A Multiwavelength Study of the Intracluster Medium and the Characterization of the Multiwavelength Sub/millimeter Inductance Camera

The first part of this thesis combines Bolocam observations of the thermal Sunyaev-Zel’dovich (SZ) effect at 140 GHz with X-ray observations from Chandra, strong lensing data from the Hubble Space Telescope (HST), and weak lensing data from HST and Subaru to constrain parametric models for the distribution of dark and baryonic matter in a sample of six massive, dynamically relaxed galaxy clusters. For five of the six clusters, the full multiwavelength dataset is well described by a relatively simple model that assumes spherical symmetry, hydrostatic equilibrium, and entirely thermal pressure support. The multiwavelength analysis yields considerably better constraints on the total mass and concentration compared to analysis of any one dataset individually. The subsample of five galaxy clusters is used to place an upper limit on the fraction of pressure support in the intracluster medium (ICM) due to nonthermal processes, such as turbulent and bulk flow of the gas. We constrain the nonthermal pressure fraction at r500c to be less than 0.11 at 95% confidence, where r500c refers to radius at which the average enclosed density is 500 times the critical density of the Universe. This is in tension with state-of-the-art hydrodynamical simulations, which predict a nonthermal pressure fraction of approximately 0.25 at r500c for the clusters in this sample.

The second part of this thesis focuses on the characterization of the Multiwavelength Sub/millimeter Inductance Camera (MUSIC), a photometric imaging camera that was commissioned at the Caltech Submillimeter Observatory (CSO) in 2012. MUSIC is designed to have a 14 arcminute, diffraction-limited field of view populated with 576 spatial pixels that are simultaneously sensitive to four bands at 150, 220, 290, and 350 GHz. It is well-suited for studies of dusty star forming galaxies, galaxy clusters via the SZ Effect, and galactic star formation. MUSIC employs a number of novel detector technologies: broadband phased-arrays of slot dipole antennas for beam formation, on-chip lumped element filters for band definition, and Microwave Kinetic Inductance Detectors (MKIDs) for transduction of incoming light to electric signal. MKIDs are superconducting micro-resonators coupled to a feedline. Incoming light breaks apart Cooper pairs in the superconductor, causing a change in the quality factor and frequency of the resonator. This is read out as amplitude and phase modulation of a microwave probe signal centered on the resonant frequency. By tuning each resonator to a slightly different frequency and sending out a superposition of probe signals, hundreds of detectors can be read out on a single feedline. This natural capability for large scale, frequency domain multiplexing combined with relatively simple fabrication makes MKIDs a promising low temperature detector for future kilopixel sub/millimeter instruments. There is also considerable interest in using MKIDs for optical through near-infrared spectrophotometry due to their fast microsecond response time and modest energy resolution. In order to optimize the MKID design to obtain suitable performance for any particular application, it is critical to have a well-understood physical model for the detectors and the sources of noise to which they are susceptible. MUSIC has collected many hours of on-sky data with over 1000 MKIDs. This work studies the performance of the detectors in the context of one such physical model. Chapter 2 describes the theoretical model for the responsivity and noise of MKIDs. Chapter 3 outlines the set of measurements used to calibrate this model for the MUSIC detectors. Chapter 4 presents the resulting estimates of the spectral response, optical efficiency, and on-sky loading. The measured detector response to Uranus is compared to the calibrated model prediction in order to determine how well the model describes the propagation of signal through the full instrument. Chapter 5 examines the noise present in the detector timestreams during recent science observations. Noise due to fluctuations in atmospheric emission dominate at long timescales (less than 0.5 Hz). Fluctuations in the amplitude and phase of the microwave probe signal due to the readout electronics contribute significant 1/f and drift-type noise at shorter timescales. The atmospheric noise is removed by creating a template for the fluctuations in atmospheric emission from weighted averages of the detector timestreams. The electronics noise is removed by using probe signals centered off-resonance to construct templates for the amplitude and phase fluctuations. The algorithms that perform the atmospheric and electronic noise removal are described. After removal, we find good agreement between the observed residual noise and our expectation for intrinsic detector noise over a significant fraction of the signal bandwidth.

Structure-function studies of serine hydrolases: synthesis of a gene for ∝-lytic protease and the purification and characterization of a mutant β-lactamase

The author has constructed a synthetic gene for ∝-lytic protease. Since the DNA sequence of the protein is not known, the gene was designed by using the reverse translation of ∝-lytic protease's amino acid sequence. Unique restriction sites are carefully sought in the degenerate DNA sequence to aid in future mutagenesis studies. The unique restriction sites are designed approximately 50 base pairs apart and their appropriate codons used in the DNA sequence. The codons used to construct the DNA sequence of ∝-lytic protease are preferred codons in E-coli or used in the production of β-lactamase. Codon usage is also distributed evenly to ensure that one particular codon is not heavily used. The gene is essentially constructed from the outside in. The gene is built in a stepwise fashion using plasmids as the vehicles for the ∝-lytic oligomers. The use of plasmids allows the replication and isolation of large quantities of the intermediates during gene synthesis. The ∝-lytic DNA is a double-stranded oligomer that has sufficient overhang and sticky ends to anneal correctly in the vector. After six steps of incorporating ∝-lytic DNA, the gene is completed and sequenced to ensure that the correct DNA sequence is present and that no mutations occurred in the structural gene.

β-lactamase is the other serine hydrolase studied in this thesis. The author used the class A RTEM-1 β- lactamase encoded on the plasmid pBR322 to investigate the roll of the conserved threonine residue at position 71. Cassette mutagenesis was previously used to generate all possible amino acid substitutions at position 71. The work presented here describes the purification and kinetic characterization of a T71H mutant previously constructed by S. Schultz. The mutated gene was transferred into plasmid pJN for expression and induced with IPTG. The enzyme is purified by column chromatography and FPLC to homogeneity. Kinetic studies reveal that the mutant has lower k_(cat) values on benzylpenicillin, cephalothin and 6-aminopenicillanic acid but no changes in k_m except for cephalothin which is approximately 4 times higher. The mutant did not change siginificantly in its pH profile compared to the wild-type enzyme. Also, the mutant is more sensitive to thermal denaturation as compared to the wild-type enzyme. However, experimental evidence indicates that the probable generation of a positive charge at position 71 thermally stabilized the mutant.

Detecting actions of fruit flies

In this thesis we describe a system that tracks fruit flies in video and automatically detects and classifies their actions. We introduce Caltech Fly-vs-Fly Interactions, a new dataset that contains hours of video showing pairs of fruit flies engaging in social interactions, and is published with complete expert annotations and articulated pose trajectory features. We compare experimentally the value of a frame-level feature representation with the more elaborate notion of bout features that capture the structure within actions. Similarly, we compare a simple sliding window classifier architecture with a more sophisticated structured output architecture, and find that window based detectors outperform the much slower structured counterparts, and approach human performance. In addition we test the top performing detector on the CRIM13 mouse dataset, finding that it matches the performance of the best published method.

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.

SteelConverter and Caltech VirtualShaker: Rapid Nonlinear Cloud-Based Structural Model Conversion and Analysis

STEEL, the Caltech created nonlinear large displacement analysis software, is currently used by a large number of researchers at Caltech. However, due to its complexity, lack of visualization tools (such as pre- and post-processing capabilities) rapid creation and analysis of models using this software was difficult. SteelConverter was created as a means to facilitate model creation through the use of the industry standard finite element solver ETABS. This software allows users to create models in ETABS and intelligently convert model information such as geometry, loading, releases, fixity, etc., into a format that STEEL understands. Models that would take several days to create and verify now take several hours or less. The productivity of the researcher as well as the level of confidence in the model being analyzed is greatly increased.

It has always been a major goal of Caltech to spread the knowledge created here to other universities. However, due to the complexity of STEEL it was difficult for researchers or engineers from other universities to conduct analyses. While SteelConverter did help researchers at Caltech improve their research, sending SteelConverter and its documentation to other universities was less than ideal. Issues of version control, individual computer requirements, and the difficulty of releasing updates made a more centralized solution preferred. This is where the idea for Caltech VirtualShaker was born. Through the creation of a centralized website where users could log in, submit, analyze, and process models in the cloud, all of the major concerns associated with the utilization of SteelConverter were eliminated. Caltech VirtualShaker allows users to create profiles where defaults associated with their most commonly run models are saved, and allows them to submit multiple jobs to an online virtual server to be analyzed and post-processed. The creation of this website not only allowed for more rapid distribution of this tool, but also created a means for engineers and researchers with no access to powerful computer clusters to run computationally intensive analyses without the excessive cost of building and maintaining a computer cluster.

In order to increase confidence in the use of STEEL as an analysis system, as well as verify the conversion tools, a series of comparisons were done between STEEL and ETABS. Six models of increasing complexity, ranging from a cantilever column to a twenty-story moment frame, were analyzed to determine the ability of STEEL to accurately calculate basic model properties such as elastic stiffness and damping through a free vibration analysis as well as more complex structural properties such as overall structural capacity through a pushover analysis. These analyses showed a very strong agreement between the two softwares on every aspect of each analysis. However, these analyses also showed the ability of the STEEL analysis algorithm to converge at significantly larger drifts than ETABS when using the more computationally expensive and structurally realistic fiber hinges. Following the ETABS analysis, it was decided to repeat the comparisons in a software more capable of conducting highly nonlinear analysis, called Perform. These analyses again showed a very strong agreement between the two softwares in every aspect of each analysis through instability. However, due to some limitations in Perform, free vibration analyses for the three story one bay chevron brace frame, two bay chevron brace frame, and twenty story moment frame could not be conducted. With the current trend towards ultimate capacity analysis, the ability to use fiber based models allows engineers to gain a better understanding of a building’s behavior under these extreme load scenarios.

Following this, a final study was done on Hall’s U20 structure [1] where the structure was analyzed in all three softwares and their results compared. The pushover curves from each software were compared and the differences caused by variations in software implementation explained. From this, conclusions can be drawn on the effectiveness of each analysis tool when attempting to analyze structures through the point of geometric instability. The analyses show that while ETABS was capable of accurately determining the elastic stiffness of the model, following the onset of inelastic behavior the analysis tool failed to converge. However, for the small number of time steps the ETABS analysis was converging, its results exactly matched those of STEEL, leading to the conclusion that ETABS is not an appropriate analysis package for analyzing a structure through the point of collapse when using fiber elements throughout the model. The analyses also showed that while Perform was capable of calculating the response of the structure accurately, restrictions in the material model resulted in a pushover curve that did not match that of STEEL exactly, particularly post collapse. However, such problems could be alleviated by choosing a more simplistic material model.

I. Nuclear magnetic resonance analysis of ferrocenylcarbonium ion. II. Ferrocene catalyzed photochemistry

I. Nuclear magnetic resonance spectra of appropriately substituted ferrocenylcarbonium ions reveal the α-protons of the substituted ring to be more shielded than β-protons. The observation is discussed in terms of various models proposed for the ferrocenylcarbonium ion and is found to support a model in which the iron is bonded to all six carbona of the substituted ring.

II. Ferrocene catalyzes the photoisomerization of the piperylenes and the photodimerization of isoprene. Our results suggest a mechanism in which a complex of ferrocene and diene is excited to its second singlet state which dissociates to a triplet-state ferrocene molecule and a triplet-state diene molecule. The triplet-state diene, then, proceeds to isomerize or attack ground-state diene to form dimers.