An atom-photon pair laser

We study the quantum dynamics of an ultracold atomic gas in a deep optical lattice within an optical high-$Q$ resonator. The atoms are coherently illuminated with the cavity resonance tuned to a blue vibrational sideband, so that photon scattering to the resonator mode is accompanied by vibrational cooling of the atoms. This system exhibits a threshold above which pairwise stimulated generation of a cavity photon and an atom in the lowest vibrational band dominates spontaneous scattering and we find a combination of optical lasing with a buildup of a macroscopic population in the lowest lattice band. Including output coupling of ground-state atoms and replenishing of hot atoms into the cavity volume leads to a coherent, quantum correlated atom-photon pair source very analogous to twin light beam generation in a nondegenerate optical parametric oscillator.Comment: 10 pages, 4 figure

Performance Improvements for the ATLAS Detector Simulation Framework

Many physics and performance studies carried out with the ATLAS detector at the Long Hadron Collider (LHC) require very large event samples. A detailed simulation for the detector, however, requires a great amount of CPU resources. In addition to detailed simulation, fast techniques and new setups are developed and extensively used to supply large event samples. In addition to the development of new techniques and setups, it is still possible to find some performance improvements in the existing simulation technologies. This work shows some possible ways to increase the performance for different full and fast ATLAS detector simulation setups, using new libraries and code improvements in the ATLAS detector simulation framework. Besides of the improvements, measured time consumptions of different setups are shown and possible further improvements are the other main focuses of this project

The ATLAS Track Extrapolation Package

The extrapolation of track parameters and their associated covariances to destination surfaces of different types is a very frequent process in the event reconstruction of high energy physics experiments. This is amongst other reasons due to the fact that most track and vertex fitting techniques are based on the first and second momentum of the underlying probability density distribution. The correct stochastic or deterministic treatment of interactions with the traversed detector material is hereby crucial for high quality track reconstruction throughout the entire momentum range of final state particles that are produced in high energy physics collision experiments. This document presents the main concepts, the algorithms and the implementation of the newly developed, powerful ATLAS track extrapolation engine. It also emphasises on validation procedures, timing measurements and the integration into the ATLAS offline reconstruction software

Molecular Characterization of Two Endothelin Pathways in East African Cichlid Fishes

The adaptive radiations of cichlid fishes in East Africa have been associated with the acquisition of evolutionary novelties as well as the ecological opportunities existing in the East African Great lakes. Two remarkable evolutionary innovations are the pharyngeal jaw apparatus, found in all cichlid species, and the anal fin egg-spots of mouthbrooding cichlids. Based on their conserved functions during the development of both the jaw apparatus and pigmentation, the endothelin ligands and receptors form a putative link between these naturally and sexually selected traits. Here we study the evolutionary history of four members of two endothelin pathways (Edn1/EdnrAa and Edn3b/EdnrB1a) to elucidate their possible roles during the evolution and development of key innovations in East African cichlids species. The analyses performed on partial sequences (ca. 6,000bp per taxon) show that all four endothelin family members evolved under purifying selection, although both ligands are characterized by an accelerated rate of protein evolution in comparison to the receptors. In accordance with earlier findings, we show that the mature protein sequence of Edn1 and Edn3 are highly conserved, also in cichlids, whereas the preproendothelin parts are variable indicating relaxed selective constraints. In the receptors, nonsynonymous substitutions were mainly found in the ligand-binding domains suggesting functional divergence. Gene expression assays with Real-Time PCR indeed reveal that the two studied endothelin pathways are expressed in the cichlid pharyngeal jaw and in the haplochromine egg-spot (among other pigment-cell containing tissues), suggesting their involvement during morphogenesis of naturally and sexually selected traits in cichlid

TANDEM: integrating automated allele binning into genetics and genomics workflows

Summary: Computer programs for the statistical analysis of microsatellite data use allele length variation to infer, e.g. population genetic parameters, to detect quantitative trait loci or selective sweeps. However, observed allele lengths are usually inaccurate and may deviate from the expected periodicity of repeats. The common practice of rounding to the nearest whole number frequently results in miscalls and underestimations of allelic richness. Manual sorting of allele lengths into discrete classes, a process called binning, is tedious and error-prone. Here, we present a new program for the automated binning of microsatellite allele lengths to overcome these problems and to facilitate high-throughput allele binning. Availability: www.evolution.unibas.ch/salzburger/software.htm Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

In ovo omnia: diversification by duplication in fish and other vertebrates

Gene and genome duplications are considered to be the main evolutionary mechanisms contributing to the unrivalled biodiversity of bony fish. New studies of vitellogenin yolk proteins, including a report in BMC Evolutionary Biology, reveal that the genes underlying key evolutionary innovations and adaptations have undergone complex patterns of duplication and functional evolution

Tracing evolutionary decoupling of oral and pharyngeal jaws in cichlid fishes

Evolutionary innovations can facilitate diversification if the novel trait enables a lineage to exploit new niches or by expanding character space. The elaborate pharyngeal jaw apparatus of cichlid fishes is often referred to as an evolutionary "key innovation" that has promoted the spectacular adaptive radiations in these fishes. This goes back to the idea that the structural and functional independence of the oral and pharyngeal jaws for food capturing and food processing, respectively, permitted each jaw type to follow independent evolutionary trajectories. This "evolutionary decoupling" is thought to have facilitated novel trait combinations and, hence, ecological specialization, ultimately allowing more species to coexist in sympatry. Here, we test the hypotheses of evolutionary decoupling of the oral and pharyngeal jaws in the massive adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on phylogenetic comparative analyses of oral jaw morphology and lower pharyngeal jaw shape across most of the ∼240 cichlid species occurring in that lake, we show that the two jaws evolved coupled along the main axes of morphological variation, yet most other components of these trait complexes evolved largely independently over the course of the radiation. Further, we find limited correlations between the two jaws in both overall divergence and evolutionary rates. Moreover, we show that the two jaws were evolutionary decoupled at a late stage of the radiation, suggesting that decoupling contributed to micro-niche partitioning and the associated rapidly increasing trophic diversity during this phase

The non-gradual nature of adaptive radiation

Adaptive radiation is a major source of biodiversity. Still, many aspects of this evolutionary process remain poorly understood. Our recent integrative examination of the cichlid adaptive radiation in African Lake Tanganyika provides new insights into the process of explosive diversification. The in-depth phylogenetic comparative analysis of nearly all species occurring in that lake permitted us to trace patterns of eco-morphological evolution throughout the phylogenetic history of the radiation and revealed that it occurred in a non-gradual manner, in the form of time-shifted bursts of accelerated evolution. The temporal pattern of divergence along different axes of morphological evolution provides empirical support for a scenario that potentially unifies two popular models of adaptive radiation, the "early burst model" and the "stages model"

The ATLAS Tracking Geometry Description

Track reconstruction requires a detector geometry description for the usage in track extrapolation processes and material effects integration during track finding and track fitting. Since, in general, the more realistic detector description used in full detector simulation causes an unacceptable increase of CPU time consumption when being used in track reconstruction, the reconstruction geometry is realised as a simplified description of the actual detector layout. This documents presents the data classes of the newly developed ATLAS reconstruction geometry and describes its building process for the ATLAS CSC detector layouts. Additionally a comparison of the material budget described by the reconstruction geometry with one used in full detector simulation will be presented for the Inner Detector and the Calorimeter