Related papers: Combinatorics of $\gamma$-structures
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $\ge 4$. Let ${\sf T}_{k,\sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
In this paper we compute the bivariate generating function of $\gamma$-matchings over two backbones, filtered by the number of arcs and the topological genus. $\gamma$-matchings over two backbones are chord-diagrams, obtained via…
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…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
In this paper we study the distribution of stacks in $k$-noncrossing, $\tau$-canonical RNA pseudoknot structures ($<k,\tau> $-structures). An RNA structure is called $k$-noncrossing if it has no more than $k-1$ mutually crossing arcs and…
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…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
We introduce gamma structures on regular hypergeometric D--modules in dimension 1 as special one--parametric systems of solutions on the compact subtorus. We note that a balanced gamma product is in the Paley--Wiener class and show that the…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
$\Gamma$-structures are weak forms of multiplications on closed oriented manifolds. As shown by Hopf the rational cohomology algebras of manifolds admitting $\Gamma$-structures are free over odd degree generators. We prove that this…
The Gamma-class is a characteristic class for complex manifolds with transcendental coefficients. It defines an integral structure of quantum cohomology, or more precisely, an integral lattice in the space of flat sections of the quantum…
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 present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
There exists many complicated $k$-noncrossing pseudoknot RNA structures in nature based on some special conditions. The special characteristic of RNA structures gives us great challenges in researching the enumeration, prediction and the…
The implicit signature k consists of the multiplication and the ({\omega}-1)-power. We describe a procedure to transform each {\kappa}-term over a finite alphabet A into a certain canonical form and show that different canonical forms have…
Binary idempotent semirings govern classical path algebras. Their multiplicative structure is dyadic. We examine whether this restriction is structural or accidental. We define ternary idempotent $\Gamma$-semirings as higher-arity ordered…
The notion of the Gamma integral structure for the quantum cohomology of an algebraic variety was introduced by Iritani, Katzarkov-Kontsevich-Pantev. In this paper, we define the Gamma integral structure for an invertible polynomial of…