DNA tile self-assembly for 3D-surfaces: Towards genus identification

TL;DR

This paper introduces a DNA tile self-assembly model on 3D surfaces called SFTAM, which can determine the genus of certain polycube structures by specific tile patterns, aiding topological surface analysis.

Contribution

The paper presents a novel SFTAM model for self-assembly on 3D surfaces and a system to identify the genus of order-1 cuboids, advancing topological surface characterization.

Findings

The tile system distinguishes genus 0 and genus 1 cuboids.

Assemblies on genus 1 cuboids always contain tiles from set Y.

The approach generalizes to other shape families.

Abstract

We introduce a new DNA tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. The bonds are flexible, so that the assembly can bind on the edges of the polycube. We are interested in the study of SFTAM self-assemblies on 3D surfaces which are not always embeddable in the Euclidean plane, in order to compare their different behaviors and to compute the topological properties of the host surfaces. We focus on a family of polycubes called cuboids. Order-0 cuboids are polycubes that have six rectangular faces, and order-1 cuboids are made from two order-0 cuboids by substracting one from the other. Thus, order-1 cuboids can be of genus 0 or of genus 1 (then they contain a tunnel). We are interested in the genus of these structures, and we present a SFTAM tile assembly system that determines the genus of a given order-1 cuboid. The SFTAM tile assembly system which we design, contains a specific set $Y$ of tile types with the following properties. If the assembly is made on a host order-1 cuboid $C$ of genus 0, no tile of $Y$ appears in any producible assembly, but if $C$ has genus 1, every terminal assembly contains at least one tile of $Y$. Thus, we are able to distinguish the host surfaces according to their genus, by the tiles used in the assembly. This system is specific to order-1 cuboids but the techniques we use should be generalizable to other families of shapes.