which consists of equal length sticks. Rawdon and Scharein [12] found upper bounds for the…
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…
Negami found an upper bound on the stick number $s(K)$ of a nontrivial knot $K$ in terms of the minimal crossing number $c(K)$ of the knot which is $s(K) \leq 2 c(K)$. Furthermore McCabe proved $s(K) \leq c(K) + 3$ for a $2$-bridge knot or…
A sequence covering array, denoted \textsf{SCA}$(N;t,v)$, is a set of $N$ permutations of $\{0, \dots, v-1 \}$ such that each sequence of $t$ distinct elements of $\{0, \dots, v-1\}$ reads left to right in at least one permutation. The…
A {\em pseudo-arc} in $\mathrm{PG}(3n-1,q)$ is a set of $(n-1)$-spaces such that any three of them span the whole space. A pseudo-arc of size $q^n+1$ is a {\em pseudo-oval}. If a pseudo-oval $\mathcal{O}$ is obtained by applying field…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…