Related papers: RNA-LEGO: Combinatorial Design of Pseudoknot RNA
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…
It has been argued by Thom and Palm that sparsely-connected neural networks (SCNs) show improved performance over fully-connected networks (FCNs). Super-regular networks (SRNs) are neural networks composed of a set of stacked sparse layers…
Two independent edges in ordered graphs can be nested, crossing or separated. These relations define six types of subgraphs, depending on which relations are forbidden. We refine a remark by Erd\H{o}s and Rado that every 2-coloring of the…
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…
In this paper, we give infinitely many examples of (non-isomorphic) connected $k$-regular graphs with smallest eigenvalue in half open interval $[-1-\sqrt2, -2)$ and also infinitely many examples of (non-isomorphic) connected $k$-regular…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
We introduce an alternative stratification of knots: by the size of lattice on which a knot can be first met. Using this classification, we find ratio of unknots and knots with more than 10 minimal crossings inside different lattices and…
Scale-free networks (SFN) arise from simple growth processes, which can encourage efficient, centralized and fault tolerant communication (1). Recently its been shown that stable network hub structure is governed by a phase transition at…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
Let $n\geqslant 4$ be a natural number, and let $K$ be a set $K\subseteq [n]:={1,2,...,n}$. We study the problem to find the smallest possible size of a maximal family $\mathcal{A}$ of subsets of $[n]$ such that $\mathcal{A}$ contains only…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
Let $ex(n, P)$ be the maximum possible number of ones in any 0-1 matrix of dimensions $n \times n$ that avoids $P$. Matrix $P$ is called minimally non-linear if $ex(n, P) = \omega(n)$ but $ex(n, P') = O(n)$ for every strict subpattern $P'$…
MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression by binding to the 3' UTR of the corresponding messenger RNAs. We construct miRNA co-target networks for 22 different species using a target prediction database,…
A snark is a bridgeless cubic graph which is not 3-edge-colourable. The oddness of a bridgeless cubic graph is the minimum number of odd components in any 2-factor of the graph. Lukot'ka, M\'acajov\'a, Maz\'ak and \v{S}koviera showed in…
It is known that graphs on n vertices with minimum degree at least 3 have spanning trees with at least n/4+2 leaves and that this can be improved to (n+4)/3 for cubic graphs without the diamond K_4-e as a subgraph. We generalize the second…
Nonlinear complexity, as an important measure for assessing the randomness of sequences, is defined as the length of the shortest feedback shift registers that can generate a given sequence. In this paper, the structure of n-periodic binary…
Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…
MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…