Deterministic soliton automata with at most one cycle

AbstractSoliton valves have been proposed as molecular switching elements. Their mathematical model is the soliton graph and the soliton automaton (Dassow and Jürgensen, J. Comput. System Sci.40 (1990), 154–181). In this paper we continue the study of the logic aspects of soliton switching. There are two cases of special importance: those of deterministic and those of strongly deterministic soliton automata. The former have deterministic state transitions in the usual sense of automaton theory. The latter do not only have deterministic state transitions, but also deterministic soliton paths—a much stronger property, as it turns out. In op cit. a characterization of indecomposable, strongly deterministic soliton automata was proved and it was shown that their transition monoids are primitive groups of permutations. Roughly speaking, the main difference between deterministic and strongly deterministic soliton automata is that in the former the underlying soliton graphs may contain cycles of odd lengths while such cycles are not permitted in the soliton graphs belonging to strongly deterministic soliton automata. In the present paper, we focus on a special class of deterministic soliton automata, that of deterministic soliton automata whose underlying graphs contain at most one cycle. For this class we derive structural descriptions. Our main results concern the elimination of certain types of loops, the treatment of soliton paths with repeated edges, the structure of cycles of odd length, and the transition monoid. As an application we show that the memory element proposed in the literature (Carter, in Bioelectronics, edited by Aizawa, Research and Development Report 50, CMC Press, Denver, CO, 1984) can be transformed in into a soliton tree, thus turning a deterministic device into a logically equivalent strongly deterministic device

Decision Problems For Convex Languages

In this paper we examine decision problems associated with various classes of convex languages, studied by Ang and Brzozowski (under the name "continuous languages"). We show that we can decide whether a given language L is prefix-, suffix-, factor-, or subword-convex in polynomial time if L is represented by a DFA, but that the problem is PSPACE-hard if L is represented by an NFA. In the case that a regular language is not convex, we prove tight upper bounds on the length of the shortest words demonstrating this fact, in terms of the number of states of an accepting DFA. Similar results are proved for some subclasses of convex languages: the prefix-, suffix-, factor-, and subword-closed languages, and the prefix-, suffix-, factor-, and subword-free languages.Comment: preliminary version. This version corrected one typo in Section 2.1.1, line

A Fast Algorithm Finding the Shortest Reset Words

In this paper we present a new fast algorithm finding minimal reset words for finite synchronizing automata. The problem is know to be computationally hard, and our algorithm is exponential. Yet, it is faster than the algorithms used so far and it works well in practice. The main idea is to use a bidirectional BFS and radix (Patricia) tries to store and compare resulted subsets. We give both theoretical and practical arguments showing that the branching factor is reduced efficiently. As a practical test we perform an experimental study of the length of the shortest reset word for random automata with $n$ states and 2 input letters. We follow Skvorsov and Tipikin, who have performed such a study using a SAT solver and considering automata up to $n=100$ states. With our algorithm we are able to consider much larger sample of automata with up to $n=300$ states. In particular, we obtain a new more precise estimation of the expected length of the shortest reset word $\approx 2.5\sqrt{n-5}$.Comment: COCOON 2013. The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-642-38768-5_1

Algebraic synchronization criterion and computing reset words

We refine a uniform algebraic approach for deriving upper bounds on reset thresholds of synchronizing automata. We express the condition that an automaton is synchronizing in terms of linear algebra, and obtain upper bounds for the reset thresholds of automata with a short word of a small rank. The results are applied to make several improvements in the area. We improve the best general upper bound for reset thresholds of finite prefix codes (Huffman codes): we show that an $n$-state synchronizing decoder has a reset word of length at most $O(n \log^3 n)$. In addition to that, we prove that the expected reset threshold of a uniformly random synchronizing binary $n$-state decoder is at most $O(n \log n)$. We also show that for any non-unary alphabet there exist decoders whose reset threshold is in $\varTheta(n)$. We prove the \v{C}ern\'{y} conjecture for $n$-state automata with a letter of rank at most $\sqrt[3]{6n-6}$. In another corollary, based on the recent results of Nicaud, we show that the probability that the \v{C}ern\'y conjecture does not hold for a random synchronizing binary automaton is exponentially small in terms of the number of states, and also that the expected value of the reset threshold of an $n$-state random synchronizing binary automaton is at most $n^{3/2+o(1)}$. Moreover, reset words of lengths within all of our bounds are computable in polynomial time. We present suitable algorithms for this task for various classes of automata, such as (quasi-)one-cluster and (quasi-)Eulerian automata, for which our results can be applied.Comment: 18 pages, 2 figure

Site-Directed Insertion: Decision Problems, Maximality and Minimality

Site-directed insertion is an overlapping insertion operation that can be viewed as analogous to the overlap assembly or chop operations that concatenate strings by overlapping a suffix and a prefix of the argument strings. We consider decision problems and language equations involving site-directed insertion. By relying on the tools provided by semantic shuffle on trajectories we show that one variable equations involving site-directed insertion and regular constants can be solved. We consider also maximal and minimal variants of the site-directed insertion operation

Implementation of Code Properties via Transducers

The FAdo system is a symbolic manipulator of formal language objects, implemented in Python. In this work, we extend its capabilities by implementing methods to manipulate transducers and we go one level higher than existing formal language systems and implement methods to manipulate objects representing classes of independent languages (widely known as code properties). Our methods allow users to define their own code properties and combine them between themselves or with fixed properties such as prefix codes, suffix codes, error detecting codes, etc. The satisfaction and maximality decision questions are solvable for any of the definable properties. The new online system LaSer allows one to query about a code property and obtain the answer in a batch mode. Our work is founded on independence theory as well as the theory of rational relations and transducers, and contributes with improved algorithms on these objects

Coherent multi-flavour spin dynamics in a fermionic quantum gas

Microscopic spin interaction processes are fundamental for global static and dynamical magnetic properties of many-body systems. Quantum gases as pure and well isolated systems offer intriguing possibilities to study basic magnetic processes including non-equilibrium dynamics. Here, we report on the realization of a well-controlled fermionic spinor gas in an optical lattice with tunable effective spin ranging from 1/2 to 9/2. We observe long-lived intrinsic spin oscillations and investigate the transition from two-body to many-body dynamics. The latter results in a spin-interaction driven melting of a band insulator. Via an external magnetic field we control the system's dimensionality and tune the spin oscillations in and out of resonance. Our results open new routes to study quantum magnetism of fermionic particles beyond conventional spin 1/2 systems.Comment: 9 pages, 5 figure

Diversity and activity of sugar transporters in nematode-induced root syncytia

The plant-parasitic nematode Heterodera schachtii stimulates plant root cells to form syncytial feeding structures which synthesize all nutrients required for successful nematode development. Cellular re-arrangements and modified metabolism of the syncytia are accompanied by massive intra- and intercellular solute allocations. In this study the expression of all genes annotated as sugar transporters in the Arabidopsis Membrane Protein Library was investigated by Affymetrix gene chip analysis in young and fully developed syncytia compared with non-infected Arabidopsis thaliana roots. The expression of three highly up-regulated (STP12, MEX1, and GTP2) and three highly down-regulated genes (SFP1, STP7, and STP4) was analysed by quantitative RT-PCR (qRT-PCR). The most up-regulated gene (STP12) was chosen for further in-depth studies using in situ RT-PCR and a nematode development assay with a T-DNA insertion line revealing a significant reduction of male nematode development. The specific role of STP12 expression in syncytia of male juveniles compared with those of female juveniles was further shown by qRT-PCR. In order to provide evidence for sugar transporter activity across the plasma membrane of syncytia, fluorescence-labelled glucose was used and membrane potential recordings following the application of several sugars were performed. Analyses of soluble sugar pools revealed a highly specific composition in syncytia. The presented work demonstrates that sugar transporters are specifically expressed and active in syncytia, indicating a profound role in inter- and intracelluar transport processes

Well-established nucleon resonances revisited by double-polarization measurements

The first measurement is reported of the double-polarization observable G in photoproduction of neutral pions off protons, covering the photon energy range from 620 to 1120 MeV and the full solid angle. G describes the correlation between the photon polarization plane and the scattering plane for protons polarized along the direction of the incoming photon. The observable is highly sensitive to contributions from baryon resonances. The new results are compared to the predictions from SAID, MAID, and BnGa partial wave analyses. In spite of the long-lasting efforts to understand {\gamma}p -> p{\pi} 0 as the simplest photoproduction reaction, surprisingly large differences between the new data and the latest predictions are observed which are traced to different contributions of the N (1535) with spin-parity J^P = 1/2^- and N (1520) with J^P = 3/2^- . In the third resonance region, where N (1680) with J^P = 5/2^+ production dominates, the new data are reasonably close to the predictions.Comment: Submitted for publication in PR