Related papers: Stacks in canonical RNA pseudoknot structures
We offer a pedestrian level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In non-trivial situations,…
It is known that every proper minor-closed class of graphs has bounded stack-number (a.k.a. book thickness and page number). While this includes notable graph families such as planar graphs and graphs of bounded genus, many other graph…
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…
Invariant ensemble, which are characterised by the joint distribution of eigenvalues $P(\lambda_1,\ldots,\lambda_N)$, play a central role in random matrix theory. We consider the truncated linear statistics $L_K = \sum_{n=1}^K f(\lambda_n)$…
We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a…
Rank-2 toric code (R2TC), a prototypical archetype of the discrete rank-2 symmetric gauge theory, has properties that differ from those of the standard toric code. Specifically, it features a blending of UV and IR in its ground state,…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
We show that for an infinitely many natural numbers $k$ there are $k$-uniform hypergraphs which admit a `rescaling phenomenon' as described in [9]. More precisely, let $\mathcal{A}(k,I, n)$ denote the class of $k$-graphs on $n$ vertices in…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
We describe rational knots with any of the possible combinations of the properties (a)chirality, (non-)positivity, (non-)fiberedness, and unknotting number one (or higher), and determine exactly their number for a given number of crossings…
Given a set $S$ of $v \ge 2$ symbols, and integers $k \ge t \ge 2$ and $N \ge 1$, an $N \times k$ array $A \in S^{N \times k}$ is an $(N; t, k, v)$-covering array if all sequences in $S^t$ appear as rows in every $N \times t$ subarray of…
We consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure. We consider two free-energy models where…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
For reaction networks arising in systems biology, the capacity for two or more steady states, that is, multistationarity, is an important property that underlies biochemical switches. Another property receiving much attention recently is…
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…
We develop the technique of weight truncation in the context of wall-crossings in birational cobordisms, parallel to that in [HL15, BFK19]. More precisely, for each such wall-crossing, we embed the bounded above derived category of coherent…
We have the generating function which determines the number of $2$-bridge knot groups admitting epimorphisms onto the knot group of a given $2$-bridge knot, in terms of crossing number. In this paper, we will refine this formula by taking…
The Gram matrix is a classical object formed from the pairwise inner products of a collection of vectors, with fundamental roles in functional analysis, statistics, combinatorics, and coding theory. In the realm of sequence design,…
This paper investigates the \textbf{graphical $r$-Stirling numbers of the first kind}, denoted by $\str{G}{k}$, which enumerate partitions of a vertex set $V(G)$ into $k$ disjoint cycles such that $r$ specified vertices occupy distinct…