The search for gravitational waves from the coalescence of black hole binary systems in data from the LIGO and Virgo detectors. Or: A dark walk through a random forest

The LIGO and Virgo gravitational-wave observatories are complex and extremely sensitive strain detectors that can be used to search for a wide variety of gravitational waves from astrophysical and cosmological sources. In this thesis, I motivate the search for the gravitational wave signals from coalescing black hole binary systems with total mass between 25 and 100 solar masses. The mechanisms for formation of such systems are not well-understood, and we do not have many observational constraints on the parameters that guide the formation scenarios. Detection of gravitational waves from such systems — or, in the absence of detection, the tightening of upper limits on the rate of such coalescences — will provide valuable information that can inform the astrophysics of the formation of these systems. I review the search for these systems and place upper limits on the rate of black hole binary coalescences with total mass between 25 and 100 solar masses. I then show how the sensitivity of this search can be improved by up to 40% by the the application of the multivariate statistical classifier known as a random forest of bagged decision trees to more effectively discriminate between signal and non-Gaussian instrumental noise. I also discuss the use of this classifier in the search for the ringdown signal from the merger of two black holes with total mass between 50 and 450 solar masses and present upper limits. I also apply multivariate statistical classifiers to the problem of quantifying the non-Gaussianity of LIGO data. Despite these improvements, no gravitational-wave signals have been detected in LIGO data so far. However, the use of multivariate statistical classification can significantly improve the sensitivity of the Advanced LIGO detectors to such signals.

Fiber-optic integration and efficient detection schemes for optomechanical resonators

With the advent of the laser in the year 1960, the field of optics experienced a renaissance from what was considered to be a dull, solved subject to an active area of development, with applications and discoveries which are yet to be exhausted 55 years later. Light is now nearly ubiquitous not only in cutting-edge research in physics, chemistry, and biology, but also in modern technology and infrastructure. One quality of light, that of the imparted radiation pressure force upon reflection from an object, has attracted intense interest from researchers seeking to precisely monitor and control the motional degrees of freedom of an object using light. These optomechanical interactions have inspired myriad proposals, ranging from quantum memories and transducers in quantum information networks to precision metrology of classical forces. Alongside advances in micro- and nano-fabrication, the burgeoning field of optomechanics has yielded a class of highly engineered systems designed to produce strong interactions between light and motion.

Optomechanical crystals are one such system in which the patterning of periodic holes in thin dielectric films traps both light and sound waves to a micro-scale volume. These devices feature strong radiation pressure coupling between high-quality optical cavity modes and internal nanomechanical resonances. Whether for applications in the quantum or classical domain, the utility of optomechanical crystals hinges on the degree to which light radiating from the device, having interacted with mechanical motion, can be collected and detected in an experimental apparatus consisting of conventional optical components such as lenses and optical fibers. While several efficient methods of optical coupling exist to meet this task, most are unsuitable for the cryogenic or vacuum integration required for many applications. The first portion of this dissertation will detail the development of robust and efficient methods of optically coupling optomechanical resonators to optical fibers, with an emphasis on fabrication processes and optical characterization.

I will then proceed to describe a few experiments enabled by the fiber couplers. The first studies the performance of an optomechanical resonator as a precise sensor for continuous position measurement. The sensitivity of the measurement, limited by the detection efficiency of intracavity photons, is compared to the standard quantum limit imposed by the quantum properties of the laser probe light. The added noise of the measurement is seen to fall within a factor of 3 of the standard quantum limit, representing an order of magnitude improvement over previous experiments utilizing optomechanical crystals, and matching the performance of similar measurements in the microwave domain.

The next experiment uses single photon counting to detect individual phonon emission and absorption events within the nanomechanical oscillator. The scattering of laser light from mechanical motion produces correlated photon-phonon pairs, and detection of the emitted photon corresponds to an effective phonon counting scheme. In the process of scattering, the coherence properties of the mechanical oscillation are mapped onto the reflected light. Intensity interferometry of the reflected light then allows measurement of the temporal coherence of the acoustic field. These correlations are measured for a range of experimental conditions, including the optomechanical amplification of the mechanics to a self-oscillation regime, and comparisons are drawn to a laser system for phonons. Finally, prospects for using phonon counting and intensity interferometry to produce non-classical mechanical states are detailed following recent proposals in literature.

Model systems for the study of drug hypersensitivity

I. It was not possible to produce anti-tetracycline antibody in laboratory animals by any of the methods tried. Tetracycline protein conjugates were prepared and characterized. It was shown that previous reports of the detection of anti-tetracycline antibody by in vitro-methods were in error. Tetracycline precipitates non-specifically with serum proteins. The anaphylactic reaction reported was the result of misinterpretation, since the observations were inconsistent with the known mechanism of anaphylaxis and the supposed antibody would not sensitize guinea pig skin. The hemagglutination reaction was not reproducible and was extremely sensitive to minute amounts of microbial contamination. Both free tetracyclines and the conjugates were found to be poor antigens.

II. Anti-aspiryl antibodies were produced in rabbits using 3 protein carriers. The method of inhibition of precipitation was used to determine the specificity of the antibody produced. ε-Aminocaproate was found to be the most effective inhibitor of the haptens tested, indicating that the combining hapten of the protein is ε-aspiryl-lysyl. Free aspirin and salicylates were poor inhibitors and did not combine with the antibody to a significant extent. The ortho group was found to participate in the binding to antibody. The average binding constants were measured.

Normal rabbit serum was acetylated by aspirin under in vitro conditions, which are similar to physiological conditions. The extent of acetylation was determined by immunochemical tests. The acetylated serum proteins were shown to be potent antigens in rabbits. It was also shown that aspiryl proteins were partially acetylated. The relation of these results to human aspirin intolerance is discussed.

III. Aspirin did not induce contact sensitivity in guinea pigs when they were immunized by techniques that induce sensitivity with other reactive compounds. The acetylation mechanism is not relevant to this type of hypersensitivity, since sensitivity is not produced by potent acetylating agents like acetyl chloride and acetic anhydride. Aspiryl chloride, a totally artificial system, is a good sensitizer. Its specificity was examined.

IV. Protein conjugates were prepared with p-aminosalicylic acid and various carriers using azo, carbodiimide and mixed anhydride coupling. These antigens were injected into rabbits and guinea pigs and no anti-hapten IgG or IgM response was obtained. Delayed hypersensitivity was produced in guinea pigs by immunization with the conjugates, and its specificity was determined. Guinea pigs were not sensitized by either injections or topical application of p-amino-salicylic acid or p-aminosalicylate.

A computer-aided investigation of motion detection units in the fly

This work deals with two related areas: processing of visual information in the central nervous system, and the application of computer systems to research in neurophysiology.

Certain classes of interneurons in the brain and optic lobes of the blowfly Calliphora phaenicia were previously shown to be sensitive to the direction of motion of visual stimuli. These units were identified by visual field, preferred direction of motion, and anatomical location from which recorded. The present work is addressed to the questions: (1) is there interaction between pairs of these units, and (2) if such relationships can be found, what is their nature. To answer these questions, it is essential to record from two or more units simultaneously, and to use more than a single recording electrode if recording points are to be chosen independently. Accordingly, such techniques were developed and are described.

One must also have practical, convenient means for analyzing the large volumes of data so obtained. It is shown that use of an appropriately designed computer system is a profitable approach to this problem. Both hardware and software requirements for a suitable system are discussed and an approach to computer-aided data analysis developed. A description is given of members of a collection of application programs developed for analysis of neuro-physiological data and operated in the environment of and with support from an appropriate computer system. In particular, techniques developed for classification of multiple units recorded on the same electrode are illustrated as are methods for convenient graphical manipulation of data via a computer-driven display.

By means of multiple electrode techniques and the computer-aided data acquisition and analysis system, the path followed by one of the motion detection units was traced from open optic lobe through the brain and into the opposite lobe. It is further shown that this unit and its mirror image in the opposite lobe have a mutually inhibitory relationship. This relationship is investigated. The existence of interaction between other pairs of units is also shown. For pairs of units responding to motion in the same direction, the relationship is of an excitatory nature; for those responding to motion in opposed directions, it is inhibitory.

Experience gained from use of the computer system is discussed and a critical review of the current system is given. The most useful features of the system were found to be the fast response, the ability to go from one analysis technique to another rapidly and conveniently, and the interactive nature of the display system. The shortcomings of the system were problems in real-time use and the programming barrier—the fact that building new analysis techniques requires a high degree of programming knowledge and skill. It is concluded that computer system of the kind discussed will play an increasingly important role in studies of the central nervous system.

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

I. The structure and properties of closed circular duplex DNA. II. Chemically interacting systems at equilibrium in a buoyant density gradient

I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.

New generation of two-dimensional spintronic systems realized by coupling of Rashba and Dirac fermions

Intriguing phenomena and novel physics predicted for two-dimensional (2D) systems formed by electrons in Dirac or Rashba states motivate an active search for new materials or combinations of the already revealed ones. Being very promising ingredients in themselves, interplaying Dirac and Rashba systems can provide a base for next generation of spintronics devices, to a considerable extent, by mixing their striking properties or by improving technically significant characteristics of each other. Here, we demonstrate that in BiTeI@PbSb2Te4 composed of a BiTeI trilayer on top of the topological insulator (TI) PbSb2Te4 weakly- and strongly-coupled Dirac-Rashba hybrid systems are realized. The coupling strength depends on both interface hexagonal stacking and trilayer-stacking order. The weakly-coupled system can serve as a prototype to examine, e.g., plasmonic excitations, frictional drag, spin-polarized transport, and charge-spin separation effect in multilayer helical metals. In the strongly-coupled regime, within similar to 100 meV energy interval of the bulk TI projected bandgap a helical state substituting for the TI surface state appears. This new state is characterized by a larger momentum, similar velocity, and strong localization within BiTeI. We anticipate that our findings pave the way for designing a new type of spintronics devices based on Rashba-Dirac coupled systems.

Experimental demonstration of a record high 11.25Gb/s real-time optical OFDM transceiver supporting 25km SMF end-to-end transmission in simple IMDD systems.

The fastest ever 11.25Gb/s real-time FPGA-based optical orthogonal frequency division multiplexing (OOFDM) transceivers utilizing 64-QAM encoding/decoding and significantly improved variable power loading are experimentally demonstrated, for the first time, incorporating advanced functionalities of on-line performance monitoring, live system parameter optimization and channel estimation. Real-time end-to-end transmission of an 11.25Gb/s 64-QAM-encoded OOFDM signal with a high electrical spectral efficiency of 5.625bit/s/Hz over 25km of standard and MetroCor single-mode fibres is successfully achieved with respective power penalties of 0.3dB and -0.2dB at a BER of 1.0 x 10(-3) in a directly modulated DFB laser-based intensity modulation and direct detection system without in-line optical amplification and chromatic dispersion compensation. The impacts of variable power loading as well as electrical and optical components on the transmission performance of the demonstrated transceivers are experimentally explored in detail. In addition, numerical simulations also show that variable power loading is an extremely effective means of escalating system performance to its maximum potential.

Adaptively modulated optical OFDM modems utilizing RSOAs as intensity modulators in IMDD SMF transmission systems.

Detailed investigations of the transmission performance of adaptively modulated optical orthogonal frequency division multiplexed (AMOOFDM) signals converted using reflective semiconductor optical amplifiers (RSOAs) are undertaken over intensity-modulation and direct-detection (IMDD) single-mode fiber (SMF) transmission systems for WDM-PONs. The theoretical RSOA model adopted for modulating the AMOOFDM signals is experimentally verified rigorously in the aforementioned transmission systems incorporating recently developed real-time end-to-end OOFDM transceivers. Extensive performance comparisons are also made between RSOA and SOA intensity modulators. Optimum RSOA operating conditions are identified, which are independent of RSOA rear-facet reflectivity and very similar to those corresponding to SOAs. Under the identified optimum operating conditions, the RSOA and SOA intensity modulators support the identical AMOOFDM transmission performance of 30Gb/s over 60km SMFs. Under low-cost optical component-enabled practical operating conditions, RSOA intensity modulators with rear-facet reflectivity values of >0.3 outperform considerably SOA intensity modulators in transmission performance, which decreases significantly with reducing RSOA rear-facet reflectivity and optical input power. In addition, results also show that use can be made of the RSOA/SOA intensity modulation-induced negative frequency chirp to improve the AMOOFDM transmission performance in IMDD SMF systems.

Significant improvements in optical power budgets of real-time optical OFDM PON systems.

Based on a comprehensive theoretical optical orthogonal frequency division multiplexing (OOFDM) system model rigorously verified by comparing numerical results with end-to-end real-time experimental measurements at 11.25Gb/s, detailed explorations are undertaken, for the first time, of the impacts of various physical factors on the OOFDM system performance over directly modulated DFB laser (DML)-based, intensity modulation and direct detection (IMDD), single-mode fibre (SMF) systems without in-line optical amplification and chromatic dispersion compensation. It is shown that the low extinction ratio (ER) of the DML modulated OOFDM signal is the predominant factor limiting the maximum achievable optical power budget, and the subcarrier intermixing effect associated with square-law photon detection in the receiver reduces the optical power budget by at least 1dB. Results also indicate that, immediately after the DML in the transmitter, the insertion of a 0.02nm bandwidth optical Gaussian bandpass filter with a 0.01nm wavelength offset with respect to the optical carrier wavelength can enhance the OOFDM signal ER by approximately 1.24dB, thus resulting in a 7dB optical power budget improvement at a total channel BER of 1 × 10(-3).

Real-time experimental demonstration of low-cost VCSEL intensity-modulated 11.25 Gb/s optical OFDM signal transmission over 25 km PON systems.

The feasibility of utilising low-cost, un-cooled vertical cavity surface-emitting lasers (VCSELs) as intensity modulators in real-time optical OFDM (OOFDM) transceivers is experimentally explored, for the first time, in terms of achievable signal bit rates, physical mechanisms limiting the transceiver performance and performance robustness. End-to-end real-time transmission of 11.25 Gb/s 64-QAM-encoded OOFDM signals over simple intensity modulation and direct detection, 25 km SSMF PON systems is experimentally demonstrated with a power penalty of 0.5 dB. The low extinction ratio of the VCSEL intensity-modulated OOFDM signal is identified to be the dominant factor determining the maximum obtainable transmission performance. Experimental investigations indicate that, in addition to the enhanced transceiver performance, adaptive power loading can also significantly improve the system performance robustness to variations in VCSEL operating conditions. As a direct result, the aforementioned capacity versus reach performance is still retained over a wide VCSEL bias (driving) current (voltage) range of 4.5 mA to 9 mA (275 mVpp to 320 mVpp). This work is of great value as it demonstrates the possibility of future mass production of cost-effective OOFDM transceivers for PON applications.

Automated Detection of Exposed Reinforcement in Post-Earthquake Safety and Structural Evaluations

The world is at the threshold of emerging technologies, where new systems in construction, materials, and civil and architectural design are poised to make the world better from a structural and construction perspective. Exciting developments, that are too many to name individually, take place yearly, affecting design considerations and construction practices. This edited book brings together modern methods and advances in structural engineering and construction, fulfilling the mission of ISEC Conferences, which is to enhance communication and understanding between structural and construction engineers for successful design and construction of engineering projects. The articles in this book are those accepted for publication and presentation at the 6th International Structural Engineering and Construction Conference in Zurich. The 6th ISEC Conference in Zurich, Switzerland, follows the overwhelming reception and success of previous ISEC conference in Las Vegas, USA in 2009; Melbourne, Australia in 2007; Shunan, Japan in 2005; Rome, Italy in 2003; and Honolulu, USA in 2001. Many topics are covered in this book, ranging from legal affairs and contracting, to innovations and risk analysis in infrastructure projects, analysis and design of structural systems, materials, architecture, and construction. The articles here are a lasting testimony to the excellent research being undertaken around the world. These articles provide a platform for the exchange of ideas, research efforts and networking in the structural engineering and construction communities. We congratulate and thank the authors for these articles that were selected after intensive peer-review, and our gratitude extends to all reviewers and members of the International Technical Committee. It is their combined contributions that have made this book a reality.

Electrical detection of trapped charge displacements using an ultra-thin SOI percolation transistor

Electrical detection of solid-state charge qubits requires ultrasensitive charge measurement, typically using a quantum point contact or single-electron-transistor, which imposes strict limits on operating temperature, voltage and current. A conventional FET offers relaxed operating conditions, but the back-action of the channel charge is a problem for such small quantum systems. Here, we discuss the use of a percolation transistor as a measurement device, with regard to charge sensing and backaction. The transistor is based on a 10nm thick SOI channel layer and is designed to measure the displacement of trapped charges in a nearby dielectric. At cryogenic temperatures, the trapped charges result in strong disorder in the channel layer, so that current is constrained to a percolation pathway in sub-threshold conditions. A microwave driven spatial Rabi oscillation of the trapped charge causes a change in the percolation pathway, which results in a measurable change in channel current. © The Electrochemical Society.