Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Parallelism and Time in Hierarchical Self-Assembly   We study the role that parallelism plays in time complexity of Winfree's
abstract Tile Assembly Model (aTAM), a model of molecular algorithmic
self-assembly. In the "hierarchical" aTAM, two assemblies, both consisting of
multiple tiles, are allowed to aggregate together, whereas in the "seeded"
aTAM, tiles attach one at a time to a growing assembly. Adleman, Cheng, Goel,
and Huang ("Running Time and Program Size for Self-Assembled Squares", STOC
2001) showed how to assemble an n x n square in O(n) time in the seeded aTAM
using O(log n / log log n) unique tile types, where both of these parameters
are optimal. They asked whether the hierarchical aTAM could allow a tile system
to use the ability to form large assemblies in parallel before they attach to
break the Omega(n) lower bound for assembly time. We show that there is a tile
system with the optimal O(log n / log log n) tile types that assembles an n x n
square using O(log^2 n) parallel "stages", which is close to the optimal
Omega(log n) stages, forming the final n x n square from four n/2 x n/2
squares, which are themselves recursively formed from n/4 x n/4 squares, etc.
However, despite this nearly maximal parallelism, the system requires
superlinear time to assemble the square. We extend the definition of *partial
order tile systems* studied by Adleman et al. in a natural way to hierarchical
assembly and show that no hierarchical partial order tile system can build any
shape with diameter N in less than time Omega(N), demonstrating that in this
case the hierarchical model affords no speedup whatsoever over the seeded
model. We strengthen the Omega(N) time lower bound for deterministic seeded
systems of Adleman et al. to nondeterministic seeded systems. Finally, we show
that for infinitely many n, a tile system can assemble an n x n' rectangle,
with n > n', in time O(n^{4/5} log n), breaking the linear-time lower bound.

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The categories of this paper are: hep-ex
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The categories of this paper are: math
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The categories of this paper are: stat
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The categories of this paper are: math-ph
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The categories of this paper are: funct-an
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The categories of this paper are: nucl-ex
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The categories of this paper are: acc-phys
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The categories of this paper are: q-alg
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The categories of this paper are: physics
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The categories of this paper are: hep-lat
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The categories of this paper are: astro-ph
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The categories of this paper are: adap-org
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The categories of this paper are: cond-mat
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The categories of this paper are: econ
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The categories of this paper are: comp-gas
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The categories of this paper are: cmp-lg