Related papers: Shapes of RNA pseudoknot structures
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
We study aspects of superstring vacua of non-compact special holonomy manifolds with conical singularities constructed systematically using soluble N = 1 superconformal field theories (SCFT's). It is known that Einstein homogeneous spaces…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
We construct canonical absolute parallelisms over real-analytic manifolds equipped with $2$-nondegenerate, hypersurface-type CR structures of arbitrary odd dimension not less than $7$ whose Levi kernel has constant rank belonging to a broad…
We study pseudo-geometric strongly regular graphs whose second subconstituent with respect to a vertex is a cover of a strongly regular graph or a complete graph. By studying the structure of such graphs, we characterize all graphs…
A translated point of a contactomorphism $\phi$ on a contact manifold with contact form $\alpha$ is a point $p$ where $\alpha$ is preserved under $\phi$ and whose image under $\phi$ lies in the same Reeb trajectory. They were introduced as…
Let $\left( g\left( x \right),xg\left( x \right) \right)$ be a Riordan matrix from the Bell subgroup. We denote ${{\left( g\left( x \right),xg\left( x \right) \right)}^{\varphi }}=\left( {{g}^{\left( \varphi \right)}}\left( x…
An unified approach to the pseudo scalar meson ($\pi, \eta$, and $K$) photoproduction off nucleons are presented. It begins with the low energy QCD Lagrangian, and the resonances in the s- and u- channels are treated in the framework of the…
In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore…
We study a new class of functions that arise naturally in quaternionic analysis, we call them "quasi regular functions". Like the well-known quaternionic regular functions, these functions provide representations of the quaternionic…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
The so-called l0 pseudonorm, or cardinality function, counts the number of nonzero components of a vector. In this paper, we analyze the l0 pseudonorm by means of so-called Capra (constant along primal rays) conjugacies, for which the…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
The automata arising from the well known conversion of regular expression to non deterministic automata have rather particular transition graphs. We refer to them as the Glushkov graphs, to honour his nice expression-to-automaton…
In this paper we consider left-invariant pseudo-K\"{a}hler structures on six-dimensional nilpotent Lie algebras. The explicit expressions of the canonical complex structures are calculated, and the curvature properties of the associated…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…
We introduce a new perspective on a procedure for generating pseudo-Anosov homemorphisms from postcritically finite interval maps. The central idea is the realization of a tree structure on one such family of pseudo-Anosovs: individual…
The Hopf-Galois structures on normal extensions $K/k$ with $G=Gal(K/k)$ are in one-to-one correspondence with the set of regular subgroups $N\leq B=Perm(G)$ that are normalized by the left regular representation $\lambda(G)\leq B$. Each…