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

Binary pattern tile set synthesis is NP-hard

In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the smallest number of tile types which will self-assemble an input pattern of $k$ colors. Of both theoretical and practical significance, $k$-PATS has been studied in a series of papers which have shown $k$-PATS to be NP-hard for $k = 60$, $k = 29$, and then $k = 11$. In this paper, we close the fundamental conjecture that 2-PATS is NP-hard, concluding this line of study. While most of our proof relies on standard mathematical proof techniques, one crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof of the four color theorem by Appel and Haken (simplified later by Robertson, Sanders, Seymour, and Thomas) or the recent important advance on the Erd\H{o}s discrepancy problem by Konev and Lisitsa using computer programs. We utilize a massively parallel algorithm and thus turn an otherwise intractable portion of our proof into a program which requires approximately a year of computation time, bringing the use of computer-assisted proofs to a new scale. We fully detail the algorithm employed by our code, and make the code freely available online

Block Copolymer at Nano-Patterned Surfaces

We present numerical calculations of lamellar phases of block copolymers at patterned surfaces. We model symmetric di-block copolymer films forming lamellar phases and the effect of geometrical and chemical surface patterning on the alignment and orientation of lamellar phases. The calculations are done within self-consistent field theory (SCFT), where the semi-implicit relaxation scheme is used to solve the diffusion equation. Two specific set-ups, motivated by recent experiments, are investigated. In the first, the film is placed on top of a surface imprinted with long chemical stripes. The stripes interact more favorably with one of the two blocks and induce a perpendicular orientation in a large range of system parameters. However, the system is found to be sensitive to its initial conditions, and sometimes gets trapped into a metastable mixed state composed of domains in parallel and perpendicular orientations. In a second set-up, we study the film structure and orientation when it is pressed against a hard grooved mold. The mold surface prefers one of the two components and this set-up is found to be superior for inducing a perfect perpendicular lamellar orientation for a wide range of system parameters