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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…

Computational Geometry · Computer Science 2015-02-20 Florent Becker , Pierre-Étienne Meunier

We show the first non-trivial positive algorithmic results (i.e. programs whose output is larger than their size), in a model of self-assembly that has so far resisted many attempts of formal analysis or programming: the planar…

Computational Geometry · Computer Science 2014-07-11 Pierre-Étienne Meunier

We discuss the self-assembly system of triangular tiles instead of square tiles, in particular right triangular tiles and equilateral triangular tiles. We show that the triangular tile assembly system, either deterministic or…

Discrete Mathematics · Computer Science 2010-03-01 Lila Kari , Shinnosuke Seki , Zhi Xu

We prove that the abstract Tile Assembly Model (aTAM) of nanoscale self-assembly is intrinsically universal. This means that there is a single tile assembly system U that, with proper initialization, simulates any tile assembly system T.…

Data Structures and Algorithms · Computer Science 2012-04-10 David Doty , Jack H. Lutz , Matthew J. Patitz , Robert T. Schweller , Scott M. Summers , Damien Woods

Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of…

Emerging Technologies · Computer Science 2016-04-27 S. Tesoro , S. E. Ahnert

This paper concerns the self-assembly of scaled-up versions of arbitrary finite shapes. We work in the multiple temperature model that was introduced by Aggarwal, Cheng, Goldwasser, Kao, and Schweller (Complexities for Generalized Models of…

Computational Complexity · Computer Science 2009-09-30 Scott M. Summers

Algorithmic self-assembly occurs when disorganized components autonomously combine to form structures and, by their design and the dynamics of the system, are forced to follow the execution of algorithms. Motivated by applications in…

Computational Geometry · Computer Science 2023-05-05 Daniel Hader , Matthew J. Patitz

In this paper we demonstrate the power of a model of tile self-assembly based on active glues which can dynamically change state. We formulate the Signal-passing Tile Assembly Model (STAM), based on the model of Padilla, Liu, and Seeman to…

In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…

Soft Condensed Matter · Physics 2022-05-25 Huang Fang , Botond Tyukodi , W. Benjamin Rogers , Michael F. Hagan

Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are…

Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…

The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of…

Soft Condensed Matter · Physics 2022-03-02 Thomas E. Videbæk , Huang Fang , Daichi Hayakawa , Botond Tyukodi , Michael F. Hagan , W. Benjamin Rogers

The field of algorithmic self-assembly is concerned with the computational and expressive power of nanoscale self-assembling molecular systems. In the well-studied cooperative, or temperature 2, abstract tile assembly model it is known that…

Computational Complexity · Computer Science 2017-05-31 Pierre-Étienne Meunier , Damien Woods

We prove a Pumping Lemma for the noncooperative abstract Tile Assembly Model, a model central to the theory of algorithmic self-assembly since the beginning of the field. This theory suggests, and our result proves, that small differences…

Computational Complexity · Computer Science 2020-02-11 Pierre-Étienne Meunier , Damien Regnault , Damien Woods

In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…

Emerging Technologies · Computer Science 2022-03-30 Andrew Alseth , Daniel Hader , Matthew J. Patitz

In this paper, we prove that in the abstract Tile Assembly Model (aTAM), an accretion-based model which only allows for a single tile to attach to a growing assembly at each step, there are no tile assembly systems capable of…

Emerging Technologies · Computer Science 2018-07-18 Jacob Hendricks , Joseph Opseth , Matthew Patitz , Scott Summers

We prove the computational weakness of a model of tile assembly that has so far resisted many attempts of formal analysis or positive constructions. Specifically, we prove that, in Winfree's abstract Tile Assembly Model, when restricted to…

Computational Complexity · Computer Science 2015-07-31 Pierre-Étienne Meunier , Damien Regnault

A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…

Statistical Mechanics · Physics 2017-02-27 Stephen Whitelam

We prove a result which strongly hints at the computational weakness of a model of tile assembly that has so far resisted many attempts of formal analysis or positive constructions. Specifically, we prove that, in Winfree's abstract Tile…

Computational Complexity · Computer Science 2016-10-28 Pierre-Étienne Meunier , Damien Regnault

In this paper, we study the minimum number of unique tile types required for the self-assembly of thin rectangles in Winfree's abstract Tile Assembly Model (aTAM), restricted to temperature-1. Using Catalan numbers, planar self-assembly and…

Computational Geometry · Computer Science 2019-06-18 David Furcy , Scott M. Summers , Christian Wendlandt