Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array

The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an underlying suffix tree. The LCP array of a string of length $n$ can be represented as an array of length $n$ words, or, in the presence of the SA, as a bit vector of $2n$ bits plus asymptotically negligible support data structures. External memory construction algorithms for the LCP array have been proposed, but those proposed so far have a space requirement of $O(n)$ words (i.e. $O(n \log n)$ bits) in external memory. This space requirement is in some practical cases prohibitively expensive. We present an external memory algorithm for constructing the $2n$ bit version of the LCP array which uses $O(n \log \sigma)$ bits of additional space in external memory when given a (compressed) BWT with alphabet size $\sigma$ and a sampled inverse suffix array at sampling rate $O(\log n)$. This is often a significant space gain in practice where $\sigma$ is usually much smaller than $n$ or even constant. We also consider the case of computing succinct LCP arrays for circular strings

Wave Energy: a Pacific Perspective

This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Royal Society and can be found at: http://rsta.royalsocietypublishing.org/.This paper illustrates the status of wave energy development in Pacific Rim countries by characterizing the available resource and introducing the region‟s current and potential future leaders in wave energy converter development. It also describes the existing licensing and permitting process as well as potential environmental concerns. Capabilities of Pacific Ocean testing facilities are described in addition to the region‟s vision of the future of wave energy

Lattice Artefacts In The Non-Abelian Debye Screening Mass In One Loop Order

We compute the electric screening mass in lattice QCD with Wilson fermions at finite temperature and chemical potential to one-loop order, and show that lattice artefacts arising from a finite lattice spacing result in an enhancement of the screening mass as compared to the continuum. We discuss the magnitude of this enhancement as a function of the temperature and chemical potential for lattices with different number of lattice sites in the temporal direction that can be implemented in lattice simulations. Most of the enhancement is found to be due to the fermion loop contribution.Comment: 23 pages, 8 figures, LaTe

Lightweight Lempel-Ziv Parsing

We introduce a new approach to LZ77 factorization that uses O(n/d) words of working space and O(dn) time for any d >= 1 (for polylogarithmic alphabet sizes). We also describe carefully engineered implementations of alternative approaches to lightweight LZ77 factorization. Extensive experiments show that the new algorithm is superior in most cases, particularly at the lowest memory levels and for highly repetitive data. As a part of the algorithm, we describe new methods for computing matching statistics which may be of independent interest.Comment: 12 page

Gauged Yukawa Matrix Models and 2-Dimensional Lattice Theories

We argue that chiral symmetry breaking in three dimensional QCD can be identified with N\'eel order in 2-dimensional quantum antiferromagnets. When operators which drive the chiral transition are added to these theories, we postulate that the resulting quantum critical behavior is in the universality class of gauged Yukawa matrix models. As a consequence, the chiral transition is typically of first order, although for a limited class of parameters it can be second order with computable critical exponents.Comment: LaTeX, 11 page

On finding minimal absent words

<p>Abstract</p> <p>Background</p> <p>The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of interest, but the existing algorithms only provide generic absent words by trivially extending the shortest ones.</p> <p>Results</p> <p>We show how absent words relate to the repetitions and structure of the data, and define a new and larger class of absent words, called minimal absent words, that still captures the essential properties of the shortest absent words introduced in recent works. The words of this new class are minimal in the sense that if their leftmost or rightmost character is removed, then the resulting word is no longer an absent word. We describe an algorithm for generating minimal absent words that, in practice, runs in approximately linear time. An implementation of this algorithm is publicly available at <url>ftp://www.ieeta.pt/~ap/maws</url>.</p> <p>Conclusion</p> <p>Because the set of minimal absent words that we propose is much larger than the set of the shortest absent words, it is potentially more useful for applications that require a richer variety of absent words. Nevertheless, the number of minimal absent words is still manageable since it grows at most linearly with the string size, unlike generic absent words that grow exponentially. Both the algorithm and the concepts upon which it depends shed additional light on the structure of absent words and complement the existing studies on the topic.</p

Heavy Quark Potentials in Quenched QCD at High Temperature

Heavy quark potentials are investigated at high temperatures. The temperature range covered by the analysis extends from $T$ values just below the deconfinement temperature up to about $4 T_c$ in the deconfined phase. We simulated the pure gauge sector of QCD on lattices with temporal extents of 4, 6 and 8 with spatial volumes of $32^3$. On the smallest lattice a tree level improved action was employed while in the other two cases the standard Wilson action was used. Below $T_c$ we find a temperature dependent logarithmic term contributing to the confinement potential and observe a string tension which decreases with rising temperature but retains a finite value at the deconfinement transition. Above $T_c$ the potential is Debye-screened, however simple perturbative predictions do not apply.Comment: 20 pages, 9 figure