The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square

In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles pre-formed by the joining of two square tiles. We show that the addition of duples allows for powerful behaviors of self-assembling systems at temperature 1, meaning systems which exclude the requirement of cooperative binding by tiles (i.e., the requirement that a tile must be able to bind to at least 2 tiles in an existing assembly if it is to attach). Cooperative binding is conjectured to be required in the standard aTAM for Turing universal computation and the efficient self-assembly of shapes, but we show that in the DaTAM these behaviors can in fact be exhibited at temperature 1. We then show that the DaTAM doesn't provide asymptotic improvements over the aTAM in its ability to efficiently build thin rectangles. Finally, we present a series of results which prove that the temperature-2 aTAM and temperature-1 DaTAM have mutually exclusive powers. That is, each is able to self-assemble shapes that the other can't, and each has systems which cannot be simulated by the other. Beyond being of purely theoretical interest, these results have practical motivation as duples have already proven to be useful in laboratory implementations of DNA-based tiles

Crystalline Assemblies and Densest Packings of a Family of Truncated Tetrahedra and the Role of Directional Entropic Forces

Polyhedra and their arrangements have intrigued humankind since the ancient Greeks and are today important motifs in condensed matter, with application to many classes of liquids and solids. Yet, little is known about the thermodynamically stable phases of polyhedrally-shaped building blocks, such as faceted nanoparticles and colloids. Although hard particles are known to organize due to entropy alone, and some unusual phases are reported in the literature, the role of entropic forces in connection with polyhedral shape is not well understood. Here, we study thermodynamic self-assembly of a family of truncated tetrahedra and report several atomic crystal isostructures, including diamond, {\beta}-tin, and high- pressure lithium, as the polyhedron shape varies from tetrahedral to octahedral. We compare our findings with the densest packings of the truncated tetrahedron family obtained by numerical compression and report a new space filling polyhedron, which has been overlooked in previous searches. Interestingly, the self-assembled structures differ from the densest packings. We show that the self-assembled crystal structures can be understood as a tendency for polyhedra to maximize face-to-face alignment, which can be generalized as directional entropic forces.Comment: Article + supplementary information. 23 pages, 10 figures, 2 table

Temperature 1 Self-Assembly: Deterministic Assembly in 3D and Probabilistic Assembly in 2D

We investigate the power of the Wang tile self-assembly model at temperature 1, a threshold value that permits attachment between any two tiles that share even a single bond. When restricted to deterministic assembly in the plane, no temperature 1 assembly system has been shown to build a shape with a tile complexity smaller than the diameter of the shape. In contrast, we show that temperature 1 self-assembly in 3 dimensions, even when growth is restricted to at most 1 step into the third dimension, is capable of simulating a large class of temperature 2 systems, in turn permitting the simulation of arbitrary Turing machines and the assembly of $n\times n$ squares in near optimal $O(\log n)$ tile complexity. Further, we consider temperature 1 probabilistic assembly in 2D, and show that with a logarithmic scale up of tile complexity and shape scale, the same general class of temperature $\tau=2$ systems can be simulated with high probability, yielding Turing machine simulation and $O(\log^2 n)$ assembly of $n\times n$ squares with high probability. Our results show a sharp contrast in achievable tile complexity at temperature 1 if either growth into the third dimension or a small probability of error are permitted. Motivated by applications in nanotechnology and molecular computing, and the plausibility of implementing 3 dimensional self-assembly systems, our techniques may provide the needed power of temperature 2 systems, while at the same time avoiding the experimental challenges faced by those systems

Automating the transformation-based analysis of visual languages

The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-009-0114-yWe present a novel approach for the automatic generation of model-to-model transformations given a description of the operational semantics of the source language in the form of graph transformation rules. The approach is geared to the generation of transformations from Domain-Specific Visual Languages (DSVLs) into semantic domains with an explicit notion of transition, like for example Petri nets. The generated transformation is expressed in the form of operational triple graph grammar rules that transform the static information (initial model) and the dynamics (source rules and their execution control structure). We illustrate these techniques with a DSVL in the domain of production systems, for which we generate a transformation into Petri nets. We also tackle the description of timing aspects in graph transformation rules, and its analysis through their automatic translation into Time Petri netsWork sponsored by the Spanish Ministry of Science and Innovation, project METEORIC (TIN2008-02081/TIN) and by the Canadian Natural Sciences and Engineering Research Council (NSERC)

Phase diagram of self-assembled rigid rods on two-dimensional lattices: Theory and Monte Carlo simulations

Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize reversibly into chains with discrete orientational degrees of freedom and, at the same time, undergo a continuous isotropic-nematic (IN) transition. A complete phase diagram was obtained as a function of temperature and density. The numerical results were compared with mean field (MF) and real space renormalization group (RSRG) analytical predictions about the IN transformation. While the RSRG approach supports the continuous nature of the transition, the MF solution predicts a first-order transition line and a tricritical point, at variance with the simulation results.Comment: 12 pages, 10 figures, supplementary informatio