Tile Assembly Model Research Articles

A biomimetic branching signal-passing tile assembly model with dynamic growth and disassembly.

Natural biological branching processes can form tree-like structures at all scales and, moreover, can perform various functions to achieve specific goals; these include receiving stimuli, performing two-way communication along their branches, and dynamically reforming (extending or retracting branches). They underlie many biological systems with considerable diversity, frequency, and geometric complexity; these include networks of neurons, organ tissue, mycorrhizal fungal networks, plant growth, foraging networks, etc. This paper presents a biomimetic DNA tile assembly model (Y-STAM) to implement dynamic branching processes. The Y-STAM is a relatively compact mathematical model providing a design space where complex, biomimetic branch-like growth and behaviour can emerge from the appropriate parametrization of the model. We also introduce a class of augmented models (Y-STAM+) that provide time- and space-dependent modulations of tile glue strengths, which enable further diverse behaviours that are not possible in the Y-STAM; these additional behaviours include refinement of network assemblies, obstacle avoidance, and programmable growth patterns. We perform and discuss extensive simulations of the Y-STAM and the Y-STAM+. We envision that these models could be applied at the mesoscale and the molecular scale to dynamically assemble branching DNA nanostructures and offer insights into complex biological self-assembly processes.

Universal shape replication via self-assembly with signal-passing tiles

AbstractIn this paper, we investigate shape-assembling power of a tile-based model of self-assembly called the Signal-Passing Tile Assembly Model (STAM). In this model, the glues that bind tiles together can be turned on and off by the binding actions of other glues via “signals”. Specifically, the problem we investigate is “shape replication” wherein, given a set of input assemblies of arbitrary shape, a system must construct an arbitrary number of assemblies with the same shapes and, with the exception of size-bounded junk assemblies that result from the process, no others. We provide the first fully universal shape replication result, namely a single tile set capable of performing shape replication on arbitrary sets of any 3-dimensional shapes without requiring any scaling or pre-encoded information in the input assemblies. Our result requires the input assemblies to be composed of signal-passing tiles whose glues can be deactivated to allow deconstruction of those assemblies, which we also prove is necessary by showing that there are shapes whose geometry cannot be replicated without deconstruction. Additionally, we modularize our construction to create systems capable of creating binary encodings of arbitrary shapes, and building arbitrary shapes from their encodings. Because the STAM is capable of universal computation, this then allows for arbitrary programs to be run within an STAM system, using the shape encodings as input, so that any computable transformation can be performed on the shapes. This is the full version, containing all construction and proof details, of a previously published extended abstract version that had most details omitted.

Self-replication via tile self-assembly

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. These modifications consist of an extension to 3D, the ability of tiles to form “flexible” bonds that allow bound tiles to rotate relative to each other, and allowing tiles of multiple shapes within the same system. We call this new model the STAM*, and we present a series of constructions within it that are capable of self-replicating behavior. Namely, the input seed assemblies to our STAM* systems can encode either “genomes” specifying the instructions for building a target shape, or can be copies of the target shape with instructions built in. A universal tile set exists for any target shape (at scale factor 2), and from a genome assembly creates infinite copies of the genome as well as the target shape. An input target structure, on the other hand, can be “deconstructed” by the universal tile set to form a genome encoding it, which will then replicate and also initiate the growth of copies of assemblies of the target shape. Since the lengths of the genomes for these constructions are proportional to the number of points in the target shape, we also present a replicator which utilizes hierarchical self-assembly to greatly reduce the size of the genomes required. The main goals of this work are to examine minimal requirements of self-assembling systems capable of self-replicating behavior, with the aim of better understanding self-replication in nature as well as understanding the complexity of mimicking it.

The Impacts of Dimensionality, Diffusion, and Directedness on Intrinsic Cross-Model Simulation in Tile-Based Self-Assembly

Motivated by applications in DNA-nanotechnology, theoretical investigations in algorithmic tile-assembly have blossomed into a mature theory. In addition to computational universality, the abstract Tile Assembly Model (aTAM) was shown to be intrinsically universal (FOCS 2012), a strong notion of completeness where a single tile set is capable of simulating the full dynamics of all systems within the model; however, this construction fundamentally required non-deterministic tile attachments. This was confirmed necessary when it was shown that the class of directed aTAM systems, those where all possible sequences of tile attachments result in the same terminal assembly, is not intrinsically universal (FOCS 2016). Furthermore, it was shown that the non-cooperative aTAM, where tiles only need to match on 1 side to bind rather than 2 or more, is not intrinsically universal (SODA 2014) nor computationally universal (STOC 2017). Building on these results to further investigate the other dynamics, Hader et al. examined several tile-assembly models which varied across (1) the numbers of dimensions used, (2) how tiles diffused through space, and (3) whether each system is directed, and determined which models exhibited intrinsic universality (SODA 2020). In this paper we extend those results to provide direct comparisons of the various models against each other by considering intrinsic simulations between models. Our results show that in some cases, one model is strictly more powerful than another, and in others, pairs of models have mutually exclusive capabilities. This paper is a greatly expanded version of that which appeared in ICALP 2023.

The Need for Seed (in the Abstract Tile Assembly Model)

The Need for Seed (in the Abstract Tile Assembly Model)

Building squares with optimal state complexity in restricted active self-assembly

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 has been shown to be powerful even with limited assembly size, but many fundamental questions have yet to be explored. Here, we study the state complexity of assembling n×n squares in seeded Tile Automata systems where growth starts from a seed and tiles attach one at a time, similar to the abstract Tile Assembly Model. We provide optimal bounds for three classes of seeded Tile Automata systems (all without detachment), which vary in the amount of complexity allowed in the transition rules. We show that, in general, seeded Tile Automata systems require Θ(log14⁡n) states. For single-transition systems, where only one state may change in a transition rule, we show a bound of Θ(log13⁡n), and for deterministic systems, where each pair of states may only have one associated transition rule, a bound of Θ((log⁡nlog⁡log⁡n)12). Along the way, we provide optimal bounds for the subroutines of building binary strings and building O(log⁡n)×n rectangles.

Fractal dimension of assemblies in the abstract tile assembly model

Fractal dimension of assemblies in the abstract tile assembly model

Complexity of verification in self-assembly with prebuilt assemblies

We analyze the complexity of two fundamental verification problems within a generalization of the two-handed tile self-assembly model (2HAM) where initial system assemblies are not restricted to be singleton tiles, but may be larger prebuilt assemblies. Within this model we consider the producibility problem, which asks if a given tile system builds, or produces, a given assembly, and the unique assembly verification (UAV) problem, which asks if a given system uniquely produces a given assembly. We show that producibility is NP-complete and UAV is coNPNP-complete even when the initial assembly size and temperature threshold are both bounded by a constant. This is in stark contrast to results in the standard model with singleton input tiles where producibility is in P and UAV is coNP-complete with constant temperature. We further provide preliminary polynomial time results for producibility and UAV in the case of 1-dimensional linear assemblies with pre-built assemblies, as well as extend our results to the abstract Tile Assembly Model (aTAM) with constant-size attachable assemblies.

Logical computation with self-assembling electric circuits.

Inspired by self-assembled biological growth, the Circuit Tile Assembly Model (cTAM) was developed to provide insights into signal propagation, information processing, and computation in bioelectric networks. The cTAM is an abstract model that produces a family of circuits of different sizes that is amenable to exact analysis. Here, the cTAM is extended to the Boolean Circuit Tile Assembly Model (bcTAM) that implements a computationally complete set of Boolean gates through self-assembled and self-controlled growth. The proposed model approximates axonal growth in neural networks and thus, investigates the computational capability of dynamic biological networks, for example, in growing networks of axons. Thus, the bcTAM models the effect of electrical activity on growth and shows how that growth might implement Boolean computations. In this sense, given a set of input voltages, the bcTAM is a system that is able to monitor and make decisions about its own growth.

Systems of axon-like circuits for self-assembled and self-controlled growth of bioelectric networks

By guiding cell and chemical migration and coupling with genetic mechanisms, bioelectric networks of potentials influence biological pattern formation and are known to have profound effects on growth processes. An abstract model that is amenable to exact analysis has been proposed in the circuit tile assembly model (cTAM) to understand self-assembled and self-controlled growth as an emergent phenomenon that is capable of complex behaviors, like self-replication. In the cTAM, a voltage source represents a finite supply of energy that drives growth until it is unable to overcome randomizing factors in the environment, represented by a threshold. Here, the cTAM is extended to the axon or alternating cTAM model (acTAM) to include a circuit similar to signal propagation in axons, exhibiting time-varying electric signals and a dependence on frequency of the input voltage. The acTAM produces systems of circuits whose electrical properties are coupled to their length as growth proceeds through self-assembly. The exact response is derived for increasingly complex circuit systems as the assembly proceeds. The model exhibits complicated behaviors that elucidate the interactive role of energy, environment, and noise with electric signals in axon-like circuits during biological growth of complex patterns and function.

Replication of Arbitrary Hole-Free Shapes via Self-assembly with Signal-Passing Tiles

In this paper, we investigate the abilities of systems of self-assembling tiles which can each pass a constant number of signals to their immediate neighbors to create replicas of input shapes. Namely, we work within the Signal-passing Tile Assembly Model (STAM), and we provide a universal STAM tile set which is capable of creating unbounded numbers of assemblies of shapes identical to those of input assemblies. The shapes of the input assemblies can be arbitrary 2-dimensional hole-free shapes. This improves previous shape replication results in self-assembly that required models in which multiple assembly stages and/or bins were required, and the shapes which could be replicated were more constrained, as well as a previous version of this result that required input shapes to be represented at scale factor 2.

On the effects of hierarchical self-assembly for reducing program-size complexity

In this paper we present a series of results which show separations between the standard seeded model of self-assembly, Winfree's abstract Tile Assembly Model (aTAM), and the “seedless” 2-Handed Assembly Model (2HAM), which incorporates the dynamics of hierarchical self-assembly. In particular, we focus on the problem of self-assembling various shapes while minimizing the sizes of tile sets, or “programs”, in each of these models in order to compare and contrast the models. A high-level overview of a subset of these results was presented in a paper by the authors in STACS 2013, but in this version we expand and improve the set of results related to showing separations between the two models according to their abilities to self-assemble various shapes. We exhibit classes of finite shapes that can be self-assembled more efficiently in each model. We also demonstrate infinite shapes that can self-assemble in one model but not in the other, as well as a shape which cannot self-assemble in either model.

Self-assembly of and optimal encoding within thin rectangles at temperature-1 in 3D

In this paper, we study the self-assembly of rectangles in a non-cooperative, 3D version of Winfree's abstract Tile Assembly Model. We prove two results. First, we give the full details for the proof of a general construction for the efficient self-assembly of thin rectangles that was first reported by Furcy, Summers and Wendlandt (2019). This construction is non-cooperative and “just-barely” 3D in the sense that it places tiles at most one step into the third dimension. Second, we give a non-cooperative, just-barely 3D optimal encoding construction that self-assembles the bits of a given binary string along the perimeter of a thin rectangle of constant height.

Covert Computation in Self-Assembled Circuits

Traditionally, computation within self-assembly models is hard to conceal because the self-assembly process generates a crystalline assembly whose computational history is inherently part of the structure itself. With no way to remove information from the computation, this computational model offers a unique problem: how can computational input and computation be hidden while still computing and reporting the final output? Designing such systems is inherently motivated by privacy concerns in biomedical computing and applications in cryptography. In this paper we propose the problem of performing “covert computation” within tile self-assembly that seeks to design self-assembly systems that “conceal” both the input and computational history of performed computations. We achieve these results within the growth-only restricted abstract Tile Assembly Model (aTAM) with positive and negative interactions. We show that general-case covert computation is possible by implementing a set of basic covert logic gates capable of simulating any circuit (functionally complete). To further motivate the study of covert computation, we apply our new framework to resolve an outstanding complexity question; we use our covert circuitry to show that the unique assembly verification problem within the growth-only aTAM with negative interactions is coNP-complete.

Model for self-replicating, self-assembling electric circuits with self-controlled growth

The authors propose a tile assembly model (rcTAM) to study self-assembly, self-controlled growth, and self-replication. The paper shows how self-replication can be achieved without biological mechanisms or organic chemistry.

A model for self‐assembling circuits with voltage‐controlled growth

SummaryThe circuit tile assembly model (cTAM) consists of a voltage source and resistive circuit tiles, configured as a voltage divider, that attach to form resistive ladders or grids if the voltage on the boundary is greater than or equal to a threshold. The model produces a family of circuits whose composition and properties change with time. As growth proceeds, the voltage decreases until it no longer exceeds a threshold, which causes growth to cease. This is referred to as self‐controlled growth, because the properties of the assembly itself are the primary determinant in controlling the extent of the assembly. The model augments tile assembly models, which are programmable through specific chemical interactions, with an alternative electrical mechanism. The ladder and grid assemblies have bounded size and unique shape that are determined by parameters from the electrical network. Using the harmonicity of the electric potential, the shape of the grid assembly is shown to be symmetric around the main diagonal. Finally, two models of growth, differentiated by whether the voltage is measured before or after attachment, are equivalent. The model and analysis have potential application to self‐assembly of nanostructures, as well as to networks whose structure changes over time.

Hierarchical growth is necessary and (sometimes) sufficient to self-assemble discrete self-similar fractals

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 self-assembling the discrete self-similar fractals known as the “H” and “U” fractals. We then show that in a related model which allows for hierarchical self-assembly, the 2-Handed Assembly Model (2HAM), there does exist a tile assembly system which self-assembles the “U” fractal and conjecture that the same holds for the “H” fractal. This is the first example of discrete self similar fractals which self-assemble in the 2HAM but not in the aTAM, providing a direct comparison of the models and greater understanding of the power of hierarchical assembly.

Self-assembly of 3-D structures using 2-D folding tiles

Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large amount of research into designing theoretical models of self-assembling systems, and even laboratory-based implementations of them, these artificial models and systems often tend to be lacking in one of the powerful features of natural systems (e.g. the assembly and folding of proteins), which is dynamic reconfigurability of structures. In this paper, we present a new mathematical model of self-assembly, based on the abstract Tile Assembly Model (aTAM), called the Flexible Tile Assembly Model (FTAM). In the FTAM, the individual components are 2-dimensional tiles as in the aTAM, but in the FTAM, bonds between the edges of tiles can be flexible, allowing bonds to flex and entire structures to reconfigure, thus allowing 2-dimensional components to form 3-dimensional structures. We analyze the powers and limitations of FTAM systems by (1) demonstrating how flexibility can be controlled to carefully build desired structures, and (2) showing how flexibility can be beneficially harnessed to form structures which can “efficiently” reconfigure into many different configurations and/or greatly varying configurations. We also show that with such power comes a heavy burden in terms of computational complexity of simulation and prediction by proving that for important properties of FTAM systems, determining their existence is intractable, even for properties which are easily computed for systems in less dynamic models.

Optimal staged self-assembly of linear assemblies

We analyze the complexity of building linear assemblies, sets of linear assemblies, and \(\mathcal {O}(1)\)-scale general shapes in the staged tile assembly model. For systems with at most b bins and t tile types, we prove that the minimum number of stages to uniquely assemble a \(1 \times n\) line is \(\varTheta (\log _t{n} + \log _b{\frac{n}{t}} + 1)\). Generalizing to \(\mathcal {O}(1) \times n\) lines, we prove the minimum number of stages is \(\mathcal {O}(\frac{\log {n} - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})\) and \(\varOmega (\frac{\log {n} - tb - t\log t}{b^2})\).

Simulation of one dimensional staged DNA tile assembly by the signal-passing hierarchical TAM

The Tile Assembly Model, and its many variants, is one of the most fundamental algorithmic assembly formalism within DNA nanotechnology. Most of the research in this field is focused on the complexity of assembling different shapes and patterns. In many cases, the assembly process is intrinsically deterministic and the final product is unique, while the assembly process might evolve through several possible assembly strategies. In this study we consider the controlled assembly of one dimensional tile structures according to predefined assembly graphs. We provide algorithmic approaches for developing such controlled assembly protocols, using the signal-passing Tile Assembly Model, as well as probabilistic approaches for investigating the assembly of such tile-based one-dimensional structures. As a byproduct, we build a generalized TAS (tile assembly system) which generate specific non-local non-associative algebraic computations and we assamble n × n squares using only one tile, which is a better efficiency compared to the staged assembly model.