Scott M. Summers

Strict self-assembly of discrete Sierpinski triangles

Winfree (1998) showed that discrete Sierpinski triangles can self-assemble in the Tile Assembly Model. A striking molecular realization of this self-assembly, using DNA tiles a few nanometers long and verifying the results by atomic-force microscopy, was achieved by Rothemund, Papadakis, and Winfree (2004). Precisely speaking, the above self-assemblies tile completely filled-in, two-dimensional regions of the plane, with labeled subsets of these tiles representing discrete Sierpinski triangles. This paper addresses the more challenging problem of the strict self-assembly of discrete Sierpinski triangles, i.e., the task of tiling a discrete Sierpinski triangle and nothing else. We first prove that the standard discrete Sierpinski triangle cannot strictly self-assemble in the Tile Assembly Model. We then define the fibered Sierpinski triangle, a discrete Sierpinski triangle with the same fractal dimension as the standard one but with thin fibers that can carry data, and show that the fibered Sierpinski triangle strictly self-assembles in the Tile Assembly Model. In contrast with the simple XOR algorithm of the earlier, non-strict self-assemblies, our strict self-assembly algorithm makes extensive, recursive use of optimal counters, coupled with measured delay and corner-turning operations. We verify our strict self-assembly using the local determinism method of Soloveichik and Winfree (2007).

ASYNCHRONOUS SIGNAL PASSING FOR TILE SELF-ASSEMBLY: FUEL EFFICIENT COMPUTATION AND EFFICIENT ASSEMBLY OF SHAPES

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 et al. [24] to be asynchronous, allowing any action of turning a glue on or off, attaching a new tile, or breaking apart an assembly to happen in any order. Within this highly generalized model we provide three new solutions to tile self-assembly problems that have been addressed within the abstract Tile Assembly Model and its variants, showing that signal passing tiles allow for substantial improvement across multiple complexity metrics. Our first result utilizes a recursive assembly process to achieve tile-type efficient assembly of linear structures, using provably fewer tile types than what is possible in standard tile assembly models. Our second system of signal-passing tiles simulates any Turing machine with high fuel efficiency by using only a constant number of tiles per computation step. Our third system assembles the discrete Sierpinski triangle, demonstrating that this pattern can be strictly self-assembled within the STAM. This result is of particular interest in that it is known that this pattern cannot self-assemble within a number of well studied tile self-assembly models. Notably, all of our constructions are at temperature 1, further demonstrating that signal-passing confers the power to bypass many restrictions found in standard tile assembly models.

Limitations of self-assembly at temperature 1

We prove that if a set X@?Z^2 weakly self-assembles at temperature 1 in a deterministic (Winfree) tile assembly system satisfying a natural condition known as pumpability, then X is a semilinear set. This shows that only the most simple of infinite shapes and patterns can be constructed using pumpable temperature 1 tile assembly systems, and gives evidence for the thesis that temperature 2 or higher is required to carry out general-purpose computation in a deterministic two-dimensional tile assembly system. We employ this result to show that, unlike the case of temperature 2 self-assembly, no discrete self-similar fractal weakly self-assembles at temperature 1 in a pumpable tile assembly system.

Computability and Complexity in Self-assembly

This paper explores the impact of geometry on computability and complexity in Winfree’s model of nanoscale self-assembly. We work in the two-dimensional tile assembly model, i.e., in the discrete Euclidean plane ℤ×ℤ. Our first main theorem says that there is a roughly quadratic function f such that a set A⊆ℤ+ is computably enumerable if and only if the set XA={(f(n),0)∣n∈A}—a simple representation of A as a set of points on the x-axis—self-assembles in Winfree’s sense. In contrast, our second main theorem says that there are decidable sets D⊆ℤ×ℤ that do not self-assemble in Winfree’s sense.Our first main theorem is established by an explicit translation of an arbitrary Turing machine M to a modular tile assembly system

Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature

\mathcal{T}_{M}

INTRINSIC UNIVERSALITY IN SELF-ASSEMBLY

, together with a proof that

Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract)

\mathcal{T}_{M}

Reducing Tile Complexity for the Self-assembly of Scaled Shapes Through Temperature Programming

carries out concurrent simulations of M on all positive integer inputs.

Self-assembly of decidable sets

We consider the problem of fault-tolerance in nanoscale algorithmic self-assembly. We employ a standard variant of Winfree’s abstract Tile Assembly Model (aTAM), the two-handed aTAM, in which square “tiles” – a model of molecules constructed from DNA for the purpose of engineering self-assembled nanostructures – aggregate according to specific binding sites of varying strengths, and in which large aggregations of tiles may attach to each other, in contrast to the seeded aTAM, in which tiles aggregate one at a time to a single specially designated “seed” assembly. We focus on a major cause of errors in tile-based self-assembly: that of unintended growth due to “weak” strength-1 bonds, which if allowed to persist, may be stabilized by subsequent attachment of neighboring tiles in the sense that at least energy 2 is now required to break apart the resulting assembly, i.e., the errant assembly is stable at temperature 2. We study a common self-assembly benchmark problem, that of assembling an n×n square using O(log n) unique tile types, under the two-handed model of self-assembly. Our main result achieves a much stronger notion of fault-tolerance than those achieved previously. Arbitrary strength-1 growth is allowed, however, any assembly that grows sufficiently to become stable at temperature 2 is guaranteed to assemble into the correct final assembly of an n×n square. In other words, errors due to insufficient attachment, which is the cause of errors studied in earlier papers on fault-tolerance, are prevented absolutely in our main construction, rather than only with high probability and for sufficiently small structures, as in previous fault tolerance studies.

Asynchronous Signal Passing for Tile Self-assembly: Fuel Efficient Computation and Efficient Assembly of Shapes

We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is capable of simulating a very wide class of tile systems, including itself. Specifically, we give a tile set that simulates the assembly of any tile assembly system in a class of systems that we call \emph{locally consistent}: each tile binds with exactly the strength needed to stay attached, and that there are no glue mismatches between tiles in any produced assembly. Our construction is reminiscent of the studies of \emph{intrinsic universality} of cellular automata by Ollinger and others, in the sense that our simulation of a tile system