Effects of LESA in Three-Dimensional Supernova Simulations with Multi-Dimensional and Ray-by-Ray-plus Neutrino Transport

A set of eight self-consistent, time-dependent supernova (SN) simulations in three spatial dimensions (3D) for 9 solar-mass and 20 solar-mass progenitors is evaluated for the presence of dipolar asymmetries of the electron lepton-number emission as discovered by Tamborra et al. and termed lepton-number emission self-sustained asymmetry (LESA). The simulations were performed with the Aenus-Alcar neutrino/hydrodynamics code, which treats the energy- and velocity-dependent transport of neutrinos of all flavors by a two-moment scheme with algebraic M1 closure. For each of the progenitors, results with fully multi-dimensional (FMD) neutrino transport and with ray-by-ray-plus (RbR+) approximation are considered for two different grid resolutions. While the 9 solar-mass models develop explosions, the 20 solar-mass progenitor does not explode with the employed version of simplified neutrino opacities. In all 3D models we observe the growth of substantial dipole amplitudes of the lepton-number (electron neutrino minus antineutrino) flux with stable or slowly time-evolving direction and overall properties fully consistent with the LESA phenomenon. Models with RbR+ transport develop LESA dipoles somewhat faster and with temporarily higher amplitudes, but the FMD calculations exhibit cleaner hemispheric asymmetries with a far more dominant dipole. In contrast, the RbR+ results display much wider multipole spectra of the neutrino-emission anisotropies with significant power also in the quadrupole and higher-order modes. Our results disprove speculations that LESA is a numerical artifact of RbR+ transport. We also discuss LESA as consequence of a dipolar convection flow inside of the nascent neutron star and establish, tentatively, a connection to Chandrasekhar's linear theory of thermal instability in spherical shells.Comment: 20 pages, 9 figures; revised version accepted by ApJ; new Figs. 6,7, and new panels in Fig.8 added; Sects. 4,5,6 considerably extended in reply to referee question

Enabling semantic queries across federated bioinformatics databases

MOTIVATION: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. RESULTS: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: [email protected] or [email protected]

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers

Three-dimensional Models of Core-collapse Supernovae From Low-mass Progenitors With Implications for Crab

We present 3D full-sphere supernova simulations of non-rotating low-mass (~9 Msun) progenitors, covering the entire evolution from core collapse through bounce and shock revival, through shock breakout from the stellar surface, until fallback is completed several days later. We obtain low-energy explosions [~(0.5-1.0)x 10^{50} erg] of iron-core progenitors at the low-mass end of the core-collapse supernova (LMCCSN) domain and compare to a super-AGB (sAGB) progenitor with an oxygen-neon-magnesium core that collapses and explodes as electron-capture supernova (ECSN). The onset of the explosion in the LMCCSN models is modelled self-consistently using the Vertex-Prometheus code, whereas the ECSN explosion is modelled using parametric neutrino transport in the Prometheus-HOTB code, choosing different explosion energies in the range of previous self-consistent models. The sAGB and LMCCSN progenitors that share structural similarities have almost spherical explosions with little metal mixing into the hydrogen envelope. A LMCCSN with less 2nd dredge-up results in a highly asymmetric explosion. It shows efficient mixing and dramatic shock deceleration in the extended hydrogen envelope. Both properties allow fast nickel plumes to catch up with the shock, leading to extreme shock deformation and aspherical shock breakout. Fallback masses of <~5x10^{-3} Msun have no significant effects on the neutron star (NS) masses and kicks. The anisotropic fallback carries considerable angular momentum, however, and determines the spin of the newly-born NS. The LMCCSNe model with less 2nd dredge-up results in a hydrodynamic and neutrino-induced NS kick of >40 km/s and a NS spin period of ~30 ms, both not largely different from those of the Crab pulsar at birth.Comment: 47 pages, 27 figures, 6 tables; minor revisions, accepted by MNRA

Object Serialization and Deserialization Using XML

Interoperability of potentially heterogeneous databases has been an ongoing research issue for a number of years in the database community. With the trend towards globalization of data location and data access and the consequent requirement for the coexistence of new data stores with legacy systems, the cooperation and data interchange between data repositories has become increasingly important. The emergence of the eXtensible Markup Language (XML) as a database independent representation for data offers a suitable mechanism for transporting data between repositories. This paper describes a research activity within a group at CERN (called CMS) towards identifying and implementing database serialization and deserialization methods that can be used to replicate or migrate objects across the network between CERN and worldwide centres using XML to serialize the contents of multiple objects resident in object-oriented databases.Comment: 14 pages 7 figure

DIANA Scheduling Hierarchies for Optimizing Bulk Job Scheduling

The use of meta-schedulers for resource management in large-scale distributed systems often leads to a hierarchy of schedulers. In this paper, we discuss why existing meta-scheduling hierarchies are sometimes not sufficient for Grid systems due to their inability to re-organise jobs already scheduled locally. Such a job re-organisation is required to adapt to evolving loads which are common in heavily used Grid infrastructures. We propose a peer-to-peer scheduling model and evaluate it using case studies and mathematical modelling. We detail the DIANA (Data Intensive and Network Aware) scheduling algorithm and its queue management system for coping with the load distribution and for supporting bulk job scheduling. We demonstrate that such a system is beneficial for dynamic, distributed and self-organizing resource management and can assist in optimizing load or job distribution in complex Grid infrastructures.Comment: 8 pages, 9 figures. Presented at the 2nd IEEE Int Conference on eScience & Grid Computing. Amsterdam Netherlands, December 200

Higher-order non-symmetric counterterms in pure Yang-Mills theory

We analyze the restoration of the Slavnov-Taylor (ST) identities for pure massless Yang-Mills theory in the Landau gauge within the BPHZL renormalization scheme with IR regulator. We obtain the most general form of the action-like part of the symmetric regularized action, obeying the relevant ST identities and all other relevant symmetries of the model, to all orders in the loop expansion. We also give a cohomological characterization of the fulfillment of BPHZL IR power-counting criterion, guaranteeing the existence of the limit where the IR regulator goes to zero. The technique analyzed in this paper is needed in the study of the restoration of the ST identities for those models, like the MSSM, where massless particles are present and no invariant regularization scheme is known to preserve the full set of ST identities of the theory.Comment: Final version published in the journa

Anomalously large oxygen-ordering contribution to the thermal expansion of untwinned YBa2Cu3O6.95 single crystals: a glass-like transition near room temperature

We present high-resolution capacitance dilatometry studies from 5 - 500 K of untwinned YBa2Cu3Ox (Y123) single crystals for x ~ 6.95 and x = 7.0. Large contributions to the thermal expansivities due to O-ordering are found for x ~ 6.95, which disappear below a kinetic glass-like transition near room temperature. The kinetics at this glass transition is governed by an energy barrier of 0.98 +- 0.07 eV, in very good agreement with other O-ordering studies. Using thermodynamic arguments, we show that O-ordering in the Y123 system is particularly sensitive to uniaxial pressure (stress) along the chain axis and that the lack of well-ordered chains in Nd123 and La123 is most likely a consequence of a chemical-pressure effect.Comment: 4 pages, 3 figures, submitted to PR