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.

Electro-optic modulation of light propagating near the optic axis with any polarization in uniaxial crystals

The electro-optic effect in uniaxial crystals for light propagating near the optic axis with any polarization has been analyzed. The passive and the electrically induced birefringences and the rotation of polarization direction in crystals have been calculated, and the conoscopic interference figures under orthogonal polariscopes for different polarizer directions have been plotted. The extinction areas caused by the rotation of polarization direction in crystals change with the polarizer direction, but the two heads of the induced optical axes do not vary, which are always on the induced principal axis with bigger refractive index. The directions of polariscopes are always extinction, and the +/- 45 degrees directions with polarizer are always complete transmission. The conoscopic interference figures for LiNbO3 crystals have been demonstrated experimentally by rotating polariscopes directions, which accord with the theoretically calculating plots. (c) 2006 Elsevier GmbH. All rights reserved.

Energy loss of light ions channeling in silicon

Experimental measurements of rate of energy loss were made for protons of energy .5 to 1.6 MeV channeling through 1 μm thick silicon targets along the <110>, <111>, and <211> axial directions, and the {100}, {110}, {111}, and {211} planar directions. A .05% resolution automatically controlled magnetic spectrometer was used. The data are presented graphically along with an extensive summary of data in the literature. The data taken cover a wider range of channels than has previously been examined, and are in agreement with the data of F. Eisen, et al., Radd. Eff. 13, 93 (1972).

The theory in the literature for channeling energy loss due to interaction with local electrons, core electrons, and distant valence electrons of the crystal atoms is summarized. Straggling is analyzed, and a computer program which calculates energy loss and straggling using this theory and the Moliere approximation to the Thomas Fermi potential, V_TF, and the detailed silicon crystal structure is described. Values for the local electron density Z_loc in each of the channels listed above are extracted from the data by graphical matching of the experimental and computer results.

Zeroth and second order contributions to Z_loc as a function of distance from the center of the channel were computed from ∇²V_TF = 4πρ for various channels in silicon. For data taken in this work and data of F. Eisen, et al., Rad. Eff. 13, 93 (1972), the calculated zeroth order contribution to Z_loc lies between the experimentally extracted Z_loc values obtained by using the peak and the leading edge of the transmission spectra, suggesting that the observed straggling is due both to statistical fluctuations and to path variation.

A study of T=1, T=3/2, and T=2 states in some light nuclei using (He^3,n) reactions

The (He³, n) reactions on B¹¹, N¹⁵, O¹⁶, and O¹⁸ targets have been studied using a pulsed-beam time-of-flight spectrometer. Special emphasis was placed upon the determination of the excitation energies and properties of states with T = 1 (in Ne¹⁸), T = 3/2 (in N¹³ and F¹⁷) and T = 2 (in Ne²⁰). The identification of the T = 3/2 and T = 2 levels is based on the structure of these states as revealed by intensities and shapes of angular distributions. The reactions are interpreted in terms of double stripping theory. Angular distributions have been compared with plane and distorted wave stripping theories. Results for the four reactions are summarized below:

1) O¹⁶ (He³, n). The reaction has been studied at incident energies up to 13.5 MeV and two previously unreported levels in Ne¹⁸ were observed at E_x = 4.55 ± .015 MeV (Γ = 70 ± 30 keV) and E_x = 5.14 ± .018 MeV (Γ = 100 ± 40 keV).

2) B¹¹ (He³, n). The reaction has been studied at incident energies up to 13.5 MeV. Three T = 3/2 levels in N¹³ have been identified at E_x = 15.068 ± .008 MeV (Γ ˂ 15 keV), E_x = 18.44 ± .04, and E_x 18.98 ± .02 MeV (Γ = 40 ± 20 keV).

3) N¹⁵ (He³, n). The reaction has been studied at incident energies up to 11.88 MeV. T = 3/2 levels in F¹⁷ have been identified at E_x = 11.195 ± .007 MeV (Γ ˂ 20 keV), E_x = 12.540 ± .010 MeV (Γ ˂ 25 keV), and E_x = 13.095 ± .009 MeV (Γ ˂ 25 keV).

4) O¹⁸ (He³, n). The reaction has been studied at incident energies up to 9.0 MeV. The excitation energy of the lowest T = 2 level in Ne²⁰ has been found to be 16.730 ± .006 MeV (Γ ˂ 20 keV).

Angular distributions of the transitions leading to the above higher isospin states are well described by double stripping theory. Analog correspondences are established by comparing the present results with recent studies (t, p) and (He³, p) reactions on the same targets.

Characterization of birefringence dispersion in polarization-maintaining fibers by use of white-light interferometry

A new method for measuring the birefringence dispersion in polarization-maintaining fibers (PMFs) with high sensitivity and accuracy is presented. The method employs white-light interferences between two orthogonally polarized modes of PMFs. The group birefringence of the fiber is calibrated first. Then the birefringence dispersion and its variation along different fiber sections are acquired by analyzing the broadening of interferograms at different fiber lengths. The main sources of error are investigated. Bireffingence dispersions of two PANDA fibers at their operation wavelength are measured to be 0.011 ps/(km nm) and 0.018 ps/(km nm). A measurement repeatability of 0.001 ps/(km nm) is achieved. (C) 2007 Optical Society of America.

Wavelength dependence of light-induced domain nucleation in MgO-doped congruent LiNbO3 crystal

Within the wavelength range from 351 to 799 nm, the different reductions of nucleation field induced by the focused continuous laser irradiation are achieved in the 5 mol % MgO-doped congruent LiNbO3 crystals. The reduction proportion increases exponentially with decreasing irradiation wavelength and decreases exponentially with increasing irradiation wavelength. At one given wavelength, the reduction proportion increases exponentially with increasing irradiation intensity. An assumption is proposed that the reduction of nucleation field is directly related to the defect structure of crystal lattice generated by the complex coaction of incident irradiation field and external electric field. (c) 2007 American Institute of Physics.

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.

Advanced Monte Carlo Simulation and Machine Learning for Frequency Domain Optical Coherence Tomography

Optical Coherence Tomography(OCT) is a popular, rapidly growing imaging technique with an increasing number of bio-medical applications due to its noninvasive nature. However, there are three major challenges in understanding and improving an OCT system: (1) Obtaining an OCT image is not easy. It either takes a real medical experiment or requires days of computer simulation. Without much data, it is difficult to study the physical processes underlying OCT imaging of different objects simply because there aren't many imaged objects. (2) Interpretation of an OCT image is also hard. This challenge is more profound than it appears. For instance, it would require a trained expert to tell from an OCT image of human skin whether there is a lesion or not. This is expensive in its own right, but even the expert cannot be sure about the exact size of the lesion or the width of the various skin layers. The take-away message is that analyzing an OCT image even from a high level would usually require a trained expert, and pixel-level interpretation is simply unrealistic. The reason is simple: we have OCT images but not their underlying ground-truth structure, so there is nothing to learn from. (3) The imaging depth of OCT is very limited (millimeter or sub-millimeter on human tissues). While OCT utilizes infrared light for illumination to stay noninvasive, the downside of this is that photons at such long wavelengths can only penetrate a limited depth into the tissue before getting back-scattered. To image a particular region of a tissue, photons first need to reach that region. As a result, OCT signals from deeper regions of the tissue are both weak (since few photons reached there) and distorted (due to multiple scatterings of the contributing photons). This fact alone makes OCT images very hard to interpret.

This thesis addresses the above challenges by successfully developing an advanced Monte Carlo simulation platform which is 10000 times faster than the state-of-the-art simulator in the literature, bringing down the simulation time from 360 hours to a single minute. This powerful simulation tool not only enables us to efficiently generate as many OCT images of objects with arbitrary structure and shape as we want on a common desktop computer, but it also provides us the underlying ground-truth of the simulated images at the same time because we dictate them at the beginning of the simulation. This is one of the key contributions of this thesis. What allows us to build such a powerful simulation tool includes a thorough understanding of the signal formation process, clever implementation of the importance sampling/photon splitting procedure, efficient use of a voxel-based mesh system in determining photon-mesh interception, and a parallel computation of different A-scans that consist a full OCT image, among other programming and mathematical tricks, which will be explained in detail later in the thesis.

Next we aim at the inverse problem: given an OCT image, predict/reconstruct its ground-truth structure on a pixel level. By solving this problem we would be able to interpret an OCT image completely and precisely without the help from a trained expert. It turns out that we can do much better. For simple structures we are able to reconstruct the ground-truth of an OCT image more than 98% correctly, and for more complicated structures (e.g., a multi-layered brain structure) we are looking at 93%. We achieved this through extensive uses of Machine Learning. The success of the Monte Carlo simulation already puts us in a great position by providing us with a great deal of data (effectively unlimited), in the form of (image, truth) pairs. Through a transformation of the high-dimensional response variable, we convert the learning task into a multi-output multi-class classification problem and a multi-output regression problem. We then build a hierarchy architecture of machine learning models (committee of experts) and train different parts of the architecture with specifically designed data sets. In prediction, an unseen OCT image first goes through a classification model to determine its structure (e.g., the number and the types of layers present in the image); then the image is handed to a regression model that is trained specifically for that particular structure to predict the length of the different layers and by doing so reconstruct the ground-truth of the image. We also demonstrate that ideas from Deep Learning can be useful to further improve the performance.

It is worth pointing out that solving the inverse problem automatically improves the imaging depth, since previously the lower half of an OCT image (i.e., greater depth) can be hardly seen but now becomes fully resolved. Interestingly, although OCT signals consisting the lower half of the image are weak, messy, and uninterpretable to human eyes, they still carry enough information which when fed into a well-trained machine learning model spits out precisely the true structure of the object being imaged. This is just another case where Artificial Intelligence (AI) outperforms human. To the best knowledge of the author, this thesis is not only a success but also the first attempt to reconstruct an OCT image at a pixel level. To even give a try on this kind of task, it would require fully annotated OCT images and a lot of them (hundreds or even thousands). This is clearly impossible without a powerful simulation tool like the one developed in this thesis.

Theoretical investigations of experimental gravitation

This thesis has two basic themes: the investigation of new experiments which can be used to test relativistic gravity, and the investigation of new technologies and new experimental techniques which can be applied to make gravitational wave astronomy a reality.

Advancing technology will soon make possible a new class of gravitation experiments: pure laboratory experiments with laboratory sources of non-Newtonian gravity and laboratory detectors. The key advance in techno1ogy is the development of resonant sensing systems with very low levels of dissipation. Chapter 1 considers three such systems (torque balances, dielectric monocrystals, and superconducting microwave resonators), and it proposes eight laboratory experiments which use these systems as detectors. For each experiment it describes the dominant sources of noise and the technology required.

The coupled electro-mechanical system consisting of a microwave cavity and its walls can serve as a gravitational radiation detector. A gravitational wave interacts with the walls, and the resulting motion induces transitions from a highly excited cavity mode to a nearly unexcited mode. Chapter 2 describes briefly a formalism for analyzing such a detector, and it proposes a particular design.

The monitoring of a quantum mechanical harmonic oscillator on which a classical force acts is important in a variety of high-precision experiments, such as the attempt to detect gravitational radiation. Chapter 3 reviews the standard techniques for monitoring the oscillator; and it introduces a new technique which, in principle, can determine the details of the force with arbitrary accuracy, despite the quantum properties of the oscillator.

The standard method for monitoring the oscillator is the "amplitude- and-phase" method (position or momentum transducer with output fed through a linear amplifier). The accuracy obtainable by this method is limited by the uncertainty principle. To do better requires a measurement of the type which Braginsky has called "quantum nondemolition." A well-known quantum nondemolition technique is "quantum counting," which can detect an arbitrarily weak force, but which cannot provide good accuracy in determining its precise time-dependence. Chapter 3 considers extensively a new type of quantum nondemolition measurement - a "back-action-evading" measurement of the real part X₁ (or the imaginary part X₂) of the oscillator's complex amplitude. In principle X₁ can be measured arbitrarily quickly and arbitrarily accurately, and a sequence of such measurements can lead to an arbitrarily accurate monitoring of the classical force.

Chapter 3 describes explicit gedanken experiments which demonstrate that X₁ can be measured arbitrarily quickly and arbitrarily accurately, it considers approximate back-action-evading measurements, and it develops a theory of quantum nondemolition measurement for arbitrary quantum mechanical systems.

In Rosen's "bimetric" theory of gravity the (local) speed of gravitational radiation v_g is determined by the combined effects of cosmological boundary values and nearby concentrations of matter. It is possible for v_g to be less than the speed of light. Chapter 4 shows that emission of gravitational radiation prevents particles of nonzero rest mass from exceeding the speed of gravitational radiation. Observations of relativistic particles place limits on v_g and the cosmological boundary values today, and observations of synchrotron radiation from compact radio sources place limits on the cosmological boundary values in the past.

Dynamic response of hysteretic systems with application to a system containing limited slip

A general class of single degree of freedom systems possessing rate-independent hysteresis is defined. The hysteretic behavior in a system belonging to this class is depicted as a sequence of single-valued functions; at any given time, the current function is determined by some set of mathematical rules concerning the entire previous response of the system. Existence and uniqueness of solutions are established and boundedness of solutions is examined.

An asymptotic solution procedure is used to derive an approximation to the response of viscously damped systems with a small hysteretic nonlinearity and trigonometric excitation. Two properties of the hysteresis loops associated with any given system completely determine this approximation to the response: the area enclosed by each loop, and the average of the ascending and descending branches of each loop.

The approximation, supplemented by numerical calculations, is applied to investigate the steady-state response of a system with limited slip. Such features as disconnected response curves and jumps in response exist for a certain range of system parameters for any finite amount of slip.

To further understand the response of this system, solutions of the initial-value problem are examined. The boundedness of solutions is investigated first. Then the relationship between initial conditions and resulting steady-state solution is examined when multiple steady-state solutions exist. Using the approximate analysis and numerical calculations, it is found that significant regions of initial conditions in the initial condition plane lead to the different asymptotically stable steady-state solutions.