In search of slow-moving ionizing massive particles

Many particles proposed by theories, such as GUT monopoles, nuclearites and 1/5 charge superstring particles, can be categorized as Slow-moving, Ionizing, Massive Particles (SIMPs).

Detailed calculations of the signal-to-noise ratios in vanous acoustic and mechanical methods for detecting such SIMPs are presented. It is shown that the previous belief that such methods are intrinsically prohibited by the thermal noise is incorrect, and that ways to solve the thermal noise problem are already within the reach of today's technology. In fact, many running and finished gravitational wave detection ( GWD) experiments are already sensitive to certain SIMPs. As an example, a published GWD result is used to obtain a flux limit for nuclearites.

The result of a search using a scintillator array on Earth's surface is reported. A flux limit of 4.7 x 10^(-12) cm^(-2)sr^(-1)s^(-1) (90% c.l.) is set for any SIMP with 2.7 x 10^(-4) less than β less than 5 x 10^(-3) and ionization greater than 1/3 of minimum ionizing muons. Although this limit is above the limits from underground experiments for typical supermassive particles (10^(16)GeV), it is a new limit in certain β and ionization regions for less massive ones (~10^9 GeV) not able to penetrate deep underground, and implies a stringent limit on the fraction of the dark matter that can be composed of massive electrically and/ or magnetically charged particles.

The prospect of the future SIMP search in the MACRO detector is discussed. The special problem of SIMP trigger is examined and a circuit proposed, which may solve most of the problems of the previous ones proposed or used by others and may even enable MACRO to detect certain SIMP species with β as low as the orbital velocity around the earth.

The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

Search for color transparency in A(e,e'p) at high momentum transfer

Rates for A(e, e'p) on the nuclei ^2H, C, Fe, and Au have been measured at momentum transfers Q^2 = 1, 3, 5, and 6.8 (GeV fc)^2 . We extract the nuclear transparency T, a measure of the importance of final state interactions (FSI) between the outgoing proton and the recoil nucleus. Some calculations based on perturbative QCD predict an increase in T with momentum transfer, a phenomenon known as Color Transparency. No statistically significant rise is seen in the present experiment.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Search for heavy neutral resonances in the dielectron channel with the CMS detector at the LHC

A search for dielectron decays of heavy neutral resonances has been performed using proton-proton collision data collected at √s = 7 TeV by the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in 2011. The data sample corresponds to an integrated luminosity of 5 fb⁻¹. The dielectron mass distribution is consistent with Standard Model (SM) predictions. An upper limit on the ratio of the cross section times branching fraction of new bosons, normalized to the cross section times branching fraction of the Z boson, is set at the 95 % confidence level. This result is translated into limits on the mass of new neutral particles at the level of 2120 GeV for the Z′ in the Sequential Standard Model, 1810 GeV for the superstring-inspired Z′_ψ resonance, and 1940 (1640) GeV for Kaluza-Klein gravitons with the coupling parameter k/M_Pl of 0.10 (0.05).

Finding needles in the haystack : a search for AM CVn systems using the Palomar Transient Factory

The AM CVn systems are a rare class of ultra-compact astrophysical binaries. With orbital periods of under an hour and as short as five minutes, they are among the closest known binary star systems and their evolution has direct relevance to the type Ia supernova rate and the white dwarf binary population. However, their faint and rare nature has made population studies of these systems difficult and several studies have found conflicting results.

I undertook a survey for AM CVn systems using the Palomar Transient Factory (PTF) astrophysical synoptic survey by exploiting the "outbursts" these systems undergo. Such events result in an increase in luminosity by a factor of up to two-hundred and are detectable in time-domain photometric data of AM CVn systems. My search resulted in the discovery of eight new systems, over 20% of the current known population. More importantly, this search was done in a systematic fashion, which allows for a population study properly accounting for biases.

Apart from the discovery of new systems, I used the time-domain data from the PTF and other synoptic surveys to better understand the long-term behavior of these systems. This analysis of the photometric behavior of the majority of known AM CVn systems has shown changes in their behavior at longer time scales than have previously been observed. This has allowed me to find relationships between the outburst properties of an individual system and its orbital period.

Even more importantly, the systematically selected sample together with these properties have allowed me to conduct a population study of the AM CVn systems. I have shown that the latest published estimates of the AM CVn system population, a factor of fifty below theoretical estimates, are consistent with the sample of systems presented here. This is particularly noteworthy since my population study is most sensitive to a different orbital period regime than earlier surveys. This confirmation of the population density will allow the AM CVn systems population to be used in the study of other areas of astrophysics.

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.

Exploring the Dynamic Radio Sky: The Search for Slow Transients with the VLA

While synoptic surveys in the optical and at high energies have revealed a rich discovery phase space of slow transients, a similar yield is still awaited in the radio. Majority of the past blind surveys, carried out with radio interferometers, have suffered from a low yield of slow transients, ambiguous transient classifications, and contamination by false positives. The newly-refurbished Karl G. Jansky Array (Jansky VLA) offers wider bandwidths for accurate RFI excision as well as substantially-improved sensitivity and survey speed compared with the old VLA. The Jansky VLA thus eliminates the pitfalls of interferometric transient search by facilitating sensitive, wide-field, and near-real-time radio surveys and enabling a systematic exploration of the dynamic radio sky. This thesis aims at carrying out blind Jansky VLA surveys for characterizing the radio variable and transient sources at frequencies of a few GHz and on timescales between days and years. Through joint radio and optical surveys, the thesis addresses outstanding questions pertaining to the rates of slow radio transients (e.g. radio supernovae, tidal disruption events, binary neutron star mergers, stellar flares, etc.), the false-positive foreground relevant for the radio and optical counterpart searches of gravitational wave sources, and the beaming factor of gamma-ray bursts. The need for rapid processing of the Jansky VLA data and near-real-time radio transient search has enabled the development of state-of-the-art software infrastructure. This thesis has successfully demonstrated the Jansky VLA as a powerful transient search instrument, and it serves as a pathfinder for the transient surveys planned for the SKA-mid pathfinder facilities, viz. ASKAP, MeerKAT, and WSRT/Apertif.

A search for fractionally charged particles in cosmic rays and a theoretical interpretation of the results

An array of two spark chambers and six trays of plastic scintillation counters was used to search for unaccompanied fractionally charged particles in cosmic rays near sea level. No acceptable events were found with energy losses by ionization between 0.04 and 0.7 that of unit-charged minimum-ionizing particles. New 90%-confidence upper limits were thereby established for the fluxes of fractionally charged particles in cosmic rays, namely, (1.04 ± 0.07)x10^-10 and (2.03 ± 0.16)x10^-10 cm^-2sr^-1sec^-1 for minimum-ionizing particles with charges 1/3 and 2/3, respectively.

In order to be certain that the spark chambers could have functioned for the low levels of ionization expected from particles with small fractional charges, tests were conducted to estimate the efficiency of the chambers as they had been used in this experiment. These tests showed that the spark-chamber system with the track-selection criteria used might have been over 99% efficient for the entire range of energy losses considered.

Lower limits were then obtained for the mass of a quark by considering the above flux limits and a particular model for the production of quarks in cosmic rays. In this model, which is one involving the multi-peripheral Regge hypothesis, the production cross section and a corresponding mass limit are critically dependent on the Regge trajectory assigned to a quark. If quarks are "elementary'' with a flat trajectory, the mass of a quark can be expected to be at least 6 ± 2 BeV/c². If quarks have a trajectory with unit slope, just as the existing hadrons do, the mass of a quark might be as small as 1.3 ± 0.2 BeV/c². For a trajectory with unit slope and a mass larger than a couple of BeV/c², the production cross section may be so low that quarks might never be observed in nature.