GRChombo: An adaptable numerical relativity code for fundamental physics

GRChombo is an open-source code for performing Numerical Relativity time evolutions, built on top of the publicly available Chombo software for the solution of PDEs. Whilst GRChombo uses standard techniques in NR, it focusses on applications in theoretical physics where adaptability, both in terms of grid structure, and in terms of code modification, are key drivers

Binary black-hole evolutions of excision and puncture data

We present a new numerical code developed for the evolution of binary black-hole spacetimes using different initial data and evolution techniques. The code is demonstrated to produce state-of-the-art simulations of orbiting and inspiralling black-hole binaries with convergent waveforms. We also present the first detailed study of the dependence of gravitational waveforms resulting from three-dimensional evolutions of different types of initial data. For this purpose we compare the waveforms generated by head-on collisions of superposed Kerr-Schild, Misner and Brill-Lindquist data over a wide range of initial separations.Comment: 21 pages, 13 figures, final version accepted for publication in PR

DNA DEAMINATION REPAIR ENZYMES IN BACTERIAL AND HUMAN SYSTEMS

DNA repair enzymes and pathways are diverse and critical for living cells to maintain correct genetic information. Single-strand-selective monofunctional uracil DNA glycosylase (SMUG1) belongs to Family 3 of the uracil DNA glycosylase superfamily. We report that a bacterial SMUG1 ortholog in Geobacter metallireducens (Gme) and the human SMUG1 enzyme are not only uracil DNA glycosylases (UDG), but also xanthine DNA glycosylases (XDG). Mutations at M57 (M57L) and H210 (H210G, H210M, H210N) can cause substantial reductions in XDG and UDG activities. Increased selectivity is achieved in the A214R mutant of Gme SMUG1 and G60Y completely abolishes XDG and UDG activity. Most interestingly, a proline substitution at the G63 position switches the Gme SMUG1 enzyme to an exclusive uracil DNA glycosylase. Mutational analysis and molecular dynamics (MD) simulations of Gme SMUG1 identify important structural determinants in conserved motifs 1 and 2. Our study offers insights on the important role that modulation of conformational flexibility may play in defining specificity and catalytic efficiency. Endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3\u27 side one nucleotide from a deaminated base lesion. This study defines the endonuclease and exonuclease activity in endonuclease V from Thermotoga maritima (Tma) in an assay condition with Mn2+ as a metal cofactor. Tma endonuclease V exhibits inosine-dependent 3\u27-exonuclease activity. Detailed kinetic analysis using 3\u27-labeled DNA indicates that Tma endonuclease V also possesses nonspecific 5\u27-exonuclease activity. The multiplicity of the endonuclease and exonuclease activity is discussed with respect to deaminated base repair. Biochemical properties of human endonuclease V with respect to repair of deaminated base lesions were reported. We determined repair activities of human endonuclease V on inosine (I)-, xanthosine (X)-, oxanosine (O)- and uridine (U)-containing DNA. Human endonuclease V is most active with inosine-containing DNA; however, with minor activity on xanthosine-containing DNA. Mg2+ and to a much less extent, Mn2+, Ni2+, Co2+ can support the endonuclease activity. Introduction of human endonuclease V into Escherichia coli cells caused two-fold reduction in mutation frequency. This is the first report of deaminated base repair activity from human endonuclease V

Probing the Nature of Black Holes with Gravitational Waves

In this thesis, I present a number of studies intended to improve our understanding of black holes using gravitational waves. Although black holes are relatively well understood from a theory perspective, many questions remain about the nature of the black holes in our Universe. According to general relativity, astrophysical black holes are fully described by just their mass and spin. Yet, relying on electromagnetic-based observatories alone, we still know very little about the distribution of black hole masses or spins. Moreover, as merging black holes are invisible to these electromagnetic observatories, we cannot rely on them to provide us with information about the binary black hole merger rate or binary black hole formation channels. However, by observing gravitational wave signals from these inherently dark binaries, we will soon have some answers to these questions. Indeed, the Laser Interferometer Gravitational-Wave Observatory (LIGO) has already revealed a great deal of new information about binary black holes; giving us an early glimpse into their mass and spin distributions and placing the first constraints on the binary black hole merger rate. This thesis contributes to the goal of probing the nature of black holes with gravitational waves. Binary black holes can form as an isolated binary in the galactic field or through dynamical encounters in high-density environments. Dynamical formation can significantly alter the binary parameters, which then become imprinted on the gravitational waveform. By simulating varying black hole populations in high-density globular clusters, we identify a population of highly eccentric binary black hole mergers that are characteristic of dynamical formation. Although these systems would circularize by the time they are visible in LIGO's frequency band, the future Laser Interferometer Space Antenna (LISA) is capable of distinguishing this population of eccentric mergers from the circular mergers expected of isolated field-formed binaries. As these dynamically formed binaries depend on the size of the underlying black hole population in globular clusters, we can utilize the dynamically formed merger rate to infer globular cluster black hole populations -- allowing us to reveal information about binary black hole birth environments. In order to properly estimate the parameters of binary black holes from detected gravitational wave signals, such as their masses and spins, high-accuracy waveforms are a needed. The highest accuracy waveforms are those produced by numerical relativity simulations, which solve the full Einstein equations. Using the Spectral Einstein Code (SpEC), we expand the reach of numerical relativity to simulate binary black holes with nearly extremal spins, i.e., black holes with spins near the maximal value χ = 1. These waveforms are used to calibrate existing waveform approximants used in LIGO data analyses. This ensures that the systematic errors in these approximants are small enough that if highly-spinning systems are observed, the spins are recovered without bias. Although rapidly spinning binaries have remained elusive thus far, these waveforms ensure that the highest-spin systems can be detected in the quest to uncover the spin distribution of black holes. The end state of a binary black hole merger is a newly born, single black hole that rings down like a struck bell, sending its last few ripples of gravitational waves out into the spacetime. Embedded in this 'ringdown' signal are a multitude of specific frequencies. Einstein's theory of general relativity precisely predicts the ringdown frequencies of a black hole with a given mass and spin. The statement that a black hole is entirely described by just these two parameters is known as the no-hair theorem. For black holes that obey the laws of general relativity (and consequently, the no-hair theorem), these frequencies serve as a fingerprint for the black hole. However, if the objects we observe are not Einstein's black holes, but instead something more exotic, the frequencies will not have this property and this would be a spectacular surprise. A minimum of two tones are required for this test, each with an associated frequency and damping time that depend only on the mass and spin. The conventional no-hair test relies on the so-called 'fundamental' tones of a black hole. A test relying on the fundamental modes is not expected to be feasible for another ~10-15 years, after detector sensitivity has improved significantly. However, by analyzing the ringdown of high-accuracy numerical relativity waveforms, we show that modes beyond the fundamental, known as 'overtones', are detectable in current detectors. The overtones are short-lived, but this is countered by the fact that they can initially be much stronger than the fundamental mode. By measuring two tones in the ringdown of GW150914 we perform a first test of the no-hair theorem. While the current constraints are rather loose, this first test serves as a proof of principle. This is just one example of the powerful tests that can be employed with overtones using present day detectors and the even more precise tests that can be accomplished with LISA in the future.</p

Identification and detection of phosphorylated proteins by laser induced breakdown spectroscopy

Thesis (Master)--Izmir Institute of Technology, Chemistry, Izmir, 2011Includes bibliographical references (leaves: 53-56)Text in English; Abstract: Turkish and Englishx, 56 leavesLaser-Induced Breakdown Spectroscopy (LIBS) is an optical atomic emission spectroscopic technique that uses an energetic laser source to generate a luminous plasma. Spectrochemical analysis of the light emitted from the plasma reveals information about the elemental composition of the sample. Phosphorylation is an important regulatory mechanism that activates or deactivates many proteins and enzymes in a wide range of cellular process. Identification and detection of phosphoproteins have a crucial importance in phosphopeptide mapping. This study is based on the assessment of the capabilities and limitations of LIBS as a quick and simple method for in-gel identification and determination of phosphorylated proteins, specifically casein and ovalbumin before mass spectrometric analysis for the elucidation of phosporylation sites. For this purpose, an optical LIBS set-up was constructed from its commercially available parts and the system was optimized for LIBS analysis of polyacrylamide gels. Nd:YAG laser operating at 532 nm wavelength and at 10 Hz frequency was used to create plasma on dry gel surfaces. Emitted light from a luminous plasma was analyzed and detected by an Echelle type spectrograph containing Intensified CCD, detector. With this study, LIBS detection of phosphorous proteins after electrophoretic separation of phosphorylated proteins has been shown, for the first time. After SDS-PAGE gel separation process, phosphoproteins were recognized from prominent P(I) lines (at 253.5 nm and 255.3 nm) in a plasma formed by the focused laser pulses on the gel, just in the center or in the vicinity of the electrophoretic spot. Spectral emission intensity of P(I) lines from LIBS data has been optimized with respect to laser energy and detector timing parameters by using standard Na2HPO4. It has been shown that phosphorylated proteins (casein and ovalbumin in mixture) can be identified by LIBS after both coomassie brilliant blue and silver staining procedures. Technique shows a great promise in microlocal spotting of phosphorylated proteins in gel before MS analysis for the determination of the phosphorylation sites

Eccentric binaries of compact objects in strong-field gravity

In dieser Arbeit untersuchen wir die Dynamik exzentrischer Binärsysteme kompakter Objekte und die resultierende Gravitationswellenstrahlung im nicht-linearen Regime der Allgemeinen Relativitätstheorie. Hierzu lösen wir die Einsteinschen Feldgleichungen numerisch in einer 3+1 Zerlegung. Wir konzentrieren uns hierbei auf spezielle Orbits, die im Zusammenhang mit nicht-stabilen Kreisbahnen entstehen, und einen rein relativistischen Effekt des Zweikörperproblems der Allgemeinen Relativitätstheorie darstellen. Diese werden bestimmt durch schnelle, quasi-zirkuläre Umläufe bei kleinen Abständen, gefolgt von langsamen radialen Bewegung auf quasi-elliptischen Trajektorien. Auf Grund der besonderen Gestalt dieser Bahnen werden sie als "Zoom-Whirl-Orbits" bezeichnet. Im ersten Teil betrachten wir Binärsysteme Schwarzer Löcher. Wir variieren die Anfangsexzentrizität, und charakterisieren die entstehende Gravitationswellen. Unsere Resultate implizieren, dass Zoom-Whirl-Orbits ohne einen hohen Grad von Feinabstimmung und auch bei moderaten Exzentrizitäten erzeugt werden können. Die Werte der Exzentrizität, für die solche Orbits entstehen, sind in disjunkten Intervallen zu finden. Im zweiten Teil untersuchen wir Binärsysteme von Neutronensternen auf exzentrischen Orbits in Allgemeiner Relativitätstheorie, was einen bisher unerforschten Bereich darstellt. Wir untersuchen deren Phänomenologie und die Folgen einer Verschmelzung für die übrigbleibende Sternmaterie. Die verschmolzenen Neutronensterne kollabieren stets zu einem Schwarzen Loch, aber im Allgemeinen bleibt eine Akkretionsscheibe nicht zu vernachlässigender Masse zurück. Für einen erheblichen Bereich von Exzentrizitäten ist die Masse der Scheibe groß genug, um einen kurzen Gammastrahlenblitz zu speisen. Die starke Gezeitenwechselwirkung modifiziert die Gravitationswellenform in charakteristischer Weise, und kann Hinweise auf die unbekannte Zustandsgleichung der Kernmaterie im Inneren von Neutronensterne geben

Proceedings of the Fall 1995 Advanced Digital Communication Systems

Coordinated Science Laboratory was formerly known as Control Systems Laborator

Articles indexats publicats per investigadors del Campus de Terrassa: 2013

Aquest informe recull els 228 treballs publicats per 177 investigadors/es del Campus de Terrassa en revistes indexades al Journal Citation Report durant el 2013Preprin

Cosmic String Radiation with Adaptive Mesh Refinement

Cosmic strings are a fundamental feature of many physically-motivated field theories which inevitably form in the early Universe, as a result of a symmetry breaking phase transition. An important example is the Peccei-Quinn mechanism, from which strings emerge as a potential source of dark matter axions. They are also a strong source of gravitational wave (GW) emission, with the potential for detection by the Laser Interferometer Gravitational-Wave Observatory (LIGO) and other GW experiments. The nonlinear evolution of cosmic strings has been extensively studied using large-scale numerical simulations. However, the vast difference in scale between a typical string width and the string curvature poses a significant computational challenge. This is usually addressed by approximating the string to have either zero or fixed comoving width, resulting in inconsistencies in predictions between different methods. One technique that can address this issue is adaptive mesh refinement (AMR), which allows the resolution of the numerical grid to adapt to the scale of the features of interest in the simulation. This thesis uses GRChombo, a sophisticated code originally designed for numerical relativity, to perform the first AMR simulations of global cosmic strings. We also present our numerical contributions to GRChombo as a core developer, including novel diagnostic tools and performance enhancement. We perform a detailed quantitative investigation of single sinusoidally displaced string configurations, comparing oscillating string trajectories with a backreaction model accounting for radiation energy losses. We conclude that analytic radiation modelling in the thin-string (Nambu-Goto) limit provides the appropriate picture for cosmological evolution. We also investigate the resulting massless (Goldstone boson or axion) and massive (Higgs) radiation signals, using quantitative diagnostic tools to determine their eigenmode decomposition. We find that the massless quadrupole is dominant and massive radiation is strongly suppressed with increasing mass, with a complex wavepacket structure that is sensitive to numerical resolution. String network configurations are also simulated, with advanced visualisation of radiation used to reveal new qualitative phenomena as strings reconnect and small loops decay. The thesis concludes with the cosmological implications of this work, considering dark matter axions radiated by cosmic strings and the outlook for gravitational wave signatures