Structures of Monoids Motivated by DNA Origami

TL;DR

This paper introduces origami monoids, a new class of monoids inspired by DNA origami structures and Jones monoids, including their relations, normal forms, and Green's class correspondence.

Contribution

It constructs origami monoids with novel relations, including contextual commutation, and establishes their finiteness and structural properties.

Findings

Origami monoids are finite structures.

Normal form representations are established.

Green's classes correspond to those of Jones monoids.

Abstract

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 of Jones monoids are identified and are taken as generators for the origami monoid. Motivated by plausible modifications of the DNA origami structures and the relations of the well studied Jones monoids, we then identify a set of relations that characterize the origami monoid. These relations expand the relations of the Jones monoids and include a new set of relations called contextual commutation. With contextual commutation, certain generators commute only when found within a given context. We prove that the origami monoids are finite and propose a normal form representation of their elements. We establish a correspondence between the Green's classes of the origami monoid and the Green's classes of a direct product of Jones monoids.