Related papers: $k$-noncrossing RNA structures with arc-length $\g…

It had been proposed that overstretching double stranded DNA from the 5-5 ends will produce a new fiber form of dsDNA that is narrower than the S form that has been suggested to result when the dsDNA is overstretched from the 3-3 ends. We…

The aim of this article is to study the existence of invariant SKT structures on nilmanifolds. More precisely, we give a negative answer to the question of whether there exist a $k$-step ($k>2$) complex nilmanifold admitting an invariant…

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…

It is known that the arc index of alternating knots is the minimal crossing number plus two and the arc index of prime nonalternating knots is less than or equal to the minimal crossing number. We study some cases when the arc index is…

A covering array $\mathsf{CA}(N;t,k,v)$ is an $N\times k$ array with entries in $\{1, 2, \ldots , v\}$, for which every $N\times t$ subarray contains each $t$-tuple of $\{1, 2, \ldots , v\}^t$ among its rows. Covering arrays find…

We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation and evaluation to address unique challenges…

Let $S_{g}$ denote the genus $g$ closed orientable surface. For $k\in \mathbb{N}$, a $k$-system is a collection of pairwise non-homotopic simple closed curves such that no two intersect more than $k$ times. Juvan-Malni\v{c}-Mohar…

In this paper we present an algorithm that generates $k$-noncrossing, $\sigma$-modular diagrams with uniform probability. A diagram is a labeled graph of degree $\le 1$ over $n$ vertices drawn in a horizontal line with arcs $(i,j)$ in the…

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…

The series-parallel (SP) graphs are those containing no topological $K_{_4}$ and are considered trivial. We relax the prohibition distinguishing the SP graphs by forbidding only embeddings of $K_{_4}$ whose edges with both ends 3-valent…

Non-crossing and non-nesting permutations are variations of the well-known Stirling permutations. A permutation $\pi$ on $\{1,1,2,2,\ldots, n,n\}$ is called non-crossing if it avoids the crossing patterns $\{1212,2121\}$ and is called…

In 1991, 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 $s(K) \leq 2 c(K)$. In this paper we improve this upper bound to $s(K) \leq…

Let $n,k,s$ be three integers and $\beta$ be a sufficiently small positive number such that $k\geq 3$, $0<1/n\ll \beta\ll 1/k$ and $ks+k\leq n\leq (1+\beta)ks+k-2$. A $k$-graph is called non-trivial if it has no isolated vertex. In this…

In 1994, Kranakis et al. published a conjecture about the minimum link-length of every rectilinear covering path for the $k$-dimensional grid $P(n,k) := \{0,1, \dots, n-1\} \times \{0,1, \dots, n-1\} \times \cdots \times \{0,1, \dots,…

A tangled-diagram over $[n]=\{1,...,n\}$ is a graph of degree less than two whose vertices $1,...,n$ are arranged in a horizontal line and whose arcs are drawn in the upper halfplane with a particular notion of crossings and nestings.…

Let T1, T2,..., Tk be spanning trees in a graph G. If for any pair of vertices {u, v} of G, the paths between u and v in every Ti( 0 < i < k+1) do not contain common edges and common vertices, except the vertices u and v, then T1, T2,...,…

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…

We show the expected order of RNA saturated secondary structures of size $n$ is $\log_4n(1+O(\frac{\log_2n}{n}))$, if we select the saturated secondary structure uniformly at random. Furthermore, the order of saturated secondary structures…

We determine the distance-regular graphs with diameter at least $3$ and $c_2\geq 2$ but without induced $K_{1,4}$-subgraphs.

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…