相关论文: RNA-LEGO: Combinatorial Design of Pseudoknot RNA

We revisit several maximization problems for geometric networks design under the non-crossing constraint, first studied by Alon, Rajagopalan and Suri (ACM Symposium on Computational Geometry, 1993). Given a set of $n$ points in the plane in…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

We introduce k-crossings and k-nestings of permutations. We show that the crossing number and the nesting number of permutations have a symmetric joint distribution. As a corollary, the number of k-noncrossing permutations is equal to the…

We show that the number of linear spaces on a set of $n$ points and the number of rank-3 matroids on a ground set of size $n$ are both of the form $(cn+o(n))^{n^2/6}$, where $c=e^{\sqrt 3/2-3}(1+\sqrt 3)/2$. This is the final piece of the…

A knot is a closed loop in space without self-intersection. Two knots are equivalent if there is a self homeomorphism of space bringing one onto the other. An arc presentation is an embedding of a knot in the union of finitely many half…

The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…

Let $D(n)$ be the number of pairwise disjoint Steiner quadruple systems. A simple counting argument shows that $D(n) \leq n-3$ and a set of $n-3$ such systems is called a large set. No nontrivial large set was constructed yet, although it…

We study the structure of $r$-uniform hypergraphs containing no Berge cycles of length at least $k$ for $k \leq r$, and determine that such hypergraphs have some special substructure. In particular we determine the extremal number of such…

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…

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…

The genus non-increasing totally positive unknotting number is the minimum number of crossing changes that transform a knot into the unknot, such that all the crossing changes are positive-to-negative crossing changes that do not increase…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure…

The family of snarks -- connected bridgeless cubic graphs that cannot be 3-edge-coloured -- is well-known as a potential source of counterexamples to several important and long-standing conjectures in graph theory. These include the cycle…

An elementary, at the undergraduate level derivation is given of precise upper bounds of the number of various RNA secondary structures. The method works when the generating function has multiple singularities at the circle of convergence,…

Let $NPO(k)$ be the smallest number $n$ such that the adjacency matrix of any undirected graph with $n$ vertices or more has at least $k$ nonpositive eigenvalues. We show that $NPO(k)$ is well-defined and prove that the values of $NPO(k)$…

A multi-crossing (or n-crossing) is a singular point in a projection at which n strands cross so that each strand bisects the crossing. We generalize the classic result of Kauffman, Murasugi, and Thistlethwaite, which gives the upper bound…

We study the evolution of a random graph under the constraint that the diameter remain constant as the graph grows. We show that if the graph maintains the form of its link distribution it must be scale-free with exponent between 2 and 3.…

In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…

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…