Doctor of Philosophy

dissertationPortable electronic devices will be limited to available energy of existing battery chemistries for the foreseeable future. However, system-on-chips (SoCs) used in these devices are under a demand to offer more functionality and increased battery life. A difficult problem in SoC design is providing energy-efficient communication between its components while maintaining the required performance. This dissertation introduces a novel energy-efficient network-on-chip (NoC) communication architecture. A NoC is used within complex SoCs due it its superior performance, energy usage, modularity, and scalability over traditional bus and point-to-point methods of connecting SoC components. This is the first academic research that combines asynchronous NoC circuits, a focus on energy-efficient design, and a software framework to customize a NoC for a particular SoC. Its key contribution is demonstrating that a simple, asynchronous NoC concept is a good match for low-power devices, and is a fruitful area for additional investigation. The proposed NoC is energy-efficient in several ways: simple switch and arbitration logic, low port radix, latch-based router buffering, a topology with the minimum number of 3-port routers, and the asynchronous advantages of zero dynamic power consumption while idle and the lack of a clock tree. The tool framework developed for this work uses novel methods to optimize the topology and router oorplan based on simulated annealing and force-directed movement. It studies link pipelining techniques that yield improved throughput in an energy-efficient manner. A simulator is automatically generated for each customized NoC, and its traffic generators use a self-similar message distribution, as opposed to Poisson, to better match application behavior. Compared to a conventional synchronous NoC, this design is superior by achieving comparable message latency with half the energy

Unbiased Cosmological Parameter Estimation from Emission Line Surveys with Interlopers

The galaxy catalogs generated from low-resolution emission line surveys often contain both foreground and background interlopers due to line misidentification, which can bias the cosmological parameter estimation. In this paper, we present a method for correcting the interloper bias by using the joint-analysis of auto- and cross-power spectra of the main and the interloper samples. In particular, we can measure the interloper fractions from the cross-correlation between the interlopers and survey galaxies, because the true cross-correlation must be negligibly small. The estimated interloper fractions, in turn, remove the interloper bias in the cosmological parameter estimation. For example, in the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) low-redshift ($z<0.5$) [O II] $\lambda3727${\AA} emitters contaminate high-redshift ($1.9<z<3.5$) Lyman-$\alpha$ line emitters. We demonstrate that the joint-analysis method yields a high signal-to-noise ratio measurement of the interloper fractions while only marginally increasing the uncertainties in the cosmological parameters relative to the case without interlopers. We also show the same is true for the high-latitude spectroscopic survey of Wide-Field Infrared Survey Telescope (WFIRST) mission where contamination occurs between the Balmer-$\alpha$ line emitters at lower redshifts ($1.1<z<1.9$) and Oxygen ([O III] $\lambda5007${\AA}) line emitters at higher redshifts ($1.7<z<2.8$).Comment: 36 pages, 26 figure

Cryo-Electron Tomography Elucidates the Molecular Architecture of Treponema pallidum, the Syphilis Spirochete

Cryo-electron tomography (CET) was used to examine the native cellular organization of Treponema pallidum, the syphilis spirochete. T. pallidum cells appeared to form flat waves, did not contain an outer coat and, except for bulges over the basal bodies and widening in the vicinity of flagellar filaments, displayed a uniform periplasmic space. Although the outer membrane (OM) generally was smooth in contour, OM extrusions and blebs frequently were observed, highlighting the structure’s fluidity and lack of attachment to underlying periplasmic constituents. Cytoplasmic filaments converged from their attachment points opposite the basal bodies to form arrays that ran roughly parallel to the flagellar filaments along the inner surface of the cytoplasmic membrane (CM). Motile treponemes stably attached to rabbit epithelial cells predominantly via their tips. CET revealed that T. pallidum cell ends have a complex morphology and assume at least four distinct morphotypes. Images of dividing treponemes and organisms shedding cell envelope-derived blebs provided evidence for the spirochete’s complex membrane biology. In the regions without flagellar filaments, peptidoglycan (PG) was visualized as a thin layer that divided the periplasmic space into zones of higher and lower electron densities adjacent to the CM and OM, respectively. Flagellar filaments were observed overlying the PG layer, while image modeling placed the PG-basal body contact site in the vicinity of the stator–P-collar junction. Bioinformatics and homology modeling indicated that the MotB proteins of T. pallidum, Treponema denticola, and Borrelia burgdorferi have membrane topologies and PG binding sites highly similar to those of their well-characterized Escherichia coli and Helicobacter pylori orthologs. Collectively, our results help to clarify fundamental differences in cell envelope ultrastructure between spirochetes and gram-negative bacteria. They also confirm that PG stabilizes the flagellar motor and enable us to propose that in most spirochetes motility results from rotation of the flagellar filaments against the PG

SuperMassive Black Holes in Bulges

We present spatially extended gas kinematics at parsec-scale resolution for the nuclear regions of four nearby disk galaxies, and model them as rotation of a gas disk in the joint potential of the stellar bulge and a putative central black hole. The targets were selected from a larger set of long-slit spectra obtained with the Hubble Space Telescope as part of the Survey of Nearby Nuclei with STIS (SUNNS). They represents the 4 galaxies (of 24) that display symmetric gas velocity curves consistent with a rotating disk. We derive the stellar mass distribution from the STIS acquisition images adopting the stellar mass-to-light ratio normalized so as to match ground-based velocity dispersion measurements over a large aperture. Subsequently, we constrain the mass of a putative black hole by matching the gas rotation curve, following two distinct approaches. In the most general case we explore all the possible disk orientations, alternatively we constrain the gas disk orientation from the dust-lane morphology at similar radii. In the latter case the kinematic data indicate the presence of a central black hole for three of the four objects, with masses of 10^7 - 10^8 solar masses, representing up to 0.025 % of the host bulge mass. For one object (NGC2787) the kinematic data alone provide clear evidence for the presence of a central black hole even without external constraints on the disk orientation. These results illustrate directly the need to determine black-hole masses by differing methods for a large number of objects, demonstrate that the variance in black hole/bulge mass is much larger than previously claimed, and reinforce the recent finding that the black-hole mass is tightly correlated with the bulge stellar velocity dispersion.Comment: 26 pages, 11 Postscript figures, accepted for publication on Ap

Skeletal variation in bird domestication: limb proportions and sternum in chicken, with comparisons to mallard ducks and Muscovy ducks

Background Domestication, including selective breeding, can lead to morphological changes of biomechanical relevance. In birds, limb proportions and sternum characteristics are of great importance and have been studied in the past for their relation with flight, terrestrial locomotion and animal welfare. In this work we studied the effects of domestication and breed formation in limb proportions and sternum characteristics in chicken (Gallus gallus), mallard ducks (Anas plathyrhynchos) and Muscovy ducks (Cairina moschata). Methods First, we quantified the proportional length of three long bones of the forelimb (humerus, radius, and carpometacarpus) and the hind limb (femur, tibiotarsus, and tarsometatarsus) in domestic chickens, mallard ducks, and Muscovy ducks and their wild counterparts. For this, we took linear measurements of these bones and compared their proportions in the wild vs. the domestic group in each species. In chicken, these comparisons could also be conducted among different breeds. We then evaluated the proportional differences in the context of static and ontogenetic allometry. Further, we compared discrete sternum characteristics in red jungle fowl and chicken breeds. In total, we examined limb bones of 287 specimens and keel bones of 63 specimens. Results We found a lack of significant change in the proportions of limb bones of chicken and Muscovy duck due to domestication, but significant differences in the case of mallard ducks. Variation of evolvability, allometric scaling, and heterochrony may serve to describe some of the patterns of change we report. Flight capacity loss in mallard ducks resulting from domestication may have a relation with the difference in limb proportions. The lack of variation in proportions that could distinguish domestic from wild forms of chicken and Muscovy ducks may reflect no selection for flight capacity during the domestication process in these groups. In chicken, some of the differences identified in the traits discussed are breed-dependent. The study of the sternum revealed that the condition of crooked keel was not unique to domestic chicken, that some sternal characteristics were more frequent in certain chicken breeds than in others, and that overall there were no keel characteristics that are unique for certain chicken breeds. Despite some similar morphological changes identified across species, this study highlights the lack of universal patterns in domestication and breed formation

Measuring the mass of the central black hole in the bulgeless galaxy ngc 4395 from gas dynamical modeling

NGC 4395 is a bulgeless spiral galaxy, harboring one of the nearest known type 1 Seyfert nuclei. Although there is no consensus on the mass of its central engine, several estimates suggest it is one of the lightest massive black holes (MBHs) known. We present the first direct dynamical measurement of the mass of this MBH from a combination of two-dimensional gas kinematic data, obtained with the adaptive optics assisted near-infrared integral field spectrograph Gemini/NIFS and high-resolution multiband photometric data from Hubble Space Telescope's Wide Field Camera 3. We use the photometric data to model the shape and stellar mass-to-light ratio of the nuclear star cluster (NSC). From the Gemini/NIFS observations, we derive the kinematics of warm molecular hydrogen gas as traced by emission through the H2 1–0 S(1) transition. These kinematics show a clear rotational signal, with a position angle orthogonal to NGC 4395's radio jet. Our best-fitting tilted ring models of the kinematics of the molecular hydrogen gas contain a black hole with mass M={4}-3+8× {10}5 M⊙ (3σ uncertainties) embedded in an NSC of mass M=2× {10}6 M⊙. Our black hole mass measurement is in excellent agreement with the reverberation mapping mass estimate of Peterson et al. but shows some tension with other mass measurement methods based on accretion signals

The Active Galactic Nuclei in the Hobby-Eberly Telescope Dark Energy Experiment Survey (HETDEX). III. A Red Quasar with Extremely High Equivalent Widths Showing Powerful Outflows

We report an active galactic nucleus (AGN) with an extremely high equivalent width (EW), EWLyα+N V,rest ≳921 Å, in the rest frame, at z ∼ 2.24 in the Hobby-Eberly Telescope Dark Energy Experiment Survey (HETDEX), as a representative case of the high-EW AGN population. The continuum level is a nondetection in the HETDEX spectrum; thus the measured EW is a lower limit. The source is detected with significant emission lines (>7σ) at Lyα + N v λ1241, C iv λ1549, and a moderate emission line (∼4σ) at He ii λ1640 within the wavelength coverage of HETDEX (3500-5500 Å). The r-band magnitude is 24.57 from the Hyper Suprime-Cam-HETDEX joint survey with a detection limit of r = 25.12 at 5σ. The Lyα emission line spans a clearly resolved region of ∼10″ (85 kpc) in diameter. The Lyα line profile is strongly double peaked. The spectral decomposed blue gas and red gas Lyα emission are separated by ∼1.″2 (10.1 kpc) with a line-of-sight velocity offset of ∼1100 km s−1. This source is probably an obscured AGN with powerful winds

Using Dark Energy Explorers and Machine Learning to Enhance the Hobby-Eberly Telescope Dark Energy Experiment

We present analysis using a citizen science campaign to improve the cosmological measures from the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX). The goal of HETDEX is to measure the Hubble expansion rate, $H(z)$, and angular diameter distance, $D_A(z)$, at $z =$ 2.4, each to percent-level accuracy. This accuracy is determined primarily from the total number of detected Lyman-$\alpha$ emitters (LAEs), the false positive rate due to noise, and the contamination due to [O II] emitting galaxies. This paper presents the citizen science project, Dark Energy Explorers, with the goal of increasing the number of LAEs, decreasing the number of false positives due to noise and the [O II] galaxies. Initial analysis shows that citizen science is an efficient and effective tool for classification most accurately done by the human eye, especially in combination with unsupervised machine learning. Three aspects from the citizen science campaign that have the most impact are 1) identifying individual problems with detections, 2) providing a clean sample with 100% visual identification above a signal-to-noise cut, and 3) providing labels for machine learning efforts. Since the end of 2022, Dark Energy Explorers has collected over three and a half million classifications by 11,000 volunteers in over 85 different countries around the world. By incorporating the results of the Dark Energy Explorers we expect to improve the accuracy on the $D_A(z)$ and $H(z)$ parameters at $z =$ 2.4 by 10 - 30%. While the primary goal is to improve on HETDEX, Dark Energy Explorers has already proven to be a uniquely powerful tool for science advancement and increasing accessibility to science worldwide.Comment: 14 pages, 6 figures, accepted for publication in The Astrophysical Journa