Related papers: Canonical RNA pseudoknot structures
Let $M_n$ be the topological moduli space of all parallel n-cables of long framed oriented knots in 3-space. We construct in a combinatorial way for each natural number $n>1$ a 1-cocycle $R_n$ which represents a non trivial class in…
We compute icanonical basis of the quasi-split rank one modified iquantum group, by obtaining explicit transition matrices among the icanonical basis, monomial basis, and standardized canonical basis; all these bases can be naturally…
A graph construction that produces a k-regular graph on n vertices for any choice of k >= 3 and n = m(k+1) for integer m >= 2 is described. The number of Hamiltonian cycles in such graphs can be explicitly determined as a function of n and…
A virtual knot that has a homologically trivial representative $\mathscr{K}$ in a thickened surface $\Sigma \times [0,1]$ is said to be an almost classical (AC) knot. $\mathscr{K}$ then bounds a Seifert surface $F\subset \Sigma \times…
Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…
Truncated Neumann series $S_k(A)=I+A+\cdots+A^{k-1}$ are used in approximate matrix inversion and polynomial preconditioning. In dense settings, matrix-matrix products dominate the cost of evaluating $S_k$. Naive evaluation needs $k-1$…
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…
Spatial transcriptomics (ST) measures mRNA expression while preserving spatial organization, but multi-slice analysis faces two coupled difficulties: large non-rigid deformations across slices and inter-slice batch effects when alignment…
A {\em pseudo-arc} in $\mathrm{PG}(3n-1,q)$ is a set of $(n-1)$-spaces such that any three of them span the whole space. A pseudo-arc of size $q^n+1$ is a {\em pseudo-oval}. If a pseudo-oval $\mathcal{O}$ is obtained by applying field…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
In clinical and biomedical research, multiple high-dimensional datasets are nowadays routinely collected from omics and imaging devices. Multivariate methods, such as Canonical Correlation Analysis (CCA), integrate two (or more) datasets to…
A Sidon set $S$ in $\mathbb{F}_2^n$ is a set such that $x+y=z+w$ has no solutions $x,y,z,w \in S$ with $x,y,z,w$ all distinct. In this paper, we prove various results on Sidon sets by using or generalizing known cryptographic results. In…
A covering array CA(N; t; k; v) is an N x k array on v symbols such that every N x t subarray contains as a row each t-tuple over the v symbols at least once. The minimum N for which a CA(N; t; k; v) exists is called the covering array…
Revised analysis of $\Sigma$ beam asymmetry for the $\eta$ photoproduction on the free proton reveals a structure at $W\sim 1.69$ GeV. Fit of the experimental data based on the E429 solution of the SAID partial wave analysis suggests a…
We describe two new algorithms for the generation of all non-isomorphic cubic graphs with girth at least $k\ge 5$ which are very efficient for $5\le k \le 7$ and show how these algorithms can be efficiently restricted to generate snarks…
An $(n,k)$-perfect sequence covering array with multiplicity $\lambda$, denoted PSCA$(n,k,\lambda)$, is a multiset whose elements are permutations of the sequence $(1,2, \dots, n)$ and which collectively contain each ordered length $k$…
A novel Genetic Algorithm is described that is suitable for determining the global minimum energy configurations of crystal structures and which can also be used as a polymorph search technique. This algorithm requires no prior assumptions…
We show that computing canonical representations for circular-arc (CA) graphs reduces to computing certain subsets of vertices called flip sets. For a broad class of CA graphs, which we call uniform, it suffices to compute a CA…
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…
This work deals with the construction of networks of topological defects in models described by a single complex scalar field. We take advantage of the deformation procedure recently used to describe kinklike defects in order to build…