Know When to Fold 'Em: Self-Assembly of Shapes by Folding in Oritatami

TL;DR

This paper introduces a theoretical model of shape self-assembly through co-transcriptional folding called oritatami, exploring its capabilities, limitations, and the influence of delay parameters on the folding process.

Contribution

It demonstrates fundamental differences from tile-assembly systems, establishes NP-hardness of shape folding, and shows how delay affects the ability to fold shapes at various scales.

Findings

Certain infinite shapes cannot be folded by OS but can be tile-assembled.

Any shape can be folded from a small seed at scale n≥3 with delay 1.

Shapes can be folded at scale 2 with unbounded delay.

Abstract

An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the $\delta$ most recently produced beads dynamically fold so as to maximize the number of bonds formed, self-assemblying into a shape incrementally. The parameter $\delta$ is called the delay and is related to the transcription rate in nature. This article initiates the study of shape self-assembly using oritatami. A shape is a connected set of points in the triangular lattice. We first show that oritatami systems differ fundamentally from tile-assembly systems by exhibiting a family of infinite shapes that can be tile-assembled but cannot be folded by any OS. As it is NP-hard in general to determine whether there is an OS that folds into (self-assembles) a given finite shape, we explore the folding of upscaled versions of finite shapes. We show that any shape can be folded from a constant size seed, at any scale n >= 3, by an OS with delay 1. We also show that any shape can be folded at the smaller scale 2 by an OS with unbounded delay. This leads us to investigate the influence of delay and to prove that, for all {\delta} > 2, there are shapes that can be folded (at scale 1) with delay {\delta} but not with delay {\delta}'<{\delta}. These results serve as a foundation for the study of shape-building in this new model of self-assembly, and have the potential to provide better understanding of cotranscriptional folding in biology, as well as improved abilities of experimentalists to design artificial systems that self-assemble via this complex dynamical process.