A Tale of Two Narrow-Line Regions: Ionization, Kinematics, and Spectral Energy Distributions for a Local Pair of Merging Obscured Active Galaxies

We explore the gas ionization and kinematics, as well as the optical--IR spectral energy distributions for UGC 11185, a nearby pair of merging galaxies hosting obscured active galactic nuclei (AGNs), also known as SDSS J181611.72+423941.6 and J181609.37+423923.0 (J1816NE and J1816SW, $z \approx 0.04$). Due to the wide separation between these interacting galaxies ($\sim 23$ kpc), observations of these objects provide a rare glimpse of the concurrent growth of supermassive black holes at an early merger stage. We use BPT line diagnostics to show that the full extent of the narrow line emission in both galaxies is photoionized by an AGN and confirm the existence of a 10-kpc-scale ionization cone in J1816NE, while in J1816SW the AGN narrow-line region is much more compact (1--2 kpc) and relatively undisturbed. Our observations also reveal the presence of ionized gas that nearly spans the entire distance between the galaxies which is likely in a merger-induced tidal stream. In addition, we carry out a spectral analysis of the X-ray emission using data from {\em XMM-Newton}. These galaxies represent a useful pair to explore how the [\ion{O}{3}] luminosity of an AGN is dependent on the size of the region used to explore the extended emission. Given the growing evidence for AGN "flickering" over short timescales, we speculate that the appearances and impact of these AGNs may change multiple times over the course of the galaxy merger, which is especially important given that these objects are likely the progenitors of the types of systems commonly classified as "dual AGNs."Comment: 15 pages, 10 figures, accepted by the Astrophysical Journa

Learning to Fix Build Errors with Graph2Diff Neural Networks

Professional software developers spend a significant amount of time fixing builds, but this has received little attention as a problem in automatic program repair. We present a new deep learning architecture, called Graph2Diff, for automatically localizing and fixing build errors. We represent source code, build configuration files, and compiler diagnostic messages as a graph, and then use a Graph Neural Network model to predict a diff. A diff specifies how to modify the code’s abstract syntax tree, represented in the neural network as a sequence of tokens and of pointers to code locations. Our network is an instance of a more general abstraction which we call Graph2Tocopo, which is potentially useful in any development tool for predicting source code changes. We evaluate the model on a dataset of over 500k real build errors and their resolutions from professional developers. Compared to the approach of DeepDelta [23], our approach tackles the harder task of predicting a more precise diff but still achieves over double the accuracy

Bayesian modelling of high-throughput sequencing assays with malacoda.

NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell\u27s output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. So far, the statistical methods used have been rudimentary, employing transformations on count level data and disregarding experimental and technical structure while failing to quantify uncertainty in the statistical model. We have developed an extensive framework for the analysis of NGS functionalization screens available as an R package called malacoda (available from github.com/andrewGhazi/malacoda). Our software implements a probabilistic, fully Bayesian model of screen data. The model uses the negative binomial distribution with gamma priors to model sequencing counts while accounting for effects from input library preparation and sequencing depth. The method leverages the high-throughput nature of the assay to estimate the priors empirically. External annotations such as ENCODE data or DeepSea predictions can also be incorporated to obtain more informative priors-a transformative capability for data integration. The package also includes quality control and utility functions, including automated barcode counting and visualization methods. To validate our method, we analyzed several datasets using malacoda and alternative MPRA analysis methods. These data include experiments from the literature, simulated assays, and primary MPRA data. We also used luciferase assays to experimentally validate several hits from our primary data, as well as variants for which the various methods disagree and variants detectable only with the aid of external annotations

Selective interlayer ferromagnetic coupling between the Cu spins in YBa2_2 Cu3_3 O7−x_{7-x} grown on top of La0.7_{0.7} Ca0.3_{0.3} MnO3_3

Studies to date on ferromagnet/d-wave superconductor heterostructures focus mainly on the effects at or near the interfaces while the response of bulk properties to heterostructuring is overlooked. Here we use resonant soft x-ray scattering spectroscopy to reveal a novel c-axis ferromagnetic coupling between the in-plane Cu spins in YBa$_2$ Cu$_3$ O$_{7-x}$ (YBCO) superconductor when it is grown on top of ferromagnetic La$_{0.7}$ Ca$_{0.3}$ MnO$_3$ (LCMO) manganite layer. This coupling, present in both normal and superconducting states of YBCO, is sensitive to the interfacial termination such that it is only observed in bilayers with MnO_2but not with La$_{0.7}$ Ca$_{0.3}$ interfacial termination. Such contrasting behaviors, we propose, are due to distinct energetic of CuO chain and CuO$_2$ plane at the La$_{0.7}$ Ca$_{0.3}$ and MnO$_2$ terminated interfaces respectively, therefore influencing the transfer of spin-polarized electrons from manganite to cuprate differently. Our findings suggest that the superconducting/ferromagnetic bilayers with proper interfacial engineering can be good candidates for searching the theorized Fulde-Ferrel-Larkin-Ovchinnikov (FFLO) state in cuprates and studying the competing quantum orders in highly correlated electron systems.Comment: Please note the change of the title. Text might be slightly different from the published versio

Warped Kaluza-Klein Dark Matter

Warped compactifications of type IIB string theory contain natural dark matter candidates: Kaluza-Klein modes along approximate isometry directions of long warped throats. These isometries are broken by the full compactification, including moduli stabilization; we present a thorough survey of Kaluza-Klein mode decay rates into light supergravity modes and Standard Model particles. We find that these dark matter candidates typically have lifetimes longer than the age of the universe. Interestingly, some choices for embedding the Standard Model in the compactification lead to decay rates large enough to be observed, so this dark matter sector may provide constraints on the parameter space of the compactification.Comment: 37pp; v2. references, minor clarificatio

A Scalable Correlator Architecture Based on Modular FPGA Hardware, Reuseable Gateware, and Data Packetization

A new generation of radio telescopes is achieving unprecedented levels of sensitivity and resolution, as well as increased agility and field-of-view, by employing high-performance digital signal processing hardware to phase and correlate large numbers of antennas. The computational demands of these imaging systems scale in proportion to BMN^2, where B is the signal bandwidth, M is the number of independent beams, and N is the number of antennas. The specifications of many new arrays lead to demands in excess of tens of PetaOps per second. To meet this challenge, we have developed a general purpose correlator architecture using standard 10-Gbit Ethernet switches to pass data between flexible hardware modules containing Field Programmable Gate Array (FPGA) chips. These chips are programmed using open-source signal processing libraries we have developed to be flexible, scalable, and chip-independent. This work reduces the time and cost of implementing a wide range of signal processing systems, with correlators foremost among them,and facilitates upgrading to new generations of processing technology. We present several correlator deployments, including a 16-antenna, 200-MHz bandwidth, 4-bit, full Stokes parameter application deployed on the Precision Array for Probing the Epoch of Reionization.Comment: Accepted to Publications of the Astronomy Society of the Pacific. 31 pages. v2: corrected typo, v3: corrected Fig. 1

Measurement-based quantum computation in a 2D phase of matter

Recently it has been shown that the non-local correlations needed for measurement based quantum computation (MBQC) can be revealed in the ground state of the Affleck-Kennedy-Lieb-Tasaki (AKLT) model involving nearest neighbor spin-3/2 interactions on a honeycomb lattice. This state is not singular but resides in the disordered phase of ground states of a large family of Hamiltonians characterized by short-range-correlated valence bond solid states. By applying local filtering and adaptive single particle measurements we show that most states in the disordered phase can be reduced to a graph of correlated qubits that is a scalable resource for MBQC. At the transition between the disordered and Neel ordered phases we find a transition from universal to non-universal states as witnessed by the scaling of percolation in the reduced graph state.Comment: 8 pages, 6 figures, comments welcome. v2: published versio

Thermal receptivity of free convective flow from a heated vertical surface: linear waves

Numerical techniques are used to study the receptivity to small-amplitude thermal disturbances of the boundary layer flow of air which is induced by a heated vertical flat plate. The fully elliptic nonlinear, time-dependent Navier–Stokes and energy equations are first solved to determine the steady state boundary-layer flow, while a linearised version of the same code is used to determine the stability characteristics. In particular we investigate (i) the ultimate fate of a localised thermal disturbance placed in the region near the leading edge and (ii) the effect of small-scale surface temperature oscillations as means of understanding the stability characteristics of the boundary layer. We show that there is a favoured frequency of excitation for the time-periodic disturbance which maximises the local response in terms of the local rate of heat transfer. However the magnitude of the favoured frequency depends on precisely how far from the leading edge the local response is measured. We also find that the instability is advective in nature and that the response of the boundary layer consists of a starting transient which eventually leaves the computational domain, leaving behind the large-time time-periodic asymptotic state. Our detailed numerical results are compared with those obtained using parallel flow theory