Two roads to planet detection

One of the most exciting discoveries in astrophysics of the last last decade is of the sheer diversity of planetary systems. These include "hot Jupiters", giant planets so close to their host stars that they orbit once every few days; "Super-Earths", planets with sizes intermediate to those of Earth and Neptune, of which no analogs exist in our own solar system; multi-planet systems with planets smaller than Mars to larger than Jupiter; planets orbiting binary stars; free-floating planets flying through the emptiness of space without any star; even planets orbiting pulsars. Despite these remarkable discoveries, the field is still young, and there are many areas about which precious little is known. In particular, we don't know the planets orbiting Sun-like stars nearest to our own solar system, and we know very little about the compositions of extrasolar planets. This thesis provides developments in those directions, through two instrumentation projects.

The first chapter of this thesis concerns detecting planets in the Solar neighborhood using precision stellar radial velocities, also known as the Doppler technique. We present an analysis determining the most efficient way to detect planets considering factors such as spectral type, wavelengths of observation, spectrograph resolution, observing time, and instrumental sensitivity. We show that G and K dwarfs observed at 400-600 nm are the best targets for surveys complete down to a given planet mass and out to a specified orbital period. Overall we find that M dwarfs observed at 700-800 nm are the best targets for habitable-zone planets, particularly when including the effects of systematic noise floors caused by instrumental imperfections. Somewhat surprisingly, we demonstrate that a modestly sized observatory, with a dedicated observing program, is up to the task of discovering such planets.

We present just such an observatory in the second chapter, called the "MINiature Exoplanet Radial Velocity Array," or MINERVA. We describe the design, which uses a novel multi-aperture approach to increase stability and performance through lower system etendue, as well as keeping costs and time to deployment down. We present calculations of the expected planet yield, and data showing the system performance from our testing and development of the system at Caltech's campus. We also present the motivation, design, and performance of a fiber coupling system for the array, critical for efficiently and reliably bringing light from the telescopes to the spectrograph. We finish by presenting the current status of MINERVA, operational at Mt. Hopkins observatory in Arizona.

The second part of this thesis concerns a very different method of planet detection, direct imaging, which involves discovery and characterization of planets by collecting and analyzing their light. Directly analyzing planetary light is the most promising way to study their atmospheres, formation histories, and compositions. Direct imaging is extremely challenging, as it requires a high performance adaptive optics system to unblur the point-spread function of the parent star through the atmosphere, a coronagraph to suppress stellar diffraction, and image post-processing to remove non-common path "speckle" aberrations that can overwhelm any planetary companions.

To this end, we present the "Stellar Double Coronagraph," or SDC, a flexible coronagraphic platform for use with the 200" Hale telescope. It has two focal and pupil planes, allowing for a number of different observing modes, including multiple vortex phase masks in series for improved contrast and inner working angle behind the obscured aperture of the telescope. We present the motivation, design, performance, and data reduction pipeline of the instrument. In the following chapter, we present some early science results, including the first image of a companion to the star delta Andromeda, which had been previously hypothesized but never seen.

A further chapter presents a wavefront control code developed for the instrument, using the technique of "speckle nulling," which can remove optical aberrations from the system using the deformable mirror of the adaptive optics system. This code allows for improved contrast and inner working angles, and was written in a modular style so as to be portable to other high contrast imaging platforms. We present its performance on optical, near-infrared, and thermal infrared instruments on the Palomar and Keck telescopes, showing how it can improve contrasts by a factor of a few in less than ten iterations.

One of the large challenges in direct imaging is sensing and correcting the electric field in the focal plane to remove scattered light that can be much brighter than any planets. In the last chapter, we present a new method of focal-plane wavefront sensing, combining a coronagraph with a simple phase-shifting interferometer. We present its design and implementation on the Stellar Double Coronagraph, demonstrating its ability to create regions of high contrast by measuring and correcting for optical aberrations in the focal plane. Finally, we derive how it is possible to use the same hardware to distinguish companions from speckle errors using the principles of optical coherence. We present results observing the brown dwarf HD 49197b, demonstrating the ability to detect it despite it being buried in the speckle noise floor. We believe this is the first detection of a substellar companion using the coherence properties of light.

Wide Field-of-view Microscopes and Endoscopes for Time-lapse Imaging and High-throughput Screening

Wide field-of-view (FOV) microscopy is of high importance to biological research and clinical diagnosis where a high-throughput screening of samples is needed. This thesis presents the development of several novel wide FOV imaging technologies and demonstrates their capabilities in longitudinal imaging of living organisms, on the scale of viral plaques to live cells and tissues.

The ePetri Dish is a wide FOV on-chip bright-field microscope. Here we applied an ePetri platform for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm at 30 min intervals. A density-based clustering algorithm is used to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. We also demonstrate the capabilities of the ePetri in viral titer count and dynamically monitoring plaque formation, growth, and the influence of antiviral drugs.

We developed another wide FOV imaging technique, the Talbot microscope, for the fluorescence imaging of live cells. The Talbot microscope takes advantage of the Talbot effect and can generate a focal spot array to scan the fluorescence samples directly on-chip. It has a resolution of 1.2 μm and a FOV of ~13 mm². We further upgraded the Talbot microscope for the long-term time-lapse fluorescence imaging of live cell cultures, and analyzed the cells’ dynamic response to an anticancer drug.

We present two wide FOV endoscopes for tissue imaging, named the AnCam and the PanCam. The AnCam is based on the contact image sensor (CIS) technology, and can scan the whole anal canal within 10 seconds with a resolution of 89 μm, a maximum FOV of 100 mm × 120 mm, and a depth-of-field (DOF) of 0.65 mm. We also demonstrate the performance of the AnCam in whole anal canal imaging in both animal models and real patients. In addition to this, the PanCam is based on a smartphone platform integrated with a panoramic annular lens (PAL), and can capture a FOV of 18 mm × 120 mm in a single shot with a resolution of 100─140 μm. In this work we demonstrate the PanCam’s performance in imaging a stained tissue sample.

Computational microscopy: turning megapixels into gigapixels

The layout of a typical optical microscope has remained effectively unchanged over the past century. Besides the widespread adoption of digital focal plane arrays, relatively few innovations have helped improve standard imaging with bright-field microscopes. This thesis presents a new microscope imaging method, termed Fourier ptychography, which uses an LED to provide variable sample illumination and post-processing algorithms to recover useful sample information. Examples include increasing the resolution of megapixel-scale images to one gigapixel, measuring quantitative phase, achieving oil-immersion quality resolution without an immersion medium, and recovering complex three dimensional sample structure.

Part I. A study of the velocity structure of the earth by the use of core phases. Part II. The 1971 San Fernando earthquake series focal mechanisms and tectonics

The initial objective of Part I was to determine the nature of upper mantle discontinuities, the average velocities through the mantle, and differences between mantle structure under continents and oceans by the use of P'dP', the seismic core phase P'P' (PKPPKP) that reflects at depth d in the mantle. In order to accomplish this, it was found necessary to also investigate core phases themselves and their inferences on core structure. P'dP' at both single stations and at the LASA array in Montana indicates that the following zones are candidates for discontinuities with varying degrees of confidence: 800-950 km, weak; 630-670 km, strongest; 500-600 km, strong but interpretation in doubt; 350-415 km, fair; 280-300 km, strong, varying in depth; 100-200 km, strong, varying in depth, may be the bottom of the low-velocity zone. It is estimated that a single station cannot easily discriminate between asymmetric P'P' and P'dP' for lead times of about 30 sec from the main P'P' phase, but the LASA array reduces this uncertainty range to less than 10 sec. The problems of scatter of P'P' main-phase times, mainly due to asymmetric P'P', incorrect identification of the branch, and lack of the proper velocity structure at the velocity point, are avoided and the analysis shows that one-way travel of P waves through oceanic mantle is delayed by 0.65 to 0.95 sec relative to United States mid-continental mantle.

A new P-wave velocity core model is constructed from observed times, dt/dΔ's, and relative amplitudes of P'; the observed times of SKS, SKKS, and PKiKP; and a new mantle-velocity determination by Jordan and Anderson. The new core model is smooth except for a discontinuity at the inner-core boundary determined to be at a radius of 1215 km. Short-period amplitude data do not require the inner core Q to be significantly lower than that of the outer core. Several lines of evidence show that most, if not all, of the arrivals preceding the DF branch of P' at distances shorter than 143° are due to scattering as proposed by Haddon and not due to spherically symmetric discontinuities just above the inner core as previously believed. Calculation of the travel-time distribution of scattered phases and comparison with published data show that the strongest scattering takes place at or near the core-mantle boundary close to the seismic station.

In Part II, the largest events in the San Fernando earthquake series, initiated by the main shock at 14 00 41.8 GMT on February 9, 1971, were chosen for analysis from the first three months of activity, 87 events in all. The initial rupture location coincides with the lower, northernmost edge of the main north-dipping thrust fault and the aftershock distribution. The best focal mechanism fit to the main shock P-wave first motions constrains the fault plane parameters to: strike, N 67° (± 6°) W; dip, 52° (± 3°) NE; rake, 72° (67°-95°) left lateral. Focal mechanisms of the aftershocks clearly outline a downstep of the western edge of the main thrust fault surface along a northeast-trending flexure. Faulting on this downstep is left-lateral strike-slip and dominates the strain release of the aftershock series, which indicates that the downstep limited the main event rupture on the west. The main thrust fault surface dips at about 35° to the northeast at shallow depths and probably steepens to 50° below a depth of 8 km. This steep dip at depth is a characteristic of other thrust faults in the Transverse Ranges and indicates the presence at depth of laterally-varying vertical forces that are probably due to buckling or overriding that causes some upward redirection of a dominant north-south horizontal compression. Two sets of events exhibit normal dip-slip motion with shallow hypocenters and correlate with areas of ground subsidence deduced from gravity data. Several lines of evidence indicate that a horizontal compressional stress in a north or north-northwest direction was added to the stresses in the aftershock area 12 days after the main shock. After this change, events were contained in bursts along the downstep and sequencing within the bursts provides evidence for an earthquake-triggering phenomenon that propagates with speeds of 5 to 15 km/day. Seismicity before the San Fernando series and the mapped structure of the area suggest that the downstep of the main fault surface is not a localized discontinuity but is part of a zone of weakness extending from Point Dume, near Malibu, to Palmdale on the San Andreas fault. This zone is interpreted as a decoupling boundary between crustal blocks that permits them to deform separately in the prevalent crustal-shortening mode of the Transverse Ranges region.

Fluorescence optofluidic microscopy and fluorescence microscopy based on the Talbot effect

Light microscopy has been one of the most common tools in biological research, because of its high resolution and non-invasive nature of the light. Due to its high sensitivity and specificity, fluorescence is one of the most important readout modes of light microscopy. This thesis presents two new fluorescence microscopic imaging techniques: fluorescence optofluidic microscopy and fluorescent Talbot microscopy. The designs of the two systems are fundamentally different from conventional microscopy, which makes compact and portable devices possible. The components of the devices are suitable for mass-production, making the microscopic imaging system more affordable for biological research and clinical diagnostics.

Fluorescence optofluidic microscopy (FOFM) is capable of imaging fluorescent samples in fluid media. The FOFM employs an array of Fresnel zone plates (FZP) to generate an array of focused light spots within a microfluidic channel. As a sample flows through the channel and across the array of focused light spots, a filter-coated CMOS sensor collects the fluorescence emissions. The collected data can then be processed to render a fluorescence microscopic image. The resolution, which is determined by the focused light spot size, is experimentally measured to be 0.65 μm.

Fluorescence Talbot microscopy (FTM) is a fluorescence chip-scale microscopy technique that enables large field-of-view (FOV) and high-resolution imaging. The FTM method utilizes the Talbot effect to project a grid of focused excitation light spots onto the sample. The sample is placed on a filter-coated CMOS sensor chip. The fluorescence emissions associated with each focal spot are collected by the sensor chip and are composed into a sparsely sampled fluorescence image. By raster scanning the Talbot focal spot grid across the sample and collecting a sequence of sparse images, a filled-in high-resolution fluorescence image can be reconstructed. In contrast to a conventional microscope, a collection efficiency, resolution, and FOV are not tied to each other for this technique. The FOV of FTM is directly scalable. Our FTM prototype has demonstrated a resolution of 1.2 μm, and the collection efficiency equivalent to a conventional microscope objective with a 0.70 N.A. The FOV is 3.9 mm × 3.5 mm, which is 100 times larger than that of a 20X/0.40 N.A. conventional microscope objective. Due to its large FOV, high collection efficiency, compactness, and its potential for integration with other on-chip devices, FTM is suitable for diverse applications, such as point-of-care diagnostics, large-scale functional screens, and long-term automated imaging.

Coupled plasmonic systems and devices : applications in visible metamaterials, nanophotonic circuits, and CMOS imaging

With the size of transistors approaching the sub-nanometer scale and Si-based photonics pinned at the micrometer scale due to the diffraction limit of light, we are unable to easily integrate the high transfer speeds of this comparably bulky technology with the increasingly smaller architecture of state-of-the-art processors. However, we find that we can bridge the gap between these two technologies by directly coupling electrons to photons through the use of dispersive metals in optics. Doing so allows us to access the surface electromagnetic wave excitations that arise at a metal/dielectric interface, a feature which both confines and enhances light in subwavelength dimensions - two promising characteristics for the development of integrated chip technology. This platform is known as plasmonics, and it allows us to design a broad range of complex metal/dielectric systems, all having different nanophotonic responses, but all originating from our ability to engineer the system surface plasmon resonances and interactions. In this thesis, we demonstrate how plasmonics can be used to develop coupled metal-dielectric systems to function as tunable plasmonic hole array color filters for CMOS image sensing, visible metamaterials composed of coupled negative-index plasmonic coaxial waveguides, and programmable plasmonic waveguide network systems to serve as color routers and logic devices at telecommunication wavelengths.

Crustal structure in Southern California from array data

Crustal structure in Southern California is investigated using travel times from over 200 stations and thousands of local earthquakes. The data are divided into two sets of first arrivals representing a two-layer crust. The Pg arrivals have paths that refract at depths near 10 km and the Pn arrivals refract along the Moho discontinuity. These data are used to find lateral and azimuthal refractor velocity variations and to determine refractor topography.

In Chapter 2 the Pn raypaths are modeled using linear inverse theory. This enables statistical verification that static delays, lateral slowness variations and anisotropy are all significant parameters. However, because of the inherent size limitations of inverse theory, the full array data set could not be processed and the possible resolution was limited. The tomographic backprojection algorithm developed for Chapters 3 and 4 avoids these size problems. This algorithm allows us to process the data sequentially and to iteratively refine the solution. The variance and resolution for tomography are determined empirically using synthetic structures.

The Pg results spectacularly image the San Andreas Fault, the Garlock Fault and the San Jacinto Fault. The Mojave has slower velocities near 6.0 km/s while the Peninsular Ranges have higher velocities of over 6.5 km/s. The San Jacinto block has velocities only slightly above the Mojave velocities. It may have overthrust Mojave rocks. Surprisingly, the Transverse Ranges are not apparent at Pg depths. The batholiths in these mountains are possibly only surficial.

Pn velocities are fast in the Mojave, slow in Southern California Peninsular Ranges and slow north of the Garlock Fault. Pn anisotropy of 2% with a NWW fast direction exists in Southern California. A region of thin crust (22 km) centers around the Colorado River where the crust bas undergone basin and range type extension. Station delays see the Ventura and Los Angeles Basins but not the Salton Trough, where high velocity rocks underlie the sediments. The Transverse Ranges have a root in their eastern half but not in their western half. The Southern Coast Ranges also have a thickened crust but the Peninsular Ranges have no major root.