Related papers: $k$-noncrossing RNA structures with arc-length $\g…
In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…
Nonnesting permutations are permutations of the multiset $\{1,1,2,2,\dots,n,n\}$ that avoid subsequences of the form $abba$ for any $a\neq b$. These permutations have recently been studied in connection to noncrossing (also called…
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 =…
The ropelength of a knot is the minimum contour length of a tube of unit radius that traces out the knot in three dimensional space without self-overlap, colloquially the minimum amount of rope needed to tie a given knot. Theoretical upper…
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…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
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…
We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
We give a correspondence between graphs with a given degree sequence and fillings of Ferrers diagrams by nonnegative integers with prescribed row and column sums. In this setting, k-crossings and k-nestings of the graph become occurrences…
If a knot K in a closed, orientable 3-manifold M has a bridge surface T with distance at least 3 in the curve complex of T - K, then the genus of any essential surface in its exterior with non-empty, non-meridional boundary gives rise to an…
We present computational results about quasi-alternating knots and links and odd homology obtained by looking at link families in the Conway notation. More precisely, we list quasi-alternating links up to 12 crossings and the first examples…
Let $K$ be a nontrivial knot in $S^{3}$ and $t(K)$ its tunnel number. For any $(p\geq 2,q)$-slope in the torus boundary of a closed regular neighborhood of $ K$ in $S^{3}$, denoted by $K^{\star}$, it is a nontrivial cable knot in $S^{3}$.…
We study the impact of forbidding short cycles to the edge density of $k$-planar graphs; a $k$-planar graph is one that can be drawn in the plane with at most $k$ crossings per edge. Specifically, we consider three settings, according to…
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…
A set system $\mathcal{F}$ is $t$-\textit{intersecting}, if the size of the intersection of every pair of its elements has size at least $t$. A set system $\mathcal{F}$ is $k$-\textit{Sperner}, if it does not contain a chain of length…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
The point sets of all known optimal rectilinear drawings of $K_n$ share an unmistakeable clustering property, the so--called {\em 3--decomposability}. It is widely believed that the underlying point sets of all optimal rectilinear drawings…
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…