BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization

New High-Performance Computing architectures have been recently developed for commercial central processing unit (CPU). Yet, that has not improved the execution time of widely used bioinformatics applications, like BLAST+. This is due to a lack of optimization between the bases of the existing algorithms and the internals of the hardware that allows taking full advantage of the available CPU cores. To optimize the new architectures, algorithms must be revised and redesigned; usually rewritten from scratch. BLVector adapts the high-level concepts of BLAST+ to the x86 architectures with AVX-512, to harness their capabilities. A deep comprehensive study has been carried out to optimize the approach, with a significant reduction in time execution. BLVector reduces the execution time of BLAST+ when aligning up to mid-size protein sequences (∼750 amino acids). The gain in real scenario cases is 3.2-fold. When applied to longer proteins, BLVector consumes more time than BLAST+, but retrieves a much larger set of results. BLVector and BLAST+ are fine-tuned heuristics. Therefore, the relevant results returned by both are the same, although they behave differently specially when performing alignments with low scores. Hence, they can be considered complementary bioinformatics tools.Fil: Gálvez Rojas, Sergio. Universidad de Malaga. Escuela Técnica Superior de Ingeniería Informática. Departamento de Lenguajes y Ciencias de la Computacion.; EspañaFil: Agostini, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Caselli, Javier. Universidad de Malaga. Escuela Técnica Superior de Ingeniería Informática. Departamento de Lenguajes y Ciencias de la Computacion.; EspañaFil: Hernandez, Agustina Pilar. Consejo Superior de Investigaciones Científicas; EspañaFil: Dorado, Gabriel. Universidad de Córdoba; Españ

On data reduction methods for volcanic tremor characterization: the 2012 eruption of Copahue volcano, Southern Andes

Improving the ability to detect and characterize long-duration volcanic tremor is crucial to understand the longterm dynamics and unrest of volcanic systems. We have applied data reduction methods (permutation entropy and polarization degree, among others) to characterize the seismic wave field near Copahue volcano (Southern Andes) between June 2012 and January 2013, when phreatomagmatic episodes occurred. During the selected period, a total of 52 long-duration events with energy above the background occurred. Among them, 32 were classified as volcanic tremors and the remaining as noise bursts. Characterizing each event by averaging its reduced parameters, allowed us to study the range of variability of the different events types. We found that, compared to noise burst, tremors have lower permutation entropies and higher dominant polarization degrees. This characterization is a suitable tool for detecting long-duration volcanic tremors in the ambient seismic wave field, even if the SNR is low.Project BRAVOSEIS of the Spanish Ministry of Science CTM2016.77315National University of Rio Negro PI40-A-54

Herschel HIFI observations of O2_2 toward Orion: special conditions for shock enhanced emission

We report observations of molecular oxygen (O$_2$) rotational transitions at 487 GHz, 774 GHz, and 1121 GHz toward Orion Peak A. The O2 lines at 487 GHz and 774 GHz are detected at velocities of 10-12 km/s with line widths 3 km/s; however, the transition at 1121 GHz is not detected. The observed line characteristics, combined with the results of earlier observations, suggest that the region responsible for the O$_2$ emission is 9" (6e16 cm) in size, and is located close to the H2 Peak 1position (where vibrationally-excited H$_2$ emission peaks), and not at Peak A, 23" away. The peak O2 column density is 1.1e18/cm2. The line velocity is close to that of 621 GHz water maser emission found in this portion of the Orion Molecular Cloud, and having a shock with velocity vector lying nearly in the plane of the sky is consistent with producing maximum maser gain along the line-of-sight. The enhanced O$_2$ abundance compared to that generally found in dense interstellar clouds can be explained by passage of a low-velocity C-shock through a clump with preshock density 2e4/cm3, if a reasonable flux of UV radiation is present. The postshock O$_2$ can explain the emission from the source if its line of sight dimension is ~10 times larger than its size on the plane of the sky. The special geometry and conditions required may explain why O$_2$ emission has not been detected in the cores of other massive star-forming molecular clouds.Comment: 28 pages, 13 figure

Long-duration seismicity and their relation to Copahue volcano unrest

peer reviewedUnderstanding seismic tremor wavefields can shed light on the complex functioning of a volcanic system and, thus, improve volcano monitoring systems. Usually, several seismic stations are required to detect, characterize, and locate volcanic tremors, which can be difficult in remote areas or low-income countries. In these cases, alternative techniques have to be used. Here, we apply a data-reduction approach based on the analysis of three-component seismic data from two co-located stations operating in different times to detect and analyze long-duration tremors. We characterize the spectral content and the polarization of 355 long-duration tremors recorded by a seismic sensor located 9.5 km SE from the active vent of Copahue volcano in the period 2012–2016 and 2018–2019. We classified them as narrow- (NB) and broad-band (BB) tremors according to their spectral content. Several parameters describe the characteristic peaks composing each NB episode: polarization degree, rectilinearity, horizontal azimuth, vertical incidence. Moreover, we propose two coefficients CP and CL for describing to what extent the wavefield is polarized. For BB episodes, we extend these attributes and express them as a function of frequency. We compare the occurrence of NB and BB episodes with the volcanic activity (including the level of the crater lake, deformation, temperature, and explosive activity) to get insights into their mechanisms. This comparison suggests that the wavefield of NB tremors becomes more linearly polarized during eruptive episodes, but does not provide any specific relationship between the tremor frequency and volcanic activity. On the other hand, BB tremors show a seasonal behavior that would be related to the activity of the shallow hydrothermal system. Graphical Abstract: [Figure not available: see fulltext.

Caso de estudio: diseño e implementación del soporte tecnológico de un sistema de indicadores de turismo sostenible

Cualquier destino turístico que afronte de manera rigurosa un proceso de reconversión a un destino turístico inteligente debe dotarse de herramientas, preferiblemente automatizadas, que le permitan medir la eficacia de dicho proceso. En este trabajo se presenta una plataforma tecnológica desarrollada para el Sistema de indicadores de desarrollo turístico sostenible de Andalucía, y se analiza la viabilidad de su utilización para un Sistema de indicadores de destinos turísticos inteligentes.Any tourist destination that faces a rigorous process to became a smart destination must develop a set of tools, preferably automated, that allow to measure the efficiency this process. This paper presents a technological platform developed for the Indicators System for Sustainable Tourism Development of Andalucia, and analyzes the feasibility of its use for a system of indicators to evaluate smart tourist destinations.La presente comunicación se enmarca en el Proyecto de Investigación «Nuevos enfoques para la planificación y gestión del territorio turístico: conceptualización, análisis de experiencias y problemas. Definición de modelos operativos para destinos turísticos inteligentes» (Proyecto CSO2014-59193-R) del Programa Estatal de I+D+I del Ministerio de Economía y Competitividad

Gravity or Turbulence? The velocity dispersion-size relation

We discuss the nature of the velocity dispersion vs. size relation for molecular clouds. In particular, we add to previous observational results showing that the velocity dispersions in molecular clouds and cores are not purely functions of spatial scale but involve surface gas densities as well. We emphasize that hydrodynamic turbulence is required to produce the first condensations in the progenitor medium. However, as the cloud is forming, it also becomes bound, and gravitational accelerations dominate the motions. Energy conservation in this case implies $|E_g| \sim E_k$, in agreement with observational data, and providing an interpretation for two recent observational results: the scatter in the $\delta v-R$ plane, and the dependence of the velocity dispersion on the surface density ${\delta v^2/ R} \propto \Sigma$. We argue that the observational data are consistent with molecular clouds in a state of hierarchical gravitational collapse, i.e., developing local centers of collapse throughout the whole cloud while the cloud itself is collapsing, and making equilibrium unnecessary at all stages prior to the formation of actual stars. Finally, we discuss how this mechanism need not be in conflict with the observed star formation rate.Comment: Accepted by MNRAS. 7 pages, 3 figure

High- and Low-Mass Star Forming Regions from Hierarchical Gravitational Fragmentation. High local Star Formation Rates with Low Global Efficiencies

We investigate the properties of "star forming regions" in a previously published numerical simulation of molecular cloud formation out of compressive motions in the warm neutral atomic interstellar medium, neglecting magnetic fields and stellar feedback. In this simulation, the velocity dispersions at all scales are caused primarily by infall motions rather than by random turbulence. We study the properties (density, total gas+stars mass, stellar mass, velocity dispersion, and star formation rate) of the cloud hosting the first local, isolated "star formation" event in the simulation and compare them with those of the cloud formed by a later central, global collapse event. We suggest that the small-scale, isolated collapse may be representative of low- to intermediate-mass star-forming regions, while the large-scale, massive one may be representative of massive star forming regions. We also find that the statistical distributions of physical properties of the dense cores in the region of massive collapse compare very well with those from a recent survey of the massive star forming region in the Cygnus X molecular cloud. The star formation efficiency per free-fall time (SFE_ff) of the high-mass SF clump is low, ~0.04. This occurs because the clump is accreting mass at a high rate, not because its specific SFR (SSFR) is low. This implies that a low value of the SFE_ff does not necessarily imply a low SSFR, but may rather indicate a large gas accretion rate. We suggest that a globally low SSFR at the GMC level can be attained even if local star forming sites have much larger values of the SSFR if star formation is a spatially intermittent process, so that most of the mass in a GMC is not participating of the SF process at any given time.Comment: Accepted by ApJ. Revised version, according to exchanges with referee. Original results unchanged. Extensive new discussion on the low global efficiency vs. high local efficiency of star formation. Abstract abridge

Molecular Cloud Evolution III. Accretion vs. stellar feedback

We numerically investigate the effect of feedback from the ionizing radiation heating from massive stars on the evolution of giant molecular clouds (GMCs) and their star formation efficiency (SFE). We find that the star-forming regions within the GMCs are invariably formed by gravitational contraction. After an initial period of contraction, the collapsing clouds begin forming stars, whose feedback evaporates part of the clouds' mass, opposing the continuing accretion from the infalling gas. The competition of accretion against dense gas consumption by star formation (SF) and evaporation by the feedback, regulates the clouds' mass and energy balance, as well as their SFE. We find that, in the presence of feedback, the clouds attain levels of the SFE that are consistent at all times with observational determinations for regions of comparable SF rates (SFRs). However, we observe that the dense gas mass is larger in general in the presence of feedback, while the total (dense gas + stars) is nearly insensitive to the presence of feedback, suggesting that the total mass is determined by the accretion, while the feedback inhibits mainly the conversion of dense gas to stars. The factor by which the SFE is reduced upon the inclusion of feedback is a decreasing function of the cloud's mass, for clouds of size ~ 10 pc. This naturally explains the larger observed SFEs of massive-star forming regions. We also find that the clouds may attain a pseudo-virialized state, with a value of the virial mass very similar to the actual cloud mass. However, this state differs from true virialization in that the clouds are the center of a large-scale collapse, continuously accreting mass, rather than being equilibrium entities.Comment: Submitted to ApJ (abstract abridged

Gas phase Elemental abundances in Molecular cloudS (GEMS) VIII. Unlocking the CS chemistry: the CH + S→\rightarrow CS + H and C2_2 + S→\rightarrow CS + C reactions

We revise the rates of reactions CH + S -> CS + H and C_2 + S -> CS + C, important CS formation routes in dark and diffuse warm gas. We performed ab initio calculations to characterize the main features of all the electronic states correlating to the open shell reactants. For CH+S we have calculated the full potential energy surfaces for the lowest doublet states and the reaction rate constant with a quasi-classical method. For C_2+S, the reaction can only take place through the three lower triplet states, which all present deep insertion wells. A detailed study of the long-range interactions for these triplet states allowed to apply a statistic adiabatic method to determine the rate constants. This study of the CH + S reaction shows that its rate is nearly independent on the temperature in a range of 10-500 K with an almost constant value of 5.5 10^{-11} cm^3/s at temperatures above 100~K. This is a factor \sim 2-3 lower than the value obtained with the capture model. The rate of the reaction C_2 + S depends on the temperature taking values close to 2.0 10^{-10} cm^3/s at low temperatures and increasing to 5. 10^{-10} cm^3/s for temperatures higher than 200~K. Our modeling provides a rate higher than the one currently used by factor of \sim 2. These reactions were selected for involving open-shell species with many degenerate electronic states, and the results obtained in the present detailed calculations provide values which differ a factor of \sim 2-3 from the simpler classical capture method. We have updated the sulphur network with these new rates and compare our results in the prototypical case of TMC1 (CP). We find a reasonable agreement between model predictions and observations with a sulphur depletion factor of 20 relative to the sulphur cosmic abundance, but it is not possible to fit all sulphur-bearing molecules better than a factor of 10 at the same chemical time.Comment: 13 pages, 10 figure

Water in star-forming regions with Herschel (WISH): VI. Constraints on UV and X-ray irradiation from a survey of hydrides in low- to high-mass young stellar objects

[Context] Hydrides are simple compounds containing one or a few hydrogen atoms bonded to a heavier atom. They are fundamental precursor molecules in cosmic chemistry and many hydride ions have become observable in high quality for the first time thanks to the Herschel Space Observatory. Ionized hydrides such as CH+ and OH+ (and also HCO+), which affect the chemistry of molecules such as water, provide complementary information on irradiation by far-UV (FUV) or X-rays and gas temperature.[Aims] We explore hydrides of the most abundant heavier elements in an observational survey covering young stellar objects (YSOs) with different mass and evolutionary state. The focus is on hydrides associated with the dense protostellar envelope and outflows, contrary to previous work that focused on hydrides in diffuse foreground clouds.[Methods] Twelve YSOs were observed with HIFI on Herschel in six spectral settings providing fully velocity-resolved line profiles as part of the Water in star-forming regions with Herschel (WISH) program. The YSOs include objects of low (Class 0 and I), intermediate, and high mass, with luminosities ranging from 4 L⊙ to 2 × 105 L⊙.[Results] The targeted lines of CH+, OH+, H2O+, C+, and CH are detected mostly in blue-shifted absorption. H3O+ and SH+ are detected in emission and only toward some high-mass objects. The observed line parameters and correlations suggest two different origins related to gas entrained by the outflows and to the circumstellar envelope. The derived column densities correlate with bolometric luminosity and envelope mass for all molecules, best for CH, CH+, and HCO+. The column density ratios of CH+/OH+ are estimated from chemical slab models, assuming that the H2 density is given by the specific density model of each object at the beam radius. For the low-mass YSOs the observed ratio can be reproduced for an FUV flux of 2–400 times the interstellar radiation field (ISRF) at the location of the molecules. In two high-mass objects, the UV flux is 20–200 times the ISRF derived from absorption lines, and 300–600 ISRF using emission lines. Upper limits for the X-ray luminosity can be derived from H3O+ observations for some low-mass objects.[Conclusions] If the FUV flux required for low-mass objects originates at the central protostar, a substantial FUV luminosity, up to 1.5 L⊙, is required. There is no molecular evidence for X-ray induced chemistry in the low-mass objects on the observed scales of a few 1000 AU. For high-mass regions, the FUV flux required to produce the observed molecular ratios is smaller than the unattenuated flux expected from the central object(s) at the Herschel beam radius. This is consistent with an FUV flux reduced by circumstellar extinction or by bloating of the protostar.The work on star formation at ETH Zurich was partially funded by the Swiss National Science Foundation (grant No. 200020-113556). Astrochemistry in Leiden is supported by the Netherlands Research School for Astronomy (NOVA), by a Royal Netherlands Academy of Arts and Sciences (KNAW) professor prize, and by the European Union A-ERC grant 291141 CHEMPLAN. Support for this work was also provided by NASA (Herschel OT funding) through an award issued by JPL/ Caltech