{BiQ} Analyzer {HiMod}: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives

Recent data suggest important biological roles for oxidative modifications of methylated cytosines, specifically hydroxymethylation, formylation and carboxylation. Several assays are now available for profiling these DNA modifications genome-wide as well as in targeted, locus-specific settings. Here we present BiQ Analyzer HiMod, a user-friendly software tool for sequence alignment, quality control and initial analysis of locus-specific DNA modification data. The software supports four different assay types, and it leads the user from raw sequence reads to DNA modification statistics and publication-quality plots. BiQ Analyzer HiMod combines well-established graphical user interface of its predecessor tool, BiQ Analyzer HT, with new and extended analysis modes. BiQ Analyzer HiMod also includes updates of the analysis workspace, an intuitive interface, a custom vector graphics engine and support of additional input and output data formats. The tool is freely available as a stand-alone installation package from http://biq-analyzer-himod.bioinf.mpi-inf.mpg.de/

The far-infrared/submillimeter properties of galaxies located behind the Bullet cluster

The Herschel Lensing Survey (HLS) takes advantage of gravitational lensing by massive galaxy clusters to sample a population of high-redshift galaxies which are too faint to be detected above the confusion limit of current far-infrared/submillimeter telescopes. Measurements from 100–500 μm bracket the peaks of the far-infrared spectral energy distributions of these galaxies, characterizing their infrared luminosities and star formation rates. We introduce initial results from our science demonstration phase observations, directed toward the Bullet cluster (1E0657-56). By combining our observations with LABOCA 870 μm and AzTEC 1.1 mm data we fully constrain the spectral energy distributions of 19 MIPS 24 μm-selected galaxies which are located behind the cluster. We find that their colors are best fit using templates based on local galaxies with systematically lower infrared luminosities. This suggests that our sources are not like local ultra-luminous infrared galaxies in which vigorous star formation is contained in a compact highly dust-obscured region. Instead, they appear to be scaled up versions of lower luminosity local galaxies with star formation occurring on larger physical scales

The Herschel Lensing Survey (HLS): Overview

The Herschel Lensing Survey (HLS) will conduct deep PACS and SPIRE imaging of ∼40 massive clusters of galaxies. The strong gravitational lensing power of these clusters will enable us to penetrate through the confusion noise, which sets the ultimate limit on our ability to probe the Universe with Herschel. Here we present an overview of our survey and a summary of the major results from our science demonstration phase (SDP) observations of the Bullet cluster (z = 0.297). The SDP data are rich and allow us to study not only the background high-redshift galaxies (e.g., strongly lensed and distorted galaxies at z = 2.8 and 3.2) but also the properties of cluster-member galaxies. Our preliminary analysis shows a great diversity of far-infrared/submillimeter spectral energy distributions (SEDs), indicating that we have much to learn with Herschel about the properties of galaxy SEDs. We have also detected the Sunyaev-Zel’dovich (SZ) effect increment with the SPIRE data. The success of this SDP program demonstrates the great potential of the Herschel Lensing Survey to produce exciting results in a variety of science areas

Deep Herschel view of obscured star formation in the Bullet cluster

We use deep, five band (100–500 μm) data from the Herschel Lensing Survey (HLS) to fully constrain the obscured star formation rate, SFR_(FIR), of galaxies in the Bullet cluster (z = 0.296), and a smaller background system (z = 0.35) in the same field. Herschel detects 23 Bullet cluster members with a total SFRFIR = 144±14 M_☉ yr^(-1). On average, the background system contains brighter far-infrared (FIR) galaxies, with ~50% higher SFRFIR (21 galaxies; 207 ± 9 M_☉ yr^(-1)). SFRs extrapolated from 24 μm flux via recent templates (SFR_(24 µm)) agree well with SFRFIR for ~60% of the cluster galaxies. In the remaining ~40%, SFR24 µm underestimates SFR_(FIR) due to a significant excess in observed S_(100)/S_(24) (rest frame S_(75)/S_(18)) compared to templates of the same FIR luminosity

Dynamical Structure of the Molecular Interstellar Medium in an Extremely Bright, Multiply Lensed z ≃ 3 Submillimeter Galaxy Discovered with Herschel

We report the detection of CO(J = 5 → 4), CO(J = 3 → 2), and CO(J = 1 → 0) emission in the strongly lensed, Herschel/SPIRE-selected submillimeter galaxy (SMG) HERMES J105751.1+573027 at z = 2.9574 ± 0.0001, using the Plateau de Bure Interferometer, the Combined Array for Research in Millimeter-wave Astronomy, and the Green Bank Telescope. The observations spatially resolve the molecular gas into four lensed images with a maximum separation of ~9" and reveal the internal gas dynamics in this system. We derive lensing-corrected CO line luminosities of L'_(CO(1-0)) = (4.17 ± 0.41), L'_(CO(3-2)) = (3.96 ± 0.20), and L'_(CO(5-4)) = (3.45 ± 0.20) × 10^(10) (μL/10.9)^(–1) K km s^(–1) pc^2, corresponding to luminosity ratios of r_(31) = 0.95 ± 0.10, r_(53) = 0.87 ± 0.06, and r_(51) = 0.83 ± 0.09. This suggests a total molecular gas mass of M_(gas) = 3.3×10^(10) (α_(CO)/0.8) (μ_L/10.9)^(–1) M_☉. The gas mass, gas mass fraction, gas depletion timescale, star formation efficiency, and specific star formation rate are typical for an SMG. The velocity structure of the gas reservoir suggests that the brightest two lensed images are dynamically resolved projections of the same dust-obscured region in the galaxy that are kinematically offset from the unresolved fainter images. The resolved kinematics appear consistent with the complex velocity structure observed in major, "wet" (i.e., gas-rich) mergers. Major mergers are commonly observed in SMGs and are likely to be responsible for fueling their intense starbursts at high gas consumption rates. This study demonstrates the level of detail to which galaxies in the early universe can be studied by utilizing the increase in effective spatial resolution and sensitivity provided by gravitational lensing

Observation of H_2O in a strongly lensed Herschel-ATLAS source at z = 2.3

The Herschel survey, H-ATLAS, with its large areal coverage, has recently discovered a number of bright, strongly lensed high-z submillimeter galaxies. The strong magnification makes it possible to study molecular species other than CO, which are otherwise difficult to observe in high-z galaxies. Among the lensed galaxies already identified by H-ATLAS, the source J090302.9-014127B (SDP.17b) at z = 2.305 is remarkable because of its excitation conditions and a tentative detection of the H_2O 2_(02)-1_(11) emission line (Lupu et al. 2010, ApJ, submitted). We report observations of this line in SDP.17b using the IRAM interferometer equipped with its new 277–371 GHz receivers. The H_2O line is detected at a redshift of z = 2.3049 ± 0.0006, with a flux of 7.8 ± 0.5 Jy km s^(-1) and a FWHM of 250 ± 60   km   s^(-1). The new flux is 2.4 times weaker than the previous tentative detection, although both remain marginally consistent within 1.6σ. The intrinsic line luminosity and ratio of H_2O(2_(02) − 1_(11))/CO(8 − 7) are comparable with those of the nearby starburst/enshrouded-AGN Mrk 231, and the ratio I(H_2O)/L_(FIR) is even higher, suggesting that SDP.17b could also host a luminous AGN. The detection of a strong H_2O 2_(02) − 1_(11) line in SDP.17b implies an efficient excitation mechanism of the water levels that must occur in very dense and warm interstellar gas probably similar to Mrk 231

Thermal kinetic inductance detectors for ground-based millimeter-wave cosmology

We show measurements of thermal kinetic inductance detectors (TKID) intended for millimeter wave cosmology in the 200-300 GHz atmospheric window. The TKID is a type of bolometer which uses the kinetic inductance of a superconducting resonator to measure the temperature of the thermally isolated bolometer island. We measure bolometer thermal conductance, time constant and noise equivalent power. We also measure the quality factor of our resonators as the bath temperature varies to show they are limited by effects consistent with coupling to two level systems.Comment: 8 pages, 4 figures. Submitted to Journal of Low Temperature Physic

An \emph{ab initio} method for locating characteristic potential energy minima of liquids

It is possible in principle to probe the many--atom potential surface using density functional theory (DFT). This will allow us to apply DFT to the Hamiltonian formulation of atomic motion in monatomic liquids [\textit{Phys. Rev. E} {\bf 56}, 4179 (1997)]. For a monatomic system, analysis of the potential surface is facilitated by the random and symmetric classification of potential energy valleys. Since the random valleys are numerically dominant and uniform in their macroscopic potential properties, only a few quenches are necessary to establish these properties. Here we describe an efficient technique for doing this. Quenches are done from easily generated "stochastic" configurations, in which the nuclei are distributed uniformly within a constraint limiting the closeness of approach. For metallic Na with atomic pair potential interactions, it is shown that quenches from stochastic configurations and quenches from equilibrium liquid Molecular Dynamics (MD) configurations produce statistically identical distributions of the structural potential energy. Again for metallic Na, it is shown that DFT quenches from stochastic configurations provide the parameters which calibrate the Hamiltonian. A statistical mechanical analysis shows how the underlying potential properties can be extracted from the distributions found in quenches from stochastic configurations