223,732 research outputs found
Random number selection in self-assembly
We investigate methods for exploiting nondeterminism inherent within the Tile Assembly Model in order to generate uniform random numbers. Namely, given an integer range {0,...,n − 1}, we exhibit methods for randomly selecting a number within that range. We present three constructions exhibiting a trade-off between space requirements and closeness to uniformity.
The first selector selects a random number with probability Θ(1/n) using O(log2 n) tiles. The second selector takes a user-specified parameter that guarantees the probabilities are arbitrarily close to uniform, at the cost of additional space. The third selector selects a random number with probability exactly 1/n, and uses no more space than the first selector with high probability, but uses potentially unbounded space
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
Evolutionary Dynamics in a Simple Model of Self-Assembly
We investigate the evolutionary dynamics of an idealised model for the robust
self-assembly of two-dimensional structures called polyominoes. The model
includes rules that encode interactions between sets of square tiles that drive
the self-assembly process. The relationship between the model's rule set and
its resulting self-assembled structure can be viewed as a genotype-phenotype
map and incorporated into a genetic algorithm. The rule sets evolve under
selection for specified target structures. The corresponding, complex fitness
landscape generates rich evolutionary dynamics as a function of parameters such
as the population size, search space size, mutation rate, and method of
recombination. Furthermore, these systems are simple enough that in some cases
the associated model genome space can be completely characterised, shedding
light on how the evolutionary dynamics depends on the detailed structure of the
fitness landscape. Finally, we apply the model to study the emergence of the
preference for dihedral over cyclic symmetry observed for homomeric protein
tetramers
Negative Interactions in Irreversible Self-Assembly
This paper explores the use of negative (i.e., repulsive) interaction the
abstract Tile Assembly Model defined by Winfree. Winfree postulated negative
interactions to be physically plausible in his Ph.D. thesis, and Reif, Sahu,
and Yin explored their power in the context of reversible attachment
operations. We explore the power of negative interactions with irreversible
attachments, and we achieve two main results. Our first result is an
impossibility theorem: after t steps of assembly, Omega(t) tiles will be
forever bound to an assembly, unable to detach. Thus negative glue strengths do
not afford unlimited power to reuse tiles. Our second result is a positive one:
we construct a set of tiles that can simulate a Turing machine with space bound
s and time bound t, while ensuring that no intermediate assembly grows larger
than O(s), rather than O(s * t) as required by the standard Turing machine
simulation with tiles
Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes
The emergence of replicases that can replicate themselves is a central issue
in the origin of life. Recent experiments suggest that such replicases can be
realized if an RNA polymerase ribozyme is divided into fragments short enough
to be replicable by the ribozyme and if these fragments self-assemble into a
functional ribozyme. However, the continued self-replication of such replicases
requires that the production of every essential fragment be balanced and
sustained. Here, we use mathematical modeling to investigate whether and under
what conditions fragmented replicases achieve continued self-replication. We
first show that under a simple batch condition, the replicases fail to display
continued self-replication owing to positive feedback inherent in these
replicases. This positive feedback inevitably biases replication toward a
subset of fragments, so that the replicases eventually fail to sustain the
production of all essential fragments. We then show that this inherent
instability can be resolved by small rates of random content exchange between
loose compartments (i.e., horizontal transfer). In this case, the balanced
production of all fragments is achieved through negative frequency-dependent
selection operating in the population dynamics of compartments. This selection
mechanism arises from an interaction mediated by horizontal transfer between
intracellular and intercellular symmetry breaking. The horizontal transfer also
ensures the presence of all essential fragments in each compartment, sustaining
self-replication. Taken together, our results underline compartmentalization
and horizontal transfer in the origin of the first self-replicating replicases.Comment: 14 pages, 4 figures, and supplemental materia
The difficulty of folding self-folding origami
Why is it difficult to refold a previously folded sheet of paper? We show
that even crease patterns with only one designed folding motion inevitably
contain an exponential number of `distractor' folding branches accessible from
a bifurcation at the flat state. Consequently, refolding a sheet requires
finding the ground state in a glassy energy landscape with an exponential
number of other attractors of higher energy, much like in models of protein
folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems.
As in these problems, we find that refolding a sheet requires actuation at
multiple carefully chosen creases. We show that seeding successful folding in
this way can be understood in terms of sub-patterns that fold when cut out
(`folding islands'). Besides providing guidelines for the placement of active
hinges in origami applications, our results point to fundamental limits on the
programmability of energy landscapes in sheets.Comment: 8 pages, 5 figure
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