PyCOOL - a Cosmological Object-Oriented Lattice code written in Python

There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet spot of speed, accuracy and user friendliness. This has been achieved by using the Python language with the PyCUDA interface to make a program that is easy to adapt to different scalar field models. In this paper we derive the symplectic dynamics that govern the evolution of the system and then present the implementation of the program in Python and PyCUDA. The functionality of the program is tested in a chaotic inflation preheating model, a single field oscillon case and in a supersymmetric curvaton model which leads to Q-ball production. We have also compared the performance of a consumer graphics card to a professional Tesla compute card in these simulations. We find that the program is not only accurate but also very fast. To further increase the usefulness of the program we have equipped it with numerous post-processing functions that provide useful information about the cosmological model. These include various spectra and statistics of the fields. The program can be additionally used to calculate the generated curvature perturbation. The program is publicly available under GNU General Public License at https://github.com/jtksai/PyCOOL . Some additional information can be found from http://www.physics.utu.fi/tiedostot/theory/particlecosmology/pycool/ .Comment: 23 pages, 12 figures; some typos correcte

Near-Infrared Properties of Metal-poor Globular Clusters in the Galactic Bulge Direction

Aims. J, H, and K' images obtained from the near-infrared imager CFHTIR on the Canada-France-Hawaii Telescope are used to derive the morphological parameters of the red giant branch (RGB) in the near-infrared color-magnitude diagrams for 12 metal-poor globular clusters in the Galactic bulge direction. Using the compiled data set of the RGB parameters for the observed 12 clusters, in addition to the previously studied 5 clusters, we discuss the properties of the RGB morphology for the clusters and compare them with the calibration relations for the metal-rich bulge clusters and the metal-poor halo clusters. Methods. The photometric RGB shape indices such as colors at fixed magnitudes of MK = MH = (-5.5, -5, -4, and -3), magnitudes at fixed colors of (J - K)o = (J - H)o = 0.7, and the RGB slope are measured from the fiducial normal points defined in the near- infrared color-magnitude diagrams for each cluster. The magnitudes of RGB bump and tip are also estimated from the differential and cumulative luminosity functions of the selected RGB stars. The derived RGB parameters have been used to examine the overall behaviors of the RGB morphology as a function of cluster metallicity. Results. The correlations between the near-infrared photometric RGB shape indices and the cluster metallicity for the programme clusters compare favorably with the previous observational calibration relations for metal-rich clusters in the Galactic bulge and the metal-poor halo clusters. The observed near-infrared magnitudes of the RGB bump and tip for the investigated clusters are also in accordance with the previous calibration relations for the Galactic bulge clusters.Comment: 12 pages, 9 figures, accepted for publication in Astronomy & Astrophysic

Alpha element abundances and gradients in the Milky Way bulge from FLAMES-GIRAFFE spectra of 650 K giants

We obtained FLAMES-GIRAFFE spectra (R=22,500) at the ESO Very Large Telescope for 650 bulge red giant branch (RGB) stars and performed spectral synthesis to measure Mg, Ca, Ti, and Si abundances. This sample is composed of 474 giant stars observed in 3 fields along the minor axis of the Galactic bulge and at latitudes b=-4, b=-6, b=-12. Another 176 stars belong to a field containing the globular cluster NGC 6553, located at b=-3 and 5 degrees away from the other three fields along the major axis. Our results confirm, with large number statistics, the chemical similarity between the Galactic bulge and thick disk, which are both enhanced in alpha elements when compared to the thin disk. In the same context, we analyze [alpha/Fe] vs. [Fe/H] trends across different bulge regions. The most metal rich stars, showing low [alpha/Fe] ratios at b=-4 disappear at higher Galactic latitudes in agreement with the observed metallicity gradient in the bulge. Metal-poor stars ([Fe/H]<-0.2) show a remarkable homogeneity at different bulge locations. We have obtained further constrains for the formation scenario of the Galactic bulge. A metal-poor component chemically indistinguishable from the thick disk hints for a fast and early formation for both the bulge and the thick disk. Such a component shows no variation, neither in abundances nor kinematics, among different bulge regions. A metal-rich component showing low [alpha/Fe] similar to those of the thin disk disappears at larger latitudes. This allows us to trace a component formed through fast early mergers (classical bulge) and a disk/bar component formed on a more extended timescale.Comment: 13 pages, 17 figures. Accepted for publication in Astronomy and Astrophysic

Instabilities and Mixing in SN 1993J

Rayleigh-Taylor (R-T) instabilities in the explosion of SN 1993J are investigated by means of two-dimensional hydrodynamical simulations. It is found that the extent of mixing is sensitive to the progenitor's core mass and the envelope mass. Because the helium core mass (3 - 4 \ms) is smaller than that of SN 1987A, R-T instabilities at the He/C+O interfaces develop to induce a large scale mixing in the helium core, while the instability is relatively weak at the H/He interface due to the small envelope mass. The predicted abundance distribution, in particular the amount of the \ni~ mixing, is compared with those required in the theoretical light curves and the late time optical spectra. This enables us to specify the progenitor of SN 1993J in some detail.Comment: 20 pages, LaTeX (AASTeX), to appear in Ap

Confined Population III Enrichment and the Prospects for Prompt Second-Generation Star Formation

It is widely recognized that nucleosynthetic output of the first, Population III supernovae was a catalyst defining the character of subsequent stellar generations. Most of the work on the earliest enrichment was carried out assuming that the first stars were extremely massive and that the associated supernovae were unusually energetic, enough to completely unbind the baryons in the host cosmic minihalo and disperse the synthesized metals into the intergalactic medium. Recent work, however, suggests that the first stars may in fact have been somewhat less massive, with a characteristic mass scale of a few tens of solar masses. We present a cosmological simulation following the transport of the metals synthesized in a Population III supernova assuming that it had an energy of 1e51 ergs, compatible with standard Type II supernovae. A young supernova remnant is inserted in the first star's relic HII region in the free expansion phase and is followed for 40 Myr employing adaptive mesh refinement and Lagrangian tracer particle techniques. The supernova remnant remains partially trapped within the minihalo and the thin snowplow shell develops pronounced instability and fingering. Roughly half of the ejecta turn around and fall back toward the center of the halo, with 1% of the ejecta reaching the center in 30 kyr and 10% in 10 Myr. The average metallicity of the combined returning ejecta and the pristine filaments feeding into the halo center from the cosmic web is 0.001 - 0.01 Z_sun, but the two remain unmixed until accreting onto the central hydrostatic core that is unresolved at the end of the simulation. We conclude that if Population III stars had less extreme masses, they promptly enriched the host minihalos with metals and triggered Population II star formation.Comment: 13 pages, 8 figure

Monoallelic maternal expression of STAT5A affects embryonic survival in cattle

<p>Abstract</p> <p>Background</p> <p>Reproductive disorders and infertility are surprisingly common in the human population as well as in other species. The decrease in fertility is a major cause of cow culling and economic loss in the dairy herd. The conception rate has been declining for the past 30–50 years. Conception rate is the product of fertilization and embryonic survival rates. In a previous study, we have identified associations of several single nucleotide polymorphisms (SNPs) in the signal transducer and activator 5A (<it>STAT5A</it>) with fertilization and survival rates in an <it>in </it>vitro experimental system. The objectives of this study are to fine map the <it>STAT5A </it>region in a search for causative mutations and to investigate the parent of origin expression of this gene.</p> <p>Results</p> <p>We have performed a total of 5,222 fertilizations and produced a total of 3,696 in vitro fertilized embryos using gametes from 440 cows and eight bulls. A total of 37 SNPs were developed in a 63.4-kb region of genomic sequence that includes <it>STAT5A</it>, <it>STAT3</it>, and upstream and downstream sequences of these genes. SNP153137 (G/C) in exon 8 of <it>STAT5A </it>was associated with a significant variability in embryonic survival and fertilization rate compared to all other examined SNPs. Expression analysis revealed that <it>STAT5A </it>is primarily monoallelically expressed in early embryonic stages but biallelically expressed in later fetal stages. Furthermore, the occurrence of monoallelic maternal expression of <it>STAT5A </it>was significantly higher in blastocysts, while paternal expression was more frequent in degenerative embryos.</p> <p>Conclusion</p> <p>Our results imply that <it>STAT5A </it>affects embryonic survival in a manner influenced by developmental stage and allele parent of origin.</p

Isotonic Glycerol and Sodium Hyaluronate Containing Artificial Tear Decreases Conjunctivochalasis after One and Three Months: A Self-Controlled, Unmasked Study.

Dry eye complaints are ranked as the most frequent symptoms of patients visiting ophthalmologists. Conjunctivochalasis is a common dry eye disorder, which can cause an unstable tear film and ocular discomfort. The severe conjunctivochalasis characterized by high LId-Parallel COnjunctival Folds (LIPCOF) degree usually requires surgical intervention, where a conservative therapy would be highly desirable. Here we examined the efficacy of a preservative-free, inorganic salt-free unit-dose artificial tear, called Conheal containing isotonic glycerol and 0.015% sodium hyaluronate in a prospective, unmasked, self-controlled study involving 20 patients. The regular use of the glycerol/hyaluronate artificial tear in three months caused a significant improvement in the recorded parameters. Conjunctivochalasis decreased from a mean LIPCOF degree of 2.9 ± 0.4 on both eyes to 1.4 ± 0.6 on the right (median decrease of -2 points, 95% CI from -2.0 to -1.0), and to 1.4 ± 0.7 on the left eye (median decrease of -1 points, 95% CI from -2.0 to -1.0) (p<0.001 for both sides). The tear film breakup time (TFBUT) lengthened from 4.8 ± 1.9 seconds on both eyes to 5.9 ± 2.3 seconds (mean increase of 1.1 seconds, 95% CI from 0.2 to 2.0) and 5.7 ± 1.8 seconds (mean increase of 0.9 seconds, 95% CI from 0.3 to 1.5) on the right and left eyes, respectively (p(right eyes) = 0.020, p(left eyes) = 0.004). The corneal lissamine staining (Oxford Scheme grade) was reduced from 1.3 ± 0.6 on the right and 1.4 ± 0.6 on the left eye significantly (p<0.001) to 0.3 ± 0.4 and 0.2 ± 0.4 on the right and the left eyes. The Ocular Surface Disease Index (OSDI) questionnaire score indicating the subjective complaints of the patients also decreased from a mean value of 36.2 ± 25.3 to 15.6 ± 16.7 (p<0.001). In this study, the artificial tear, Conheal decreased the grade of the conjunctivochalasis significantly after one month of regular use already, from the LIPCOF degree 3, considered as indication of conjunctival surgery, to a LIPCOF degree 2 or lower requiring a conservative therapy. Our results raise the possibility that vision-related quality of life can be significantly improved by conservative therapies even in severe conjunctivochalasis