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 $n$ unitary gates $U_1, \ldots, U_n$ and a permutation $\sigma$ of $\{1,\ldots, n\}$, in applying the unitary gates in the order specified by $\sigma$, i.e. in performing $U_{\sigma(n)}\ldots U_{\sigma(1)}$. 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 $U_i$ 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 $n^2$ calls in the query model and $\frac{n(n-1)}2$ quantum switches in the new model. We refine these results by proving that $n\log_2(n) +\Theta(n)$ quantum switches are necessary and sufficient to solve this problem, whereas $n^2-2n+4$ 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 $n^2-o(n^{7/4+\epsilon})$ queries are required, for any $\epsilon >0$. 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 $\textsf{NP}$, and the problem "is a network subset atomic with respect to a given atom set" is strongly $\textsf{NP}$-$\textsf{Complete}$. 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 $\textbf{polynomial-time algorithm}$ to decide whether a given network is reachably atomic, improving upon the result of Adleman et al. that the problem is $\textbf{decidable}$. We show that the reachability problem for reachably atomic networks is $\textsf{Pspace}$-$\textsf{Complete}$. 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