Related papers: Canonical RNA pseudoknot structures
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 show the expected order of RNA saturated secondary structures of size $n$ is $\log_4n(1+O(\frac{\log_2n}{n}))$, if we select the saturated secondary structure uniformly at random. Furthermore, the order of saturated secondary structures…
When biological foundation models such as scGPT and Geneformer process single-cell gene expression, what geometric and topological structure forms in their internal representations? Is that structure biologically meaningful or a training…
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…
We continue the study of extended T-systems of quantum affine algebras. We find a sub-system of the extended T-system of the quantum affine algebra $U_q \hat{\mathfrak{g}}$ of type $C_3$. The sub-system consisting of four systems which are…
Suppose $K$ is a knot in a 3-manifold $Y$, and that $Y$ admits a pair of distinct contact structures. Assume that $K$ has Legendrian representatives in each of these contact structures, such that the corresponding Thurston-Bennequin…
Revised analysis of Sigma beam asymmetry for eta photoproduction off the free proton from GRAAL is presented. New analysis reveals a narrow structure near W ~1.685 GeV. We describe this structure by the contribution of a narrow resonance…
We say that two knots are friends if they share the same 0-surgery. Two friends with different sliceness status would provide a counterexample to the 4-dimensional smooth Poincar\'e conjecture. Here we create a census of all friends with…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
In this paper we give a fully polynomial randomized approximation scheme (FPRAS) for the number of matchings in k-uniform hypergraphs whose intersection graphs contain few claws. Our method gives a generalization of the canonical path…
We define a knot to be half ribbon if it is the cross-section of a ribbon 2-knot, and observe that ribbon implies half ribbon implies slice. We introduce the half ribbon genus of a knot K, the minimum genus of a ribbon knotted surface of…
For a family $\mathcal{F}$ of graphs, $sat(n,\mathcal{F})$ is the minimum number of edges in a graph $G$ on $n$ vertices which does not contain any of the graphs in $\mathcal{F}$ but such that adding any new edge to $G$ creates a graph in…
A string basis is constructed for each subalgebra of invariants of the function algebra on the quantum special linear group. By analyzing the string basis for a particular subalgebra of invariants, we obtain a ``canonical basis'' for every…
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…
We present a general method for converting any family of unsatisfiable CNF formulas that is hard for one of the simplest proof systems, tree resolution, into formulas that require large rank in any proof system that manipulates polynomials…
A constructive method is provided that outputs a directed graph which is named a broken crown graph, containing $5n-9$ vertices and $k$ Hamiltonian cycles for any choice of integers $n \geq k \geq 4$. The construction is not designed to be…
The concordance crosscap number $\gamma_c(K)$ of a knot $K$ is the smallest crosscap number $\gamma_3(K')$ of any knot $K'$ concordant to $K$ (and with $\gamma_3(K')$ defined as the least first Betti number of any nonorientable surface…
We study marginal deformations of ${\cal N}=2$, $d=4$ long linear quiver CFTs using the holographic description. We find a two-parameter family of AdS$_5$ solutions that generically break all of supersymmetry, but preserve ${\cal N}=1$ for…
In this paper we present an algorithm that generates $k$-noncrossing, $\sigma$-modular diagrams with uniform probability. A diagram is a labeled graph of degree $\le 1$ over $n$ vertices drawn in a horizontal line with arcs $(i,j)$ in the…
We consider the asymptotic minimum density $f(s,k)$ of monotone $k$-subwords of words over a totally ordered alphabet of size $s$. The unrestricted alphabet case, $f(\infty,k)$, is well-studied, known for $f(\infty,3)$ and $f(\infty,4)$,…