519 research outputs found
Using Automated Reasoning Systems on Molecular Computing
This paper is focused on the interplay between automated
reasoning systems (as theoretical and formal devices to study the correctness
of a program) and DNA computing (as practical devices to
handle DNA strands to solve classical hard problems with laboratory
techniques). To illustrate this work we have proven in the PVS proof
checker, the correctness of a program, in a sticker based model for DNA
computation, solving the pairwise disjoint families problem. Also we introduce
the formalization of the Floyd–Hoare logic for imperative programs
Self-replication and evolution of DNA crystals
Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required
Quantum Weakly Nondeterministic Communication Complexity
We study the weakest model of quantum nondeterminism in which a classical
proof has to be checked with probability one by a quantum protocol. We show the
first separation between classical nondeterministic communication complexity
and this model of quantum nondeterministic communication complexity for a total
function. This separation is quadratic.Comment: 12 pages. v3: minor correction
Fuzzy splicing systems
In this paper we introduce a new variant of splicing systems, called fuzzy splicing systems, and establish some basic properties of language families generated by this type of splicing systems. We study the “fuzzy effect” on splicing operations, and show that the “fuzzification” of splicing systems can increase and decrease the computational power of splicing systems with finite components with respect to fuzzy operations and cut-points chosen for threshold languages
Quantum Circuits for the Unitary Permutation Problem
We consider the Unitary Permutation problem which consists, given unitary
gates and a permutation of , in
applying the unitary gates in the order specified by , i.e. in
performing . This problem has been
introduced and investigated by Colnaghi et al. where two models of computations
are considered. This first is the (standard) model of query complexity: the
complexity measure is the number of calls to any of the unitary gates in
a quantum circuit which solves the problem. The second model provides quantum
switches and treats unitary transformations as inputs of second order. In that
case the complexity measure is the number of quantum switches. In their paper,
Colnaghi et al. have shown that the problem can be solved within calls in
the query model and quantum switches in the new model. We
refine these results by proving that quantum switches
are necessary and sufficient to solve this problem, whereas calls
are sufficient to solve this problem in the standard quantum circuit model. We
prove, with an additional assumption on the family of gates used in the
circuits, that queries are required, for any
. The upper and lower bounds for the standard quantum circuit
model are established by pointing out connections with the permutation as
substring problem introduced by Karp.Comment: 8 pages, 5 figure
Quantum Optimization Problems
Krentel [J. Comput. System. Sci., 36, pp.490--509] presented a framework for
an NP optimization problem that searches an optimal value among
exponentially-many outcomes of polynomial-time computations. This paper expands
his framework to a quantum optimization problem using polynomial-time quantum
computations and introduces the notion of an ``universal'' quantum optimization
problem similar to a classical ``complete'' optimization problem. We exhibit a
canonical quantum optimization problem that is universal for the class of
polynomial-time quantum optimization problems. We show in a certain relativized
world that all quantum optimization problems cannot be approximated closely by
quantum polynomial-time computations. We also study the complexity of quantum
optimization problems in connection to well-known complexity classes.Comment: date change
Rapid solution of problems by nuclear-magnetic-resonance quantum computation
We offer an improved method for using a nuclear-magnetic-resonance quantum
computer (NMRQC) to solve the Deutsch-Jozsa problem. Two known obstacles to the
application of the NMRQC are exponential diminishment of density-matrix
elements with the number of bits, threatening weak signal levels, and the high
cost of preparing a suitable starting state. A third obstacle is a heretofore
unnoticed restriction on measurement operators available for use by an NMRQC.
Variations on the function classes of the Deutsch-Jozsa problem are introduced,
both to extend the range of problems advantageous for quantum computation and
to escape all three obstacles to use of an NMRQC. By adapting it to one such
function class, the Deutsch-Jozsa problem is made solvable without exponential
loss of signal. The method involves an extra work bit and a polynomially more
involved Oracle; it uses the thermal-equilibrium density matrix systematically
for an arbitrary number of spins, thereby avoiding both the preparation of a
pseudopure state and temporal averaging.Comment: 19 page
Solving the subset-sum problem with a light-based device
We propose a special computational device which uses light rays for solving
the subset-sum problem. The device has a graph-like representation and the
light is traversing it by following the routes given by the connections between
nodes. The nodes are connected by arcs in a special way which lets us to
generate all possible subsets of the given set. To each arc we assign either a
number from the given set or a predefined constant. When the light is passing
through an arc it is delayed by the amount of time indicated by the number
placed in that arc. At the destination node we will check if there is a ray
whose total delay is equal to the target value of the subset sum problem (plus
some constants).Comment: 14 pages, 6 figures, Natural Computing, 200
Computational Complexity of Atomic Chemical Reaction Networks
Informally, a chemical reaction network is "atomic" if each reaction may be
interpreted as the rearrangement of indivisible units of matter. There are
several reasonable definitions formalizing this idea. We investigate the
computational complexity of deciding whether a given network is atomic
according to each of these definitions.
Our first definition, primitive atomic, which requires each reaction to
preserve the total number of atoms, is to shown to be equivalent to mass
conservation. Since it is known that it can be decided in polynomial time
whether a given chemical reaction network is mass-conserving, the equivalence
gives an efficient algorithm to decide primitive atomicity.
Another definition, subset atomic, further requires that all atoms are
species. We show that deciding whether a given network is subset atomic is in
, and the problem "is a network subset atomic with respect to a
given atom set" is strongly -.
A third definition, reachably atomic, studied by Adleman, Gopalkrishnan et
al., further requires that each species has a sequence of reactions splitting
it into its constituent atoms. We show that there is a to decide whether a given network is reachably atomic, improving
upon the result of Adleman et al. that the problem is . We
show that the reachability problem for reachably atomic networks is
-.
Finally, we demonstrate equivalence relationships between our definitions and
some special cases of another existing definition of atomicity due to Gnacadja
Exact Cover with light
We suggest a new optical solution for solving the YES/NO version of the Exact
Cover problem by using the massive parallelism of light. The idea is to build
an optical device which can generate all possible solutions of the problem and
then to pick the correct one. In our case the device has a graph-like
representation and the light is traversing it by following the routes given by
the connections between nodes. The nodes are connected by arcs in a special way
which lets us to generate all possible covers (exact or not) of the given set.
For selecting the correct solution we assign to each item, from the set to be
covered, a special integer number. These numbers will actually represent delays
induced to light when it passes through arcs. The solution is represented as a
subray arriving at a certain moment in the destination node. This will tell us
if an exact cover does exist or not.Comment: 20 pages, 4 figures, New Generation Computing, accepted, 200
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