Related papers: Complexity of Self-Assembled Shapes
Compositionality is a key property for dealing with complexity, which has been studied from many points of view in diverse fields. Particularly, the composition of individual computations (or programs) has been widely studied almost since…
A major part of computability theory focuses on the analysis of a few structures of central importance. As a tool, the method of coding with first-order formulas has been applied with great success. For instance, in the c.e. Turing degrees,…
We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are…
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
We show the first asymptotically efficient constructions in the so-called "noncooperative planar tile assembly" model. Algorithmic self-assembly is the study of the local, distributed, asynchronous algorithms ran by molecules to…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
Adapting a result of Bazhenov, Kalimullin, and Yamaleev, we show that if a Turing degree $\textbf{d}$ is the degree of categoricity of a computable structure $\mathcal{M}$ and is not the strong degree of categoricity of any computable…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
Computations, where the number of results is much smaller than the input data and are produced through some sort of accumulation, are called Reductions. Reductions appear in many scientific applications. Usually, reductions admit an…
We introduce a new model of algorithmic tile self-assembly called size-dependent assembly. In previous models, supertiles are stable when the total strength of the bonds between any two halves exceeds some constant temperature. In this…
Tile-based self-assembly systems are capable of universal computation and algorithmically-directed growth. Systems capable of such behavior typically make use of "glue cooperation" in which the glues on at least $2$ sides of a tile must…
Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental building blocks. We aim to explore how efficiently sequence…
Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. We introduce a hypergraph-based formalism, Blocks & Bonds (B&B), that generalizes…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
We present a strict separation between the class of "mismatch free" self-assembly systems and general aTAM systems. Mismatch free systems are those systems in which concurrently grown parts must always agree with each other. Tile…
The number of distinguishable inherent structures of a liquid is the key component to understanding the thermodynamics of glass formers. In the case of hard potential systems such as hard discs, spheres and ellipsoids, an inherent structure…
When writing programs involving matrices or tensors in general, it is desirable to rule out the inconsistency of tensor shapes (i.e., the generalization of matrix sizes) before actual computation. For this purpose, some languages provide…
Self-assembly materials are traditionally designed so that molecular or meso-scale components form a single kind of large structure. Here, we propose a scheme to create "multifarious assembly mixtures", which self-assemble many different…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…