Related papers: RNA-LEGO: Combinatorial Design of Pseudoknot RNA
Enumerative studies of RNA secondary structures were initiated four decades ago by Waterman and his coworkers. Since then, RNA secondary structures have been explored according to many different structural characteristics, for instance,…
We prove that, for every positive integer k, there is an integer N such that every 4-connected non-planar graph with at least N vertices has a minor isomorphic to K_{4,k}, the graph obtained from a cycle of length 2k+1 by adding an edge…
Networks of silicon nanowires possess intriguing electronic properties surpassing the predictions based on quantum confinement of individual nanowires. Employing large-scale atomistic pseudopotential computations, as yet unexplored branched…
Experimental work suggests that the Seifert genus of a knot grows linearly with respect to the crossing number of the knot. In this article, we use a billiard table model for $2$-bridge or rational knots to show that the average genus of a…
For a non-split multi-crossing diagram $D$ of a link $L$ we show that $\alpha(L)-2 \leq c_2(D) + \sum_{n> 2}(2n-4)c_n(D)$ holds. Here $\alpha(L)$ is the arc index and $c_n(D)$ is the number of $n$-crossings of $D$. This generalizes and…
An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…
Non-coding RNA (ncRNA) are RNA sequences which don't code for a gene but instead carry important biological functions. The task of ncRNA classification consists in classifying a given ncRNA sequence into its family. While it has been shown…
In 2013, Adams introduced the $n$-crossing number of a knot $K$, denoted by $c_n(K)$. Inequalities between the $2$-, $3$-, $4$-, and $5$-crossing numbers have been previously established. We prove $c_9(K)\leq c_3(K)-2$ for all knots $K$…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
An ordered matching of size $n$ is a graph on a linearly ordered vertex set $V$, $|V|=2n$, consisting of $n$ pairwise disjoint edges. There are three different ordered matchings of size two on $V=\{1,2,3,4\}$: an alignment…
We show that for any nontrivial knot $K$ and any natural number $n$ there is a diagram $D$ of $K$ such that the unknotting number of $D$ is greater than or equal to $n$. It is well known that twice the unknotting number of $K$ is less than…
The notion of noncrossing linked partition arose from the study of certain transforms in free probability theory. It is known that the number of noncrossing linked partitions of [n+1] is equal to the n-th large Schroder number $r_n$, which…
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…
Two subsets $A,B$ of an $n$-element ground set $X$ are said to be \emph{crossing}, if none of the four sets $A\cap B$, $A\setminus B$, $B\setminus A$ and $X\setminus(A\cup B)$ are empty. It was conjectured by Karzanov and Lomonosov forty…
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 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 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…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We study relations between unknotting number and crossing number of a spatial embedding of a handcuff-graph and a theta curve. It is well known that for any non-trivial knot $K$ twice the unknotting number of $K$ is less than or equal to…
A star-simple drawing of a graph is a drawing in which adjacent edges do not cross. In contrast, there is no restriction on the number of crossings between two independent edges. When allowing empty lenses (a face in the arrangement induced…