948 research outputs found
Intrinsic Universality in Self-Assembly
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 by a tile system represents each tile
in an assembly produced by by a block of tiles in , where
is a constant depending on but not on the size of the assembly
produces (which may in fact be infinite). Also, our construction improves on
earlier simulations of tile assembly systems by other tile assembly systems (in
particular, those of Soloveichik and Winfree, and of Demaine et al.) in that we
simulate the actual process of self-assembly, not just the end result, as in
Soloveichik and Winfree's construction, and we do not discriminate against
infinite structures. Both previous results simulate only temperature 1 systems,
whereas our construction simulates tile assembly systems operating at
temperature 2
Programmable Control of Nucleation for Algorithmic Self-Assembly
Algorithmic self-assembly, a generalization of crystal growth processes, has
been proposed as a mechanism for autonomous DNA computation and for bottom-up
fabrication of complex nanostructures. A `program' for growing a desired
structure consists of a set of molecular `tiles' designed to have specific
binding interactions. A key challenge to making algorithmic self-assembly
practical is designing tile set programs that make assembly robust to errors
that occur during initiation and growth. One method for the controlled
initiation of assembly, often seen in biology, is the use of a seed or catalyst
molecule that reduces an otherwise large kinetic barrier to nucleation. Here we
show how to program algorithmic self-assembly similarly, such that seeded
assembly proceeds quickly but there is an arbitrarily large kinetic barrier to
unseeded growth. We demonstrate this technique by introducing a family of tile
sets for which we rigorously prove that, under the right physical conditions,
linearly increasing the size of the tile set exponentially reduces the rate of
spurious nucleation. Simulations of these `zig-zag' tile sets suggest that
under plausible experimental conditions, it is possible to grow large seeded
crystals in just a few hours such that less than 1 percent of crystals are
spuriously nucleated. Simulation results also suggest that zig-zag tile sets
could be used for detection of single DNA strands. Together with prior work
showing that tile sets can be made robust to errors during properly initiated
growth, this work demonstrates that growth of objects via algorithmic
self-assembly can proceed both efficiently and with an arbitrarily low error
rate, even in a model where local growth rules are probabilistic.Comment: 37 pages, 14 figure
Self-Assembly of Tiles: Theoretical Models, the Power of Signals, and Local Computing
DNA-based self-assembly is an autonomous process whereby a disordered system of DNA sequences forms an organized structure or pattern as a consequence of Watson-Crick complementarity of DNA sequences, without external direction.
Here, we propose self-assembly (SA) hypergraph automata as an automata-theoretic model for patterned self-assembly. We investigate the computational power of SA-hypergraph automata and show that for every recognizable picture language, there exists an SA-hypergraph automaton that accepts this language. Conversely, we prove that for any restricted SA-hypergraph automaton, there exists a Wang Tile System, a model for recognizable picture languages, that accepts the same language.
Moreover, we investigate the computational power of some variants of the Signal-passing Tile Assembly Model (STAM), as well as propose the concept of {\it Smart Tiles}, i.e., tiles with glues that can be activated or deactivated by signals, and which possess a limited amount of local computing capability. We demonstrate the potential of smart tiles to perform some robotic tasks such as replicating complex shapes
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