Related papers: Pseudoknot RNA Structures with Arc-Length $\ge 3$

We show that the 3-symmetric rectilinear and the 3-symmetric pseudolinear crossing numbers of $K_{33}$ are equal. Specifically, we prove that $\operatorname{sym}-\overline{\operatorname{cr}}_3(K_{33}) = 14 634 =…

Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…

Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, removal or shift of a single base pair. Using context-free…

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…

For n >1, if the Seifert form of a knotted 2n-1 sphere K in S^{2n+1} has a metabolizer, then the knot is slice. Casson and Gordon proved that this is false in dimension three (n = 1). However, in the three dimensional case it is true that…

The skewfield K(d) of rational pseudodifferential operators over a differential field K is the skewfield of fractions of the algebra of differential operators K[d]. In our previous paper we showed that any H from K(d) has a minimal…

In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…

In this paper, we use semidefinite programming and representation theory to compute new lower bounds on the crossing number of the complete bipartite graph $K_{m,n}$, extending a method from de Klerk et al. [SIAM J. Discrete Math. 20…

Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…

We provide a new lower bound on the number of $(\leq k)$-edges of a set of $n$ points in the plane in general position. We show that for $0 \leq k \leq\lfloor\frac{n-2}{2}\rfloor$ the number of $(\leq k)$-edges is at least $$ E_k(S) \geq…

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…

We report superconductivity in quasi-1D nanostructures created at the LaAlO3/SrTiO3 interface. Nanostructures having line widths w~10 nm are formed from the parent two-dimensional electron liquid using conductive atomic force microscope…

In this paper we describe all subalgebras and automorphisms of simple noncommutative Jordan superalgebras $K_3(\alpha,\beta,\gamma)$ and $D_t(\alpha,\beta,\gamma)$ and compute the derivations of the nontrivial simple finite-dimensional…

An order-$s$ Davenport-Schinzel sequence over an $n$-letter alphabet is one avoiding immediate repetitions and alternating subsequences with length $s+2$. The main problem is to determine the maximum length of such a sequence, as a function…

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…

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 present a variety of numerical data related to the growth of terms in aliquot sequences, iterations of the function $s(n) = \sigma(n) - n$. First, we compute the geometric mean of the ratio $s_k(n)/s_{k-1}(n)$ of $k$th iterates for $n…