Related papers: Shapes of RNA pseudoknot structures
Let $\mathfrak{g}$ be a real finite-dimensional Lie algebra containing pointed generating invariant closed convex cones. We determine those derivations $D$ of $\mathfrak{g}$ which induce a 3-grading of the form $\mathfrak{g} =…
In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…
We propose a nonperturbative construction of Hopf algebras that represent categories of line operators in topological quantum field theory, in terms of semi-extended operators (spark algebras) on pairs of transverse topological boundary…
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…
This note is a continuation of the paper [2] (see references). We describe some natural pseudogroup structures on almost complex manifolds of type $m$. A kind of coherency is discussed for the sheaf of almost holomorphic functions.
We introduce pseudoconformal structures on 4--dimensional manifolds and study their properties. Such structures are arising from two different complex operators which agree in a 2--dimensional subbundle of the tangent bundle; this subbundle…
We characterize general pseudo-harmonic morphisms from a Riemannian manifold to a Hermitian manifold as pseudo horizontally weakly conformal maps with an additional property. We study to what extent we can (locally) describe these…
A new symmetry of $(1,0)$ supersymmetric non-linear $\sigma$-models in two dimensions with Fermi and mass sectors is introduced. It is a generalisation of the so-called special holonomy $W$-symmetry of Howe and Papadopoulos associated with…
We investigate a phenomenon observed by W. Thurston wherein one constructs a pseudo-Anosov homeomorphism on the limit set of a certain lift of a piecewise-linear expanding interval map. We reconcile this construction with a special subclass…
Within the framework of the flux formulation of Double Field Theory (DFT) we employ a generalised Scherk-Schwarz ansatz and discuss the classification of the twists that in the presence of the strong constraint give rise to constant…
The multiplicative structure of the trivial symplectic groupoid over $\mathbb R^d$ associated to the zero Poisson structure can be expressed in terms of a generating function. We address the problem of deforming such a generating function…
Motivated by the geometry of Levi degenerate CR hypersurfaces, we define a pre-K\"ahler structure on a complex manifold as a pre-symplectic structure compatible with the almost complex structure, i.e. a closed (1,1)-form. Extending Freeman…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
We extend the notion of (smooth) stable generalized complex structures to allow for an anticanonical section with normal self-crossing singularities. This weakening not only allows for a number of natural examples in higher dimensions but…
For a normal subvariety $V$ of ${\bf C}^n$ with a good ${\bf C}^*$-action we give a simple characterization for when it has only log canonical, log terminal or rational singularities. Moreover we are able to give formulas for the…
We consider pseudo-involutions in the Riordan group where the generating function $g$ for the first column of a Riordan array satisfies a palindromic or near-palindromic functional equation. For those types of equations, we find, for very…
The symplectic graph Sp(2d, q) is the collinearity graph of the symplectic space of dimension 2d over a finite field of order q. A k-regular graph on v vertices is a divisible design graph with parameters (v, k, lambda_1, lambda_2 ,m,n) if…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
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…