Linear-time Computation of Minimal Absent Words Using Suffix Array

An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their computation provides a fast alternative for measuring approximation in sequence comparison. There exists an O(n)-time and O(n)-space algorithm for computing all minimal absent words on a fixed-sized alphabet based on the construction of suffix automata (Crochemore et al., 1998). No implementation of this algorithm is publicly available. There also exists an O(n^2)-time and O(n)-space algorithm for the same problem based on the construction of suffix arrays (Pinho et al., 2009). An implementation of this algorithm was also provided by the authors and is currently the fastest available. In this article, we bridge this unpleasant gap by presenting an O(n)-time and O(n)-space algorithm for computing all minimal absent words based on the construction of suffix arrays. Experimental results using real and synthetic data show that the respective implementation outperforms the one by Pinho et al

Fano collective resonance as complex mode in a two dimensional planar metasurface of plasmonic nanoparticles

Fano resonances are features in transmissivity/reflectivity/absorption that owe their origin to the interaction between a bright resonance and a dark (i.e., sub-radiant) narrower resonance, and may emerge in the optical properties of planar two-dimensional (2D) periodic arrays (metasurfaces) of plasmonic nanoparticles. In this Letter, we provide a thorough assessment of their nature for the general case of normal and oblique plane wave incidence, highlighting when a Fano resonance is affected by the mutual coupling in an array and its capability to support free modal solutions. We analyze the representative case of a metasurface of plasmonic nanoshells at ultraviolet frequencies and compute its absorption under TE- and TM-polarized, oblique plane-wave incidence. In particular, we find that plasmonic metasurfaces display two distinct types of resonances observable as absorption peaks: one is related to the Mie, dipolar resonance of each nanoparticle; the other is due to the forced excitation of free modes with small attenuation constant, usually found at oblique incidence. The latter is thus an array-induced collective Fano resonance. This realization opens up to manifold flexible designs at optical frequencies mixing individual and collective resonances. We explain the physical origin of such Fano resonances using the modal analysis, which allows to calculate the free modes with complex wavenumber supported by the metasurface. We define equivalent array dipolar polarizabilities that are directly related to the absorption physics at oblique incidence and show a direct dependence between array modal phase and attenuation constant and Fano resonances. We thus provide a more complete picture of Fano resonances that may lead to the design of filters, energy-harvesting devices, photodetectors, and sensors at ultraviolet frequencies.Comment: 6 pages, 5 figure

Sorting suffixes of a text via its Lyndon Factorization

The process of sorting the suffixes of a text plays a fundamental role in Text Algorithms. They are used for instance in the constructions of the Burrows-Wheeler transform and the suffix array, widely used in several fields of Computer Science. For this reason, several recent researches have been devoted to finding new strategies to obtain effective methods for such a sorting. In this paper we introduce a new methodology in which an important role is played by the Lyndon factorization, so that the local suffixes inside factors detected by this factorization keep their mutual order when extended to the suffixes of the whole word. This property suggests a versatile technique that easily can be adapted to different implementative scenarios.Comment: Submitted to the Prague Stringology Conference 2013 (PSC 2013

Representations of world coordinates in FITS

The initial descriptions of the FITS format provided a simplified method for describing the physical coordinate values of the image pixels, but deliberately did not specify any of the detailed conventions required to convey the complexities of actual image coordinates. Building on conventions in wide use within astronomy, this paper proposes general extensions to the original methods for describing the world coordinates of FITS data. In subsequent papers, we apply these general conventions to the methods by which spherical coordinates may be projected onto a two-dimensional plane and to frequency/wavelength/velocity coordinates.Comment: 15 Pages, 1 figure, LaTex with Astronomy & Astrophysics macro package, submitted to A&A, related papers at http://www.aoc.nrao.edu/~egreise