Related papers: Shapes of RNA pseudoknot structures
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
We explore the hierarchy of hidden space-time symmetries of noncritical strings in RNS formalism, realized nonlinearly. Under these symmetry transformations the variation of the matter part of the RNS action is cancelled by that of the…
We generalize Lusztig's nilpotent varieties, and Kashiwara and Saito's geometric construction of crystal graphs from the symmetric to the symmetrizable case. We also construct semicanonical functions in the convolution algebras of…
In addition to superconformal symmetry, (1,1) supersymmetric two-dimensional sigma models on special holonomy manifolds have extra symmetries that are in one-to-one correspondence with the covariantly constant forms on these manifolds. The…
Given a simple, simply laced, complex Lie algebra $\bfg$ corresponding to the Lie group $G$, let $\bfnp$ be the subalgebra generated by the positive roots. In this paper we construct a BV-algebra $\fA[\bfg]$ whose underlying graded…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
We classify the possible shapes of minimal free resolutions over a regular local ring. This illustrates the existence of free resolutions whose Betti numbers behave in surprisingly pathological ways. We also give an asymptotic…
We study structurable algebras of skew-dimension one. We present two different equivalent constructions for such algebras: one in terms of non-linear isotopies of cubic norm structures, and one in terms of hermitian cubic norm structures.…
Let $G$ be a finite group and let $\pi: G \to G'$ be a surjective group homomorphism. Consider the cocycle deformation $L = H^{\sigma}$ of the Hopf algebra $H = k^G$ of $k$-valued linear functions on $G$, with respect to some convolution…
On a (pseudo-)Riemannian manifold (MM,g), some fields of endomorphisms i.e. sections of End(TMM) may be parallel for g. They form an associative algebra A, which is also the commutant of the holonomy group of g. As any associative algebra,…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
Let $\pi$ be a set of primes and $\mathfrak{F}$ be a formation. In this article a properties of the class ${\rm w}^{*}_{\pi}\mathfrak{F}$ of all groups $G$, such that $\pi(G)\subseteq \pi(\mathfrak{F})$ and the normalizers of all Sylow…
In the paper we consider pseudo bihermitian structures - a pair of complex structures compatible with a pseudo Riemannian metric. As in the positive definite case we establish its relations with generalized (pseudo) Kaehler geometry and…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
We show that the Vassiliev invariants of orders $\leq n$ of a knot K, are obstructions to finding a regular Seifert surface, S, whose complement looks "simple" (e.g. like the complement of a disc) to the lower central series of its…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
The authors study the geometry of lightlike hypersurfaces on pseudo-Riemannian manifolds $(M, g)$ of Lorentzian signature. Such hypersurfaces are of interest in general relativity since they can be models of different types of physical…
The convolution operator is the fundamental building block of modern convolutional neural networks (CNNs), owing to its simplicity, translational equivariance, and efficient implementation. However, its structure as a fixed, linear,…
We construct Anosov diffeomorphisms on manifolds that are homeomorphic to infranilmanifolds yet have exotic smooth structures. These manifolds are obtained from standard infranilmanifolds by connected summing with certain exotic spheres.…