One-dimensional staged self-assembly

17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011. ProceedingsWe introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest stages is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(logn)-approximable problem). Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of Ω √n/log n even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice

Encoding Color Sequences in Active Tile Self-Assembly

Constructing patterns is a well-studied problem in both theoretical and experimental self-assembly with much of the work focused on multi-staged assembly. In this paper, we study building 1D patterns in a model of active self assembly: Tile Automata. This is a generalization of the 2-handed assembly model that borrows the concept of state changes from Cellular Automata. In this work we further develop the model by partitioning states as colors and show lower and upper bounds for building patterned assemblies based on an input pattern. Our first two sections utilize recent results to build binary strings along with Turing machine constructions to get Kolmogorov optimal state complexity for building patterns in Tile Automata, and show nearly optimal bounds for one case. For affinity strengthening Tile Automata, where transitions can only increase affinity so there is no detachment, we focus on scaled patterns based on Space Bounded Kolmogorov Complexity. Finally, we examine the affinity strengthening freezing case providing an upper bound based on the minimum context-free grammar. This system utilizes only one dimensional assemblies and has tiles that do not change color

Optimal Staged Self-Assembly of General Shapes

We analyze the number of tile types $t$, bins $b$, and stages necessary to assemble $n \times n$ squares and scaled shapes in the staged tile assembly model. For $n \times n$ squares, we prove $\mathcal{O}(\frac{\log{n} - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{\log{n} - tb - t\log t}{b^2})$ are necessary for almost all $n$. For shapes $S$ with Kolmogorov complexity $K(S)$, we prove $\mathcal{O}(\frac{K(S) - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{K(S) - tb - t\log t}{b^2})$ are necessary to assemble a scaled version of $S$, for almost all $S$. We obtain similarly tight bounds when the more powerful flexible glues are permitted.Comment: Abstract version appeared in ESA 201

Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract)

We consider a model of algorithmic self-assembly of geometric shapes out of square Wang tiles studied in SODA 2010, in which there are two types of tiles (e.g., constructed out of DNA and RNA material) and one operation that destroys all tiles of a particular type (e.g., an RNAse enzyme destroys all RNA tiles). We show that a single use of this destruction operation enables much more efficient construction of arbitrary shapes. In particular, an arbitrary shape can be constructed using an asymptotically optimal number of distinct tile types (related to the shape's Kolmogorov complexity), after scaling the shape by only a logarithmic factor. By contrast, without the destruction operation, the best such result has a scale factor at least linear in the size of the shape, and is connected only by a spanning tree of the scaled tiles. We also characterize a large collection of shapes that can be constructed efficiently without any scaling

Verification in Staged Tile Self-Assembly

We prove the unique assembly and unique shape verification problems, benchmark measures of self-assembly model power, are $\mathrm{coNP}^{\mathrm{NP}}$-hard and contained in $\mathrm{PSPACE}$ (and in $\mathrm{\Pi}^\mathrm{P}_{2s}$ for staged systems with $s$ stages). En route, we prove that unique shape verification problem in the 2HAM is $\mathrm{coNP}^{\mathrm{NP}}$-complete.Comment: An abstract version will appear in the proceedings of UCNC 201

Intrinsic Universality in Self-Assembly

We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is capable of simulating a very wide class of tile systems, including itself. Specifically, we give a tile set that simulates the assembly of any tile assembly system in a class of systems that we call \emph{locally consistent}: each tile binds with exactly the strength needed to stay attached, and that there are no glue mismatches between tiles in any produced assembly. Our construction is reminiscent of the studies of \emph{intrinsic universality} of cellular automata by Ollinger and others, in the sense that our simulation of a tile system $T$ by a tile system $U$ represents each tile in an assembly produced by $T$ by a $c \times c$ block of tiles in $U$, where $c$ is a constant depending on $T$ but not on the size of the assembly $T$ produces (which may in fact be infinite). Also, our construction improves on earlier simulations of tile assembly systems by other tile assembly systems (in particular, those of Soloveichik and Winfree, and of Demaine et al.) in that we simulate the actual process of self-assembly, not just the end result, as in Soloveichik and Winfree's construction, and we do not discriminate against infinite structures. Both previous results simulate only temperature 1 systems, whereas our construction simulates tile assembly systems operating at temperature 2

Polyominoes Simulating Arbitrary-Neighborhood Zippers and Tilings

This paper provides a bridge between the classical tiling theory and the complex neighborhood self-assembling situations that exist in practice. The neighborhood of a position in the plane is the set of coordinates which are considered adjacent to it. This includes classical neighborhoods of size four, as well as arbitrarily complex neighborhoods. A generalized tile system consists of a set of tiles, a neighborhood, and a relation which dictates which are the "admissible" neighboring tiles of a given tile. Thus, in correctly formed assemblies, tiles are assigned positions of the plane in accordance to this relation. We prove that any validly tiled path defined in a given but arbitrary neighborhood (a zipper) can be simulated by a simple "ribbon" of microtiles. A ribbon is a special kind of polyomino, consisting of a non-self-crossing sequence of tiles on the plane, in which successive tiles stick along their adjacent edge. Finally, we extend this construction to the case of traditional tilings, proving that we can simulate arbitrary-neighborhood tilings by simple-neighborhood tilings, while preserving some of their essential properties.Comment: Submitted to Theoretical Computer Scienc