Quantum counter automata

The question of whether quantum real-time one-counter automata (rtQ1CAs) can outperform their probabilistic counterparts has been open for more than a decade. We provide an affirmative answer to this question, by demonstrating a non-context-free language that can be recognized with perfect soundness by a rtQ1CA. This is the first demonstration of the superiority of a quantum model to the corresponding classical one in the real-time case with an error bound less than 1. We also introduce a generalization of the rtQ1CA, the quantum one-way one-counter automaton (1Q1CA), and show that they too are superior to the corresponding family of probabilistic machines. For this purpose, we provide general definitions of these models that reflect the modern approach to the definition of quantum finite automata, and point out some problems with previous results. We identify several remaining open problems.Comment: A revised version. 16 pages. A preliminary version of this paper appeared as A. C. Cem Say, Abuzer Yakary{\i}lmaz, and \c{S}efika Y\"{u}zsever. Quantum one-way one-counter automata. In R\={u}si\c{n}\v{s} Freivalds, editor, Randomized and quantum computation, pages 25--34, 2010 (Satellite workshop of MFCS and CSL 2010

Quantum computation with devices whose contents are never read

In classical computation, a "write-only memory" (WOM) is little more than an oxymoron, and the addition of WOM to a (deterministic or probabilistic) classical computer brings no advantage. We prove that quantum computers that are augmented with WOM can solve problems that neither a classical computer with WOM nor a quantum computer without WOM can solve, when all other resource bounds are equal. We focus on realtime quantum finite automata, and examine the increase in their power effected by the addition of WOMs with different access modes and capacities. Some problems that are unsolvable by two-way probabilistic Turing machines using sublogarithmic amounts of read/write memory are shown to be solvable by these enhanced automata.Comment: 32 pages, a preliminary version of this work was presented in the 9th International Conference on Unconventional Computation (UC2010

Finite state verifiers with constant randomness

We give a new characterization of $\mathsf{NL}$ as the class of languages whose members have certificates that can be verified with small error in polynomial time by finite state machines that use a constant number of random bits, as opposed to its conventional description in terms of deterministic logarithmic-space verifiers. It turns out that allowing two-way interaction with the prover does not change the class of verifiable languages, and that no polynomially bounded amount of randomness is useful for constant-memory computers when used as language recognizers, or public-coin verifiers. A corollary of our main result is that the class of outcome problems corresponding to O(log n)-space bounded games of incomplete information where the universal player is allowed a constant number of moves equals NL.Comment: 17 pages. An improved versio

Unbounded-error quantum computation with small space bounds

We prove the following facts about the language recognition power of quantum Turing machines (QTMs) in the unbounded error setting: QTMs are strictly more powerful than probabilistic Turing machines for any common space bound $s$ satisfying $s(n)=o(\log \log n)$. For "one-way" Turing machines, where the input tape head is not allowed to move left, the above result holds for $s(n)=o(\log n)$. We also give a characterization for the class of languages recognized with unbounded error by real-time quantum finite automata (QFAs) with restricted measurements. It turns out that these automata are equal in power to their probabilistic counterparts, and this fact does not change when the QFA model is augmented to allow general measurements and mixed states. Unlike the case with classical finite automata, when the QFA tape head is allowed to remain stationary in some steps, more languages become recognizable. We define and use a QTM model that generalizes the other variants introduced earlier in the study of quantum space complexity.Comment: A preliminary version of this paper appeared in the Proceedings of the Fourth International Computer Science Symposium in Russia, pages 356--367, 200

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

An Individual-based Probabilistic Model for Fish Stock Simulation

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically model-checked by giving a suitable translation into syntax accepted by existing model-checkers. In order to simulate the dynamics of a given population of soles in different environmental scenarios, an agent-based simulation environment is defined in which each agent implements the behaviour of the given EPDTA model. By varying the probabilities and the characteristic functions embedded in the EPDTA model it is possible to represent different scenarios and to tune the model itself by comparing the results of the simulations with real data about the sole stock in the North Adriatic sea, available from the recent project SoleMon. The simulator is presented and made available for its adaptation to other species.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314