Longest Common Extensions in Sublinear Space

The longest common extension problem (LCE problem) is to construct a data structure for an input string $T$ of length $n$ that supports LCE$(i,j)$ queries. Such a query returns the length of the longest common prefix of the suffixes starting at positions $i$ and $j$ in $T$. This classic problem has a well-known solution that uses $O(n)$ space and $O(1)$ query time. In this paper we show that for any trade-off parameter $1 \leq \tau \leq n$, the problem can be solved in $O(\frac{n}{\tau})$ space and $O(\tau)$ query time. This significantly improves the previously best known time-space trade-offs, and almost matches the best known time-space product lower bound.Comment: An extended abstract of this paper has been accepted to CPM 201

Average-Case Optimal Approximate Circular String Matching

Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that are at a distance at most k from x or from any of its rotations. In this article, we present a new algorithm for approximate circular string matching under the edit distance model with optimal average-case search time O(n(k + log m)/m). Optimal average-case search time can also be achieved by the algorithms for multiple approximate string matching (Fredriksson and Navarro, 2004) using x and its rotations as the set of multiple patterns. Here we reduce the preprocessing time and space requirements compared to that approach

Longest Common Extensions in Trees

The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE queries. In this paper we generalize the LCE problem to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree $T$ of size $n$, the goal is to preprocess $T$ into a compact data structure that support the following LCE queries between subpaths and subtrees in $T$. Let $v_1$, $v_2$, $w_1$, and $w_2$ be nodes of $T$ such that $w_1$ and $w_2$ are descendants of $v_1$ and $v_2$ respectively. \begin{itemize} \item \LCEPP(v_1, w_1, v_2, w_2): (path-path \LCE) return the longest common prefix of the paths $v_1 \leadsto w_1$ and $v_2 \leadsto w_2$. \item \LCEPT(v_1, w_1, v_2): (path-tree \LCE) return maximal path-path LCE of the path $v_1 \leadsto w_1$ and any path from $v_2$ to a descendant leaf. \item \LCETT(v_1, v_2): (tree-tree \LCE) return a maximal path-path LCE of any pair of paths from $v_1$ and $v_2$ to descendant leaves. \end{itemize} We present the first non-trivial bounds for supporting these queries. For \LCEPP queries, we present a linear-space solution with $O(\log^{*} n)$ query time. For \LCEPT queries, we present a linear-space solution with $O((\log\log n)^{2})$ query time, and complement this with a lower bound showing that any path-tree LCE structure of size O(n \polylog(n)) must necessarily use $\Omega(\log\log n)$ time to answer queries. For \LCETT queries, we present a time-space trade-off, that given any parameter $\tau$, $1 \leq \tau \leq n$, leads to an $O(n\tau)$ space and $O(n/\tau)$ query-time solution. This is complemented with a reduction to the the set intersection problem implying that a fast linear space solution is not likely to exist

Finite temperature phase transition for disordered weakly interacting bosons in one dimension

It is commonly accepted that there are no phase transitions in one-dimensional (1D) systems at a finite temperature, because long-range correlations are destroyed by thermal fluctuations. Here we demonstrate that the 1D gas of short-range interacting bosons in the presence of disorder can undergo a finite temperature phase transition between two distinct states: fluid and insulator. None of these states has long-range spatial correlations, but this is a true albeit non-conventional phase transition because transport properties are singular at the transition point. In the fluid phase the mass transport is possible, whereas in the insulator phase it is completely blocked even at finite temperatures. We thus reveal how the interaction between disordered bosons influences their Anderson localization. This key question, first raised for electrons in solids, is now crucial for the studies of atomic bosons where recent experiments have demonstrated Anderson localization in expanding very dilute quasi-1D clouds.Comment: 8 pages, 5 figure

Finding the region of pseudo-periodic tandem repeats in biological sequences

SUMMARY: The genomes of many species are dominated by short sequences repeated consecutively. It is estimated that over 10% of the human genome consists of tandemly repeated sequences. Finding repeated regions in long sequences is important in sequence analysis. We develop a software, LocRepeat, that finds regions of pseudo-periodic repeats in a long sequence. We use the definition of Li et al. [1] for the pseudo-periodic partition of a region and extend the algorithm that can select the repeated region from a given long sequence and give the pseudo-periodic partition of the region. AVAILABILITY: LocRepeat is available a

Flat bands as a route to high-temperature superconductivity in graphite

Superconductivity is traditionally viewed as a low-temperature phenomenon. Within the BCS theory this is understood to result from the fact that the pairing of electrons takes place only close to the usually two-dimensional Fermi surface residing at a finite chemical potential. Because of this, the critical temperature is exponentially suppressed compared to the microscopic energy scales. On the other hand, pairing electrons around a dispersionless (flat) energy band leads to very strong superconductivity, with a mean-field critical temperature linearly proportional to the microscopic coupling constant. The prize to be paid is that flat bands can generally be generated only on surfaces and interfaces, where high-temperature superconductivity would show up. The flat-band character and the low dimensionality also mean that despite the high critical temperature such a superconducting state would be subject to strong fluctuations. Here we discuss the topological and non-topological flat bands discussed in different systems, and show that graphite is a good candidate for showing high-temperature flat-band interface superconductivity.Comment: Submitted as a chapter to the book on "Basic Physics of functionalized Graphite", 21 pages, 12 figure

Inverse spin-s portrait and representation of qudit states by single probability vectors

Using the tomographic probability representation of qudit states and the inverse spin-portrait method, we suggest a bijective map of the qudit density operator onto a single probability distribution. Within the framework of the approach proposed, any quantum spin-j state is associated with the (2j+1)(4j+1)-dimensional probability vector whose components are labeled by spin projections and points on the sphere. Such a vector has a clear physical meaning and can be relatively easily measured. Quantum states form a convex subset of the 2j(4j+3) simplex, with the boundary being illustrated for qubits (j=1/2) and qutrits (j=1). A relation to the (2j+1)^2- and (2j+1)(2j+2)-dimensional probability vectors is established in terms of spin-s portraits. We also address an auxiliary problem of the optimum reconstruction of qudit states, where the optimality implies a minimum relative error of the density matrix due to the errors in measured probabilities.Comment: 23 pages, 4 figures, PDF LaTeX, submitted to the Journal of Russian Laser Researc

MuSR method and tomographic probability representation of spin states

Muon spin rotation/relaxation/resonance (MuSR) technique for studying matter structures is considered by means of a recently introduced probability representation of quantum spin states. A relation between experimental MuSR histograms and muon spin tomograms is established. Time evolution of muonium, anomalous muonium, and a muonium-like system is studied in the tomographic representation. Entanglement phenomenon of a bipartite muon-electron system is investigated via tomographic analogues of Bell number and positive partial transpose (PPT) criterion. Reconstruction of the muon-electron spin state as well as the total spin tomography of composed system is discussed.Comment: 20 pages, 4 figures, LaTeX, submitted to Journal of Russian Laser Researc

Circular pattern matching with k mismatches

The k-mismatch problem consists in computing the Hamming distance between a pattern P of length m and every length-m substring of a text T of length n, if this distance is no more than k. In many real-world applications, any cyclic shift of P is a relevant pattern, and thus one is interested in computing the minimal distance of every length-m substring of T and any cyclic shift of P. This is the circular pattern m

Quantum Measurement Theory in Gravitational-Wave Detectors

The fast progress in improving the sensitivity of the gravitational-wave (GW) detectors, we all have witnessed in the recent years, has propelled the scientific community to the point, when quantum behaviour of such immense measurement devices as kilometer-long interferometers starts to matter. The time, when their sensitivity will be mainly limited by the quantum noise of light is round the corner, and finding the ways to reduce it will become a necessity. Therefore, the primary goal we pursued in this review was to familiarize a broad spectrum of readers with the theory of quantum measurements in the very form it finds application in the area of gravitational-wave detection. We focus on how quantum noise arises in gravitational-wave interferometers and what limitations it imposes on the achievable sensitivity. We start from the very basic concepts and gradually advance to the general linear quantum measurement theory and its application to the calculation of quantum noise in the contemporary and planned interferometric detectors of gravitational radiation of the first and second generation. Special attention is paid to the concept of Standard Quantum Limit and the methods of its surmounting.Comment: 147 pages, 46 figures, 1 table. Published in Living Reviews in Relativit