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We construct a class of monoids, called origami monoids, motivated by Jones monoids and by strand organization in DNA origami structures. Two types of basic building blocks of DNA origami closely associated with the graphical representation…
We describe presentations of braid groups of type ADE and show how these presentations are compatible with mutation of quivers, building on work of Barot and Marsh for Coxeter groups. In types A and D these presentations can be understood…
Inverse braid monoid describes a structure on braids where the number of strings is not fixed. So, some strings of initial $n$ may be deleted. In the paper we show that many properties and objects based on braid groups may be extended to…
We present a construction for the holomorph of an inverse semigroup, derived from the cartesian closed structure of the category of ordered groupoids. We compare the holomorph with the monoid of mappings that preserve the ternary heap…
We show that representations of the loop braid group arise from Aharonov-Bohm like effects in finite 2-group (3+1)-dimensional topological higher gauge theory. For this we introduce a minimal categorification of biracks, which we call…
There are familiar examples of computable structures having various computable Scott ranks. There are also familiar structures, such as the Harrison ordering, which have Scott rank $\omega_1^{CK}+1$. Makkai produced a structure of Scott…
Coverings of the Riemann sphere by itself, ramified over two points, are given by so-called Shabat polynomials. The correspondence between Grothendieck's dessins d'enfants and Belyi maps then implies a bijection between Shabat polynomials…
We show that branched coverings of surfaces of large enough genus arise as characteristic maps of braided surfaces that is, lift to embeddings in the product of the surface with $\mathbb R^2$. This result is nontrivial already for…
We show how decreasing diagrams introduced in the theory of rewriting systems can be used to prove coherence type theorems in category theory. We apply this method to describe a coherent presentation of the $0$-Hecke monoid…
The objective of this paper is to study the monoid of all partial transformations of a finite set that preserve a uniform partition. In addition to proving that this monoid is a quotient of a wreath product with respect to a congruence…
We give a monoidal presentation of Coxeter and braid 2-groups, in terms of decorated planar graphs. This presentation extends the Coxeter presentation. We deduce a simple criterion for a Coxeter group or braid group to act on a category.
We construct so called Hall monoidal categories (and Hall modules thereover) and exhibit them as a categorification of classical Hall and Hecke algebras (and certain modules thereover). The input of the (functorial!) construction are…
This paper deals with graph automaton groups associated with trees and some generalizations. We start by showing some algebraic properties of tree automaton groups. Then we characterize the associated semigroup, proving that it is…
It is becoming increasingly important for machine learning methods to make predictions that are interpretable as well as accurate. In many practical applications, it is of interest which features and feature interactions are relevant to the…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
In this paper we study group-based Markov models of evolution and their mixtures. In the algebreo-geometric setting, group-based phylogenetic tree models correspond to toric varieties, while their mixtures correspond to secant and join…
The Jones polynomial can be expressed in terms of spanning trees of the graph obtained by checkerboard coloring a knot diagram. We show there exists a complex generated by these spanning trees whose homology is the reduced Khovanov…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
If a finitely generated monoid M is defined by a finite number of degree-preserving relations, then it has linear growth if and only if it can be decomposed into a finite disjoint union of subsets (which we call "sandwiches") of the form…
We describe presentations of braid groups of type $A$ arising from coloured quivers of mutation type $A$. We show that these can be interpreted geometrically as generalised triangulations of regular polygons.