Machine learning for matching astronomy catalogues

An emerging issue in the field of astronomy is the integration, management and utilization of databases from around the world to facilitate scientific discovery. In this paper, we investigate application of the machine learning techniques of support vector machines and neural networks to the problem of amalgamating catalogues of galaxies as objects from two disparate data sources: radio and optical. Formulating this as a classification problem presents several challenges, including dealing with a highly unbalanced data set. Unlike the conventional approach to the problem (which is based on a likelihood ratio) machine learning does not require density estimation and is shown here to provide a significant improvement in performance. We also report some experiments that explore the importance of the radio and optical data features for the matching problem.

Strong localization of whispering gallery modes in an optical fiber via asymmetric perturbation of the translation symmetry

Recently introduced Surface Nanoscale Axial Photonics (SNAP) is based on whispering gallery modes circulating around the optical FIber surface and undergoing slow axial propagation. In this paper we develop the theory of propagation of whispering gallery modes in a SNAP microresonator, which is formed by nanoscale asymmetric perturbation of the FIber translation symmetry and called here a nanobump microresonator. The considered modes are localized near a closed stable geodesic situated at the FIber surface. A simple condition for the stability of this geodesic corresponding to the appearance of a high Q-factor nanobump microresonator is found. The results obtained are important for engineering of SNAP devices and structures.

Advanced perturbation technique for digital backward propagation in WDM systems

An improved digital backward propagation (DBP) is proposed to compensate inter-nonlinear effects and dispersion jointly in WDM systems based on an advanced perturbation technique (APT). A non-iterative weighted concept is presented to replace the iterative in analytical recursion expression, which can dramatically simplify the complexity and improve accuracy compared to the traditional perturbation technique (TPT). Furthermore, an analytical recursion expression of the output after backward propagation is obtained initially. Numerical simulations are executed for various parameters of the transmission system. The results indicate that the advanced perturbation technique will relax the step size requirements and reduce the oversampling factor when launch power is higher than -2 dBm. We estimate this technique will reduce computational complexity by a factor of around seven with respect to the conventional DBP. © 2013 Optical Society of America.

Accurate differential group delay measurement of narrowband fiber devices with immunity to environmental perturbation

Differential group delay measurement of narrowband fiber devices using a fiber polarization scrambler with a modulation phase shift technique is demonstrated. Accurate measurement is realized with high wavelength and delay resolution and immunity to environmental perturbation.

Efficient computation of decoherent quantum walks through eigenvalue perturbation

A number of recent studies have investigated the introduction of decoherence in quantum walks and the resulting transition to classical random walks. Interestingly,it has been shown that algorithmic properties of quantum walks with decoherence such as the spreading rate are sometimes better than their purely quantum counterparts. Not only quantum walks with decoherence provide a generalization of quantum walks that naturally encompasses both the quantum and classical case, but they also give rise to new and different probability distribution. The application of quantum walks with decoherence to large graphs is limited by the necessity of evolving state vector whose sizes quadratic in the number of nodes of the graph, as opposed to the linear state vector of the purely quantum (or classical) case. In this technical report,we show how to use perturbation theory to reduce the computational complexity of evolving a continuous-time quantum walk subject to decoherence. More specifically, given a graph over n nodes, we show how to approximate the eigendecomposition of the n2×n2 Lindblad super-operator from the eigendecomposition of the n×n graph Hamiltonian.

Microbial Community Responses to Environmental Perturbation

Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.

With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.

In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them.

Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.

Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop \textrm{E} -- and \textrm{D} --TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the \textrm{E} -- and \textrm{D} --TBAs we expand the coupled-cavity \overrightarrow{E} --modes in terms of the individual \overrightarrow{E} -- and \overrightarrow{D} --modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric \textrm{D} mode amplitudes show that the \textrm{D} --TBA did not capture the correct (tangential \overrightarrow{E} --field) boundary conditions. However, the \textrm{D} --TBA did not yield significantly poorer results compared to the \textrm{E} --TBA. Our 2D analysis reveals that the \textrm{E} -- and \textrm{D} --TBAs produced nearly identical mode profiles for every structure. Plots of the relative difference between the \textrm{E} and \textrm{D} mode amplitudes show that the \textrm{D} --TBA did capture the correct (normal \overrightarrow{E} --field) boundary conditions. We found that the 2D TBA CC mode calculations were 125-150 times faster than an FDTD calculation for the same two-defect PCS. Notwithstanding this efficiency, the appropriateness of either TBA was found to depend on the geometry of the structure and the mode(s), i.e. whether or not the mode has a large normal or tangential component.

Electron acoustic soliton energy of the Kadomtsev-Petviashvili equation in the Earth’s magnetotail region at critical ion density

The nonlinear properties of small amplitude electron-acoustic solitary waves (EAWs) in a homogeneous system of unmagnetized collisionless plasma consisted of a cold electron fluid and isothermal ions with two different temperatures obeying Boltzmann type distributions have been investigated. A reductive perturbation method was employed to obtain the Kadomstev-Petviashvili (KP) equation. At the critical ion density, the KP equation is not appropriate for describing the system. Hence, a new set of stretched coordinates
is considered to derive the modified KP equation. Moreover, the solitary solution, soliton energy and the associated electric field at the critical ion density were computed. The present investigation can be of relevance to the electrostatic solitary structures observed in various space plasma environments, such as Earth’s magnetotail region.

Non-radial instabilities and progenitor asphericities in core-collapse supernovae

Since core-collapse supernova simulations still struggle to produce robust neutrino-driven explosions in 3D, it has been proposed that asphericities caused by convection in the progenitor might facilitate shock revival by boosting the activity of non-radial hydrodynamic instabilities in the post-shock region. We investigate this scenario in depth using 42 relativistic 2D simulations with multigroup neutrino transport to examine the effects of velocity and density perturbations in the progenitor for different perturbation geometries that obey fundamental physical constraints (like the anelastic condition). As a framework for analysing our results, we introduce semi-empirical scaling laws relating neutrino heating, average turbulent velocities in the gain region, and the shock deformation in the saturation limit of non-radial instabilities. The squared turbulent Mach number, 〈Ma2〉, reflects the violence of aspherical motions in the gain layer, and explosive runaway occurs for 〈Ma2〉 ≳ 0.3, corresponding to a reduction of the critical neutrino luminosity by ∼25∼25 per cent compared to 1D. In the light of this theory, progenitor asphericities aid shock revival mainly by creating anisotropic mass flux on to the shock: differential infall efficiently converts velocity perturbations in the progenitor into density perturbations δρ/ρ at the shock of the order of the initial convective Mach number Maprog. The anisotropic mass flux and ram pressure deform the shock and thereby amplify post-shock turbulence. Large-scale (ℓ = 2, ℓ = 1) modes prove most conducive to shock revival, whereas small-scale perturbations require unrealistically high convective Mach numbers. Initial density perturbations in the progenitor are only of the order of Ma2progMaprog2 and therefore play a subdominant role.

Data Science Seminar: The data science revolution in Physics and Astronomy

Abstract Heading into the 2020s, Physics and Astronomy are undergoing experimental revolutions that will reshape our picture of the fabric of the Universe. The Large Hadron Collider (LHC), the largest particle physics project in the world, produces 30 petabytes of data annually that need to be sifted through, analysed, and modelled. In astrophysics, the Large Synoptic Survey Telescope (LSST) will be taking a high-resolution image of the full sky every 3 days, leading to data rates of 30 terabytes per night over ten years. These experiments endeavour to answer the question why 96% of the content of the universe currently elude our physical understanding. Both the LHC and LSST share the 5-dimensional nature of their data, with position, energy and time being the fundamental axes. This talk will present an overview of the experiments and data that is gathered, and outlines the challenges in extracting information. Common strategies employed are very similar to industrial data! Science problems (e.g., data filtering, machine learning, statistical interpretation) and provide a seed for exchange of knowledge between academia and industry. Speaker Biography Professor Mark Sullivan Mark Sullivan is a Professor of Astrophysics in the Department of Physics and Astronomy. Mark completed his PhD at Cambridge, and following postdoctoral study in Durham, Toronto and Oxford, now leads a research group at Southampton studying dark energy using exploding stars called "type Ia supernovae". Mark has many years' experience of research that involves repeatedly imaging the night sky to track the arrival of transient objects, involving significant challenges in data handling, processing, classification and analysis.

Proficiency and mechanisms of perturbation of mature T-cell homeostasis by the TCL1 family of oncogenes

In the first part of this thesis, the oncogenic potential of TCL1A family genes was comparatively evaluated by using gamma-retroviral vectors to introduce human TCL1A, MTCP1, and TML1 into hematopoietic stem cells/hematopoietic progenitor cells (HSC/HPC) of wild type mice that were transplanted into wild type recipients. TCL1A and MTCP1 recipient mice predominantly developed B-cell malignancies after a median survival of 388 days and 394 days, respectively. The presented data indicates that TCL1A and MTCP1 are oncogenes with comparable oncogenic potential and shows for the first time that MTCP1 is not only a T-cell oncogene, but is able to transform B cells as well. The third family member TML1 induced the development of immature T-cell malignancies in only a few mice. This study provides first evidence for its oncogenic function. Additionally, the transforming potential of compartment-targeted TCL1A variants was evaluated by retroviral expression of a membrane localizing myristoylated (myr-TCL1A) and a nuclear localizing (nls-TCL1A) variant. Recipients of HSC/HPC transduced with myr-TCL1A and nls-TCL1A predominantly developed B-cell malignancies after a median survival of 360 days and 349 days, respectively. There was a significantly shorter latency period for nls-TCL1A compared to the previously described generic TCL1A. Gene expression analysis revealed higher similarities between expression profiles of tumors induced by TCL1A and nls-TCL1A. Together these data implicate that TCL1A’s predominant oncogenic function might rely on its nuclear presence. The second part of this thesis aims to understand if and how TCR stimulation affects the transforming potential of TCL1A. Mature OT-1 T cells carrying monoclonal TCR’s that specifically recognize ovalbumin (OVA) were retrovirally transduced with TCL1A and repeatedly stimulated in vivo with OVA-peptides. TCR stimulated recipient mice of TCL1A transduced T cells showed a significantly accelerated leukemic outgrowth and a reduced median survival of 305 days, when compared to unstimulated recipients (417 days). These data strongly implicate a pro-leukemogenic cooperation of TCL1A and TCR signals that might be actionable in upcoming interventional designs.

Near-infrared Instrumentation For Rapid-response Astronomy

Ɣ-ray bursts (GRBs) are the Universe's most luminous transient events. Since the discovery of GRBs was announced in 1973, efforts have been ongoing to obtain data over a broader range of the electromagnetic spectrum at the earliest possible times following the initial detection. The discovery of the theorized ``afterglow'' emission in radio through X-ray bands in the late 1990s confirmed the cosmological nature of these events. At present, GRB afterglows are among the best probes of the early Universe (z ≳ 9). In addition to informing theories about GRBs themselves, observations of afterglows probe the circum-burst medium (CBM), properties of the host galaxies and the progress of cosmic reionization. To explore the early-time variability of afterglows, I have developed a generalized analysis framework which models near-infrared (NIR), optical, ultra-violet (UV) and X-ray light curves without assuming an underlying model. These fits are then used to construct the spectral energy distribution (SED) of afterglows at arbitrary times within the observed window. Physical models are then used to explore the evolution of the SED parameter space with time. I demonstrate that this framework produces evidence of the photodestruction of dust in the CBM of GRB 120119A, similar to the findings from a previous study of this afterglow. The framework is additionally applied to the afterglows of GRB 140419A and GRB 080607. In these cases the evolution of the SEDs appears consistent with the standard fireball model. Having introduced the scientific motivations for early-time observations, I introduce the Rapid Infrared Imager-Spectrometer (RIMAS). Once commissioned on the 4.3 meter Discovery Channel Telescope (DCT), RIMAS will be used to study the afterglows of GRBs through photometric and spectroscopic observations beginning within minutes of the initial burst. The instrument will operate in the NIR, from 0.97 μm to 2.37 μm, permitting the detection of very high redshift (z ≳ 7) afterglows which are attenuated at shorter wavelengths by Lyman-ɑ absorption in the intergalactic medium (IGM). A majority of my graduate work has been spent designing and aligning RIMAS's cryogenic (~80 K) optical systems. Design efforts have included an original camera used to image the field surrounding spectroscopic slits, tolerancing and optimizing all of the instrument's optics, thermal modeling of optomechanical systems, and modeling the diffraction efficiencies for some of the dispersive elements. To align the cryogenic optics, I developed a procedure that was successfully used for a majority of the instrument's sub-assemblies. My work on this cryogenic instrument has necessitated experimental and computational projects to design and validate designs of several subsystems. Two of these projects describe simple and effective measurements of optomechanical components in vacuum and at cryogenic temperatures using an 8-bit CCD camera. Models of heat transfer via electrical harnesses used to provide current to motors located within the cryostat are also presented.