Related papers: Combinatorics of $\gamma$-structures
The canonical polynomial is an important output of the multivariable topological Poincar\'e series associated with a normal surface singularity. It can be considered as a multivariable polynomial generalization of the Seiberg--Witten…
Let $X$ be a product of locally compact rank one Hadamard spaces and $\Gamma$ a discrete group of isometries which contains two elements projecting to a pair of independent rank one isometries in each factor. In [arXiv:1308.5584] we gave a…
A tuple of commuting operators $(S_1,\dots,S_{n-1},P)$ for which the closed symmetrized polydisc $\Gamma_n$ is a spectral set is called a $\Gamma_n$-contraction. We show that every $\Gamma_n$-contraction admits a decomposition into a…
In this paper we study abstract shapes of $k$-noncrossing, $\sigma$-canonical RNA pseudoknot structures. We consider ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes, which represent a generalization of the abstract $\pi'$- and…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
We investigate the cohomology of the Milnor fibre of a reflection arrangement as a module for the group $\Gamma$ generated by the reflections, together with the cyclic monodromy. Although we succeed completely only for unitary reflection…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…
In this paper we derive polynomial time algorithms that generate random $k$-noncrossing matchings and $k$-noncrossing RNA structures with uniform probability. Our approach employs the bijection between $k$-noncrossing matchings and…
In this paper we study $k$-noncrossing RNA structures with minimum arc-length 4 and at most $k-1$ mutually crossing bonds. Let ${\sf T}_{k}^{[4]}(n)$ denote the number of $k$-noncrossing RNA structures with arc-length $\ge 4$ over $n$…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Canonical forms of positive geometries play an important role in revealing hidden structures of scattering amplitudes, from amplituhedra to associahedra. In this paper, we introduce "stringy canonical forms", which provide a natural…
Let \Gamma be a Dynkin diagram of type A,D,E and let R denote the corresponding root system. In this paper we give a categorical construction of R from \Gamma. Instead of choosing an orientation of \Gamma and studying representations of the…
With this work we aim to show how Mathematica can be a useful tool to investigate properties of combinatorial structures. Specifically, we will face enumeration problems on independent subsets of powers of paths and cycles, trying to…
The paper describes the algebraic structure of the graded algebra of differentially homogeneous polynomials of fixed finite order. We show that it is a finitely generated algebra, and we exhibit a minimal set of generators. Along the way,…
We show that, given a finitely generated group $G$ as the coordinate group of a finite system of equations over a torsion-free hyperbolic group $\Gamma$, there is an algorithm which constructs a cover of a canonical solution diagram. The…
Let \(\T\) be a commutative ternary \(\Gm\)-semiring in the sense of the triadic, \(\Gm\)-parametrized multiplication \(\{a,b,c\}_{\gamma}\). Building on the affine \(\Gm\)-spectrum \(\SpecG(\T)\), the structure sheaf, and the equivalence…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…
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…