Topology and Algebra of Bonded Knots and Braids

TL;DR

This paper develops a comprehensive mathematical framework for bonded knots and braids, incorporating new invariants and algebraic structures to model complex bonded topologies relevant in biological and chemical contexts.

Contribution

It introduces the theory of bonded knots and braids, including monoids, groups, and invariants, extending classical knot theory to bonded and open chain structures.

Findings

Defined bonded braid monoid and its generators

Formulated Alexander and Markov theorems for bonded braids

Introduced bonded knotoids and their closure operations

Abstract

In this paper we present a detailed study of \emph{bonded knots} and their related structures, integrating recent developments into a single framework. Bonded knots are classical knots endowed with embedded bonding arcs modeling physical or chemical bonds. We consider bonded knots in three categories (long, standard, and tight) according to the type of bonds, and in two categories, topological vertex and rigid vertex, according to the allowed isotopy moves, and we define invariants for each category. We then develop the theory of \emph{bonded braids}, the algebraic counterpart of bonded knots. We define the {\it bonded braid monoid}, with its generators and relations, and formulate the analogues of the Alexander and Markov theorems for bonded braids, including an $L$-equivalence for bonded braids. Next, we introduce \emph{enhanced bonded knots and braids}, incorporating two types of bonds (attracting and repelling) corresponding to different interactions. We define the enhanced bonded braid group and show how the bonded braid monoid embeds into this group. Finally, we study \emph{bonded knotoids}, which are open knot diagrams with bonds, and their closure operations, and we define the \emph{bonded closure}. We introduce \emph{bonded braidoids} as the algebraic counterpart of bonded knotoids. These models capture the topology of open chains with inter and intra-chain bonds and suggest new invariants for classifying biological macromolecules.