Abstract Tile Assembly Model (aTAM)

Informal Description of the Model

The aTAM was developed to, in some sense, be an effectivization of Wang tiling. (See Wang Tiling for more about this relationship.) Namely, it provides a defined process by which an initial (called the seed) assembly can grow into a resultant structure. This is essentially accomplished by assigning a positive integer strength value to each edge color in a set of Wang tiles and stipulating that when two tile edges are adjacent, if their colors match then the edges bind with force equivalent to the strength of the edge color. Then, starting with a preformed seed assembly (usually taken to be a single tile of a specified type), additional tiles can attach one at a time as long as the sum of the strengths of the bonds that each makes with tiles already in the assembly meets a system wide threshold value called the Temperature.

Formal Definition of the Model

We now give a brief formal definition of the aTAM. See for other developments of the model. Our notation is that of , which also contains a more complete definition.

Given a set \(T\) of tile types, an Assembly is a partial function \({\alpha}:{\mathbb{Z}^2} \dashrightarrow {T}\). An assembly is \(\tau\)-stable if it cannot be broken up into smaller assemblies without breaking bonds of total strength at least \(\tau\), for some \(\tau \in \mathbb{N}\).

Self-assembly begins with a \({\it seed assembly}\) \(\sigma\) and proceeds asynchronously and nondeterministically, with tiles adsorbing one at a time to the existing assembly in any manner that preserves \(\tau\)-stability at all times. A \({\it tile assembly system}\) (\({\it TAS}\)) is an ordered triple \(\mathcal{T} = (T, \sigma, \tau)\), where \(T\) is a finite set of tile types, \(\sigma\) is a seed assembly with finite domain, and \(\tau \in \N\). A \({\it generalized tile assembly system}\) (\({\it GTAS}\)) is defined similarly, but without the finiteness requirements. We write \(\prodasm{\mathcal{T}}\) for the set of all assemblies that can arise (in finitely many steps or in the limit) from \(\mathcal{T}\). An assembly \(\alpha \in \prodasm{\mathcal{T}}\) is \({\it terminal}\), and we write \(\alpha \in \termasm{\mathcal{T}}\), if no tile can be \(\tau\)-stably added to it. It is clear that \(\termasm{\mathcal{T}} \subseteq \prodasm{\mathcal{T}}\).

An assembly sequence in a TAS \(\mathcal{T}\) is a (finite or infinite) sequence \(\vec{\alpha} = (\alpha_0,\alpha_1,\ldots)\) of assemblies in which each \(\alpha_{i+1}\) is obtained from \(\alpha_i\) by the addition of a single tile. The \(\emph{result}\) \(\res{\vec{\alpha}}\) of such an assembly sequence is its unique limiting assembly. (This is the last assembly in the sequence if the sequence is finite.) The set \(\prodasm{T}\) is partially ordered by the relation \(\longrightarrow\) defined by

\(\begin{eqnarray*} \alpha \longrightarrow \alpha' & \textmd{iff} & \textmd{there is an assembly sequence } \vec{\alpha} = (\alpha_0,\alpha_1,\ldots) \\& & \textmd{such that } \alpha_0 = \alpha \textmd{ and } \alpha' = \res{\vec{\alpha}}\\. \end{eqnarray*}\)

We say that \(\mathcal{T}\) is \(\emph{directed}\) (a.k.a. \(\emph{deterministic}\), \(\emph{confluent}\), \(\emph{produces a unique assembly}\)) if the relation \(\longrightarrow\) is directed, i.e., if for all \(\alpha,\alpha' \in \prodasm{T}\), there exists \(\alpha'' \in \prodasm{T}\) such that \(\alpha \longrightarrow \alpha''\) and \(\alpha' \longrightarrow \alpha''\). It is easy to show that \(\mathcal{T}\) is directed if and only if there is a unique terminal assembly \(\alpha \in \prodasm{T}\) such that \(\sigma \longrightarrow \alpha\).

In general, even a directed TAS may have a very large (perhaps uncountably infinite) number of different assembly sequences leading to its terminal assembly. This seems to make it very difficult to prove that a TAS is directed. Fortunately, Soloveichik and Winfree have defined a property, {\it local determinism}, of assembly sequences and proven the remarkable fact that, if a TAS \(\mathcal{T}\) has {\it any} assembly sequence that is locally deterministic, then \(\mathcal{T}\) is directed. Intuitively, an assembly sequence \(\vec{\alpha}\) is locally deterministic if (1) each tile added in \(\vec{\alpha}\) ``just barely binds to the existing assembly (meaning that is does so with a summed strength of bonds equal to exactly \(\tau\)); (2) if a tile of type \(t_0\) at a location \(\vec{m}\) and its immediate ``output-neighbors (i.e. those adjacent tiles which bound after the tile at \(\vec{m}\)) are deleted from the \({\it result}\) of \(\vec{\alpha}\), then no tile of type \(t \ne t_0\) can attach itself to the thus-obtained configuration at location \(\vec{m}\); and (3) the result of \(\vec{\alpha}\) is terminal.

A set \(X \in \mathbb{Z}^2\) \({\it weakly self-assembles}\) if there exists a TAS \({\mathcal T} = (T, \sigma, \tau)\) and a set \(B \subseteq T\) such that \(\alpha^{-1}(B) = X\) holds for every terminal assembly \(\alpha \in \termasm{T}\). Essentially, weak self-assembly can be thought of as the creation (or ``painting) of a pattern of tiles from \(B\) (usually taken to be a unique ``color) on a possibly larger ``canvas of un-colored tiles.

A set \(X\) \(\emph{strictly self-assembles}\) if there is a TAS \(\mathcal{T}\) for which every assembly \(\alpha\in\termasm{T}\) satisfies \(\dom \alpha = X\). Essentially, strict self-assembly means that tiles are only placed in positions defined by the shape. Note that if \(X\) strictly self-assembles, then \(X\) weakly self-assembles. (Let all tiles be in \(B\).)

An example tile that has glue of strength 0 on the left (W) and bottom (S), glue of color 'a' and strength 2 on the top (N), and glue of color 'b' and strength 1 on the right (E). This tile also has label 'L'..

Tiles are often depicted as squares whose various sides contain 0, 1, or 2 attached black squares, indicating whether the glue strengths on these sides are 0, 1, or 2, respectively. Thus, for example, a tile of the type shown to the right has glue of strength 0 on the left (W) and bottom (S), glue of color `a' and strength 2 on the top (N), and glue of color `b' and strength 1 on the right (E). This tile also has a label `L', which plays no formal role but may aid our understanding and discussion of the construction.