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

Thermoelectric properties of Zn_5Sb_4In_(2-δ)(δ=0.15)

The polymorphic intermetallic compound Zn_5Sb_4In_(2−δ) (δ = 0.15(3)) shows promising thermoelectric properties at low temperatures, approaching a figure of merit ZT of 0.3 at 300 K. However, thermopower and electrical resistivity changes discontinuously at around 220 K. Measurement of the specific heat locates the previously unknown temperature of the order-disorder phase transition at around 180 K. Investigation of the charge carrier concentration and mobility by Hall measurements and infrared reflection spectroscopy indicate a mixed conduction behavior and the activation of charge carriers at temperatures above 220 K. Zn_5Sb_4In_(2−δ) has a low thermal stability, and at temperatures above 470 K samples decompose into a mixture of Zn, InSb, and Zn_4Sb_3

Photoionization Broadening of the 1S-2S Transition in a Beam of Atomic Hydrogen

We consider the excitation dynamics of the two-photon \sts transition in a beam of atomic hydrogen by 243 nm laser radiation. Specifically, we study the impact of ionization damping on the transition line shape, caused by the possibility of ionization of the 2S level by the same laser field. Using a Monte-Carlo simulation, we calculate the line shape of the \sts transition for the experimental geometry used in the two latest absolute frequency measurements (M. Niering {\it et al.}, PRL 84, 5496 (2000) and M. Fischer {\it et al.}, PRL 92, 230802 (2004)). The calculated line shift and line width are in excellent agreement with the experimentally observed values. From this comparison we can verify the values of the dynamic Stark shift coefficient for the \sts transition for the first time on a level of 15%. We show that the ionization modifies the velocity distribution of the metastable atoms, the line shape of the \sts transition, and has an influence on the derivation of its absolute frequency.Comment: 10 pages, 5 figure

Simulations of beam-beam and beam-wire interactions in RHIC

The beam-beam interaction is one of the dominant sources of emittance growth and luminosity lifetime deterioration. A current carrying wire has been proposed to compensate long-range beam-beam effects in the LHC and strong localized long-range beam-beam effects are experimentally investigated in the RHIC collider. Tune shift, beam transfer function, and beam loss rate are measured in dedicated experiments. In this paper, we report on simulations to study the effect of beam-wire interactions based on diffusive apertures, beam loss rates, and beam transfer function using a parallelized weak-strong beam simulation code (bbsimc). The simulation results are compared with measurements performed in RHIC during 2007 and 2008.Comment: 15 pages, 36 figures, submitted to HB2008 PRST-AB Special Editio

Physical Controls on Carbonate Intraclasts: Modern Flat Pebbles From Great Salt Lake, Utah

In carbonate‐forming environments, authigenic minerals can cement surface sediments into centimeter‐sized intraclasts that are later reworked into “flat‐pebble” or “edgewise” conglomerates. Flat‐pebble conglomerates comprise only a small portion of facies in modern marine environments but are common in ancient strata, implying that seafloor cements were more widespread in the past. Flat‐pebble conglomerates nearly disappeared after the Ordovician radiation, yet it is unclear if this decline was due to changing seawater chemistry or if increased infaunalization and bioturbation simply worked to break down nascent clasts. We discovered a process analog that produces flat‐pebble conglomerates around the Great Salt Lake, Utah, USA, and studied these facies using field observations, wave models, satellite imagery, petrography, and microanalytic chemical data. Clasts were sourced from wave‐rippled grainstone that cemented in situ in offshore environments. Lake floor cements formed under aragonite saturation states that are lower than modern marine settings, suggesting that physical processes are at least as important as chemical ones. Results from our wave models showed that coarse sediments near the field site experience quiescent periods of up to 6 months between suspension events, allowing isopachous cements to form. Using a simple mathematical framework, we show that the main difference between Great Salt Lake and modern, low‐energy marine settings is that the latter has enough bioturbating organisms to break up clasts. Observations from Great Salt Lake demonstrate how geologic trends in flat‐pebble abundance could largely reflect changes in total infaunal biomass and ecology without requiring regional‐to‐global changes in seawater chemistry

Short wavelength spectrum and Hamiltonian stability of vortex rings

We compare dynamical and energetical stability criteria for vortex rings. It is argued that vortex rings will be intrinsically unstable against perturbations with short wavelengths below a critical wavelength, because the canonical vortex Hamiltonian is unbounded from below for these modes. To explicitly demonstrate this behaviour, we derive the oscillation spectrum of vortex rings in incompressible, inviscid fluids, within a geometrical cutoff procedure for the core. The spectrum develops an anomalous branch of negative group velocity, and approaches the zero of energy for wavelengths which are about six times the core diameter. We show the consequences of this dispersion relation for the thermodynamics of vortex rings in superfluid $^4$He at low temperatures.Comment: 7 pages, 4 figures, final version to appear in Phys. Rev.

Causal structure of acoustic spacetimes

The so-called ``analogue models of general relativity'' provide a number of specific physical systems, well outside the traditional realm of general relativity, that nevertheless are well-described by the differential geometry of curved spacetime. Specifically, the propagation of acoustic disturbances in moving fluids are described by ``effective metrics'' that carry with them notions of ``causal structure'' as determined by an exchange of sound signals. These acoustic causal structures serve as specific examples of what can be done in the presence of a Lorentzian metric without having recourse to the Einstein equations of general relativity. (After all, the underlying fluid mechanics is governed by the equations of traditional hydrodynamics, not by the Einstein equations.) In this article we take a careful look at what can be said about the causal structure of acoustic spacetimes, focusing on those containing sonic points or horizons, both with a view to seeing what is different from standard general relativity, and to seeing what the similarities might be.Comment: 51 pages, 39 figures (23 colour figures, colour used to convey physics information.) V2: Two references added, some additional discussion of maximal analytic extension, plus minor cosmetic change

Stability of bicontinuous cubic phases in ternary amphiphilic systems with spontaneous curvature

We study the phase behavior of ternary amphiphilic systems in the framework of a curvature model with non-vanishing spontaneous curvature. The amphiphilic monolayers can arrange in different ways to form micellar, hexagonal, lamellar and various bicontinuous cubic phases. For the latter case we consider both single structures (one monolayer) and double structures (two monolayers). Their interfaces are modeled by the triply periodic surfaces of constant mean curvature of the families G, D, P, C(P), I-WP and F-RD. The stability of the different bicontinuous cubic phases can be explained by the way in which their universal geometrical properties conspire with the concentration constraints. For vanishing saddle-splay modulus $\bar \kappa$, almost every phase considered has some region of stability in the Gibbs triangle. Although bicontinuous cubic phases are suppressed by sufficiently negative values of the saddle-splay modulus $\bar \kappa$, we find that they can exist for considerably lower values than obtained previously. The most stable bicontinuous cubic phases with decreasing $\bar \kappa < 0$ are the single and double gyroid structures since they combine favorable topological properties with extreme volume fractions.Comment: Revtex, 23 pages with 10 Postscript files included, to appear in J. Chem. Phys. 112 (6) (February 2000

Immunohistological studies on neoplasms of female and male Onchocerca volvulus: filarial origin and absence of Wolbachia from tumor cells

Up to 5% of untreated female Onchocerca volvulus filariae develop potentially fatal pleomorphic neoplasms, whose incidence is increased following ivermectin treatment. We studied the occurrence of 8 filarial proteins and of Wolbachia endobacteria in the tumor cells. Onchocercomas from patients, untreated and treated with antibiotics and anthelminthics, were examined by immunohistology. Neoplasms were diagnosed in 112 of 3587 female and in 2 of 1570 male O. volvulus. The following proteins and other compounds of O. volvulus were expressed in the cells of the neoplasms: glutathione S-transferase 1, lysosomal aspartic protease, cAMP-dependent protein kinase, alpha-enolase, aspartate aminotransferase, ankyrin E1, tropomyosin, heat shock protein 60, transforming growth factor-beta, and prostaglandin E2. These findings prove the filarial origin of the neoplasms and confirm the pleomorphism of the tumor cells. Signs indicating malignancy of the neoplasms are described. Wolbachia were observed in the hypodermis, oocytes, and embryos of tumor-harbouring filariae using antibodies against Wolbachia surface protein, Wolbachia HtrA-type serine protease, and Wolbachia aspartate aminotransferase. In contrast, Wolbachia were not found in the cells of the neoplasms. Further, neoplasm-containing worms were not observed after more than 10 months after the start of sufficient treatment with doxycycline or doxycycline plus ivermectin

Hamiltonian statistical mechanics

A framework for statistical-mechanical analysis of quantum Hamiltonians is introduced. The approach is based upon a gradient flow equation in the space of Hamiltonians such that the eigenvectors of the initial Hamiltonian evolve toward those of the reference Hamiltonian. The nonlinear double-bracket equation governing the flow is such that the eigenvalues of the initial Hamiltonian remain unperturbed. The space of Hamiltonians is foliated by compact invariant subspaces, which permits the construction of statistical distributions over the Hamiltonians. In two dimensions, an explicit dynamical model is introduced, wherein the density function on the space of Hamiltonians approaches an equilibrium state characterised by the canonical ensemble. This is used to compute quenched and annealed averages of quantum observables.Comment: 8 pages, 2 figures, references adde