Related papers: Optimizing Tile Concentrations to Minimize Errors …
Perhaps the two most significant theoretical questions about the programming of self-assembling agents are: (1) necessary and sufficient conditions to produce a unique terminal assembly, and (2) error correction. We address both questions,…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal…
Tile Automata is a recently defined model of self-assembly that borrows many concepts from cellular automata to create active self-assembling systems where changes may be occurring within an assembly without requiring attachment. This model…
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…
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an…
In this paper we introduce the \emph{robust random number generation} problem where the goal is to design an abstract tile assembly system (aTAM system) whose terminal assemblies can be split into $n$ partitions such that a resulting…
We consider the problem of fault-tolerance in nanoscale algorithmic self-assembly. We employ a variant of Winfree's abstract Tile Assembly Model (aTAM), the two-handed aTAM, in which square "tiles" -- a model of molecules constructed from…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…
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.…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal…
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…
We investigate a fundamental question regarding a benchmark class of shapes in one of the simplest, yet most widely utilized abstract models of algorithmic tile self-assembly. Specifically, we study the directed tile complexity of a $k…
We investigate the role of nondeterminism in Winfree's abstract Tile Assembly Model (aTAM), which was conceived to model artificial molecular self-assembling systems constructed from DNA. Of particular practical importance is to find tile…
Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use…
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…
Nearly thirty years after its inception, the field of DNA-programmed colloidal self-assembly has begun to realize its initial promise. In this review, we summarize recent developments in designing effective interactions and understanding…
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…
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…