Electron microprobe investigations of metamorphic reactions and mineral growth histories, Kwoiek area, British Columbia

The Kwoiek Area of British Columbia contains a pendant or screen of metamorphosed sedimentary and volcanic rocks almost entirely surrounded by a portion of the Coast Range Batholith, and intruded by several dozen stocks. The major metamorphic effects were produced by the quartz diorite batholithic rocks, with minor and later effects by the quartz diorite stocks. The sequence of important metamorphic reactions in the metasedimentary and metavolcanic rocks, ranging in grade from chlorite to sillimanite, is:

1. chlorite + carbonate + muscovite → epidote + biotite

2. chlorite + carbonate → actinolite + epidote

3. chlorite + muscovite → garnet + biotite

4. chlorite + epidote → garnet + hornblende

5. chlorite + muscovite → garnet + staurolite + biotite

6. chlorite + muscovite → aluminum silicate + biotite

7. muscovite + staurolite → garnet + aluminum silicate + biotite

8. staurolite → garnet + aluminum silicate

Continuous reactions, occurring between reactions 5 and 7, are:

A. chlorite + (high Ti) biotite + Al₂O₃ (from plagioclase?)→ garnet + staurolite + (low Ti) biotite + O₂

B. muscovite (phengitic) → garnet + staurolite +muscovite (less phengitic) + O₂ (?)

Detailed electron microprobe work on garnet, staurolite, biotite, and chlorite shows that:

(1) The garnet porphyroblasts are zoned according to a depletion model, called the Rayleigh depletion model, which assumes equilibrium between the edge of a growing garnet and the minerals which are unzoned, notably biotite, chlorite, and muscovite, but which assumes disequilibrium within the garnet.

(2) The staurolite porphyroblasts are also zoned, and from their zoning patterns reactions A, B, and 5 are documented. Progressive reduction of iron with increasing grade of metamorphism is also inferred from the staurolite zoning patterns.

(3) During a late period of falling temperature garnet continued to grow and the biotite and chlorite reequilibrated. The biotite, chlorite, and garnet edge compositions can vary from point to point in a given thin section, indicating that the volume of equilibrium at the final stage of metamorphism was only a few cubic microns.

(4) The horizon within the garnet that grew at maximum temperature can be identified. The Mg/Fe ratio of this horizon, if the garnet composition is a limiting composition in the Al₂O₃ - K₂O - FeO - MgO tetrahedron, increases systematically with increasing metamorphic grade. Biotite and chlorite compositions also show a general increase in Mg/Fe ratio with increasing metamorphic grade, but staurolite appears to show the reverse effect.

(5) The Mg/Fe ratio at the maximum temperature horizon of the garnet porphyroblasts is a function of its Mn content as evidenced from the study of five garnet-bearing rocks, collected from one outcrop area, with the same assemblage but with differing proportions of minerals.

An important implication of zoned minerals is that the effective composition of a system in a phase lies on the join between the homogeneous minerals (if there are two) and not within three-or- four-phase fields when a zoned mineral, such as garnet or staurolite, is present in the assemblage.

Study of the three aluminum silicates found in the Kwoiek Area showed that a constant pressure change in polymorphs from andalusite to kyanite to sillimanite took place with increasing temperature. This transition series is best explained by the metastable formation of andalusite.

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Investigations of secondary organic aerosol formation in laboratory chambers

Secondary organic aerosol (SOA) is produced in the atmosphere by oxidation of volatile organic compounds. Laboratory chambers are used understand the formation mechanisms and evolution of SOA formed under controlled conditions. This thesis presents studies of SOA formed from anthropogenic and biogenic precursors and discusses the effects of chamber walls on suspended vapors and particles.

During a chamber experiment, suspended vapors and particles can interact with the chamber walls. Particle wall loss is relatively well-understood, but vapor wall losses have received little study. Vapor wall loss of 2,3-epoxy-1,4-butanediol (BEPOX) and glyoxal was identified, quantified, and found to depend on chamber age and relative humidity.

Particles reside in the atmosphere for a week or more and can evolve chemically during that time period, a process termed aging. Simulating aging in laboratory chambers has proven to be challenging. A protocol was developed to extend the duration of a chamber experiment to 36 h of oxidation and was used to evaluate aging of SOA produced from m-xylene. Total SOA mass concentration increased and then decreased with increasing photooxidation suggesting a transition from functionalization to fragmentation chemistry driven by photochemical processes. SOA oxidation, measured as the bulk particle elemental oxygen-to-carbon ratio and fraction of organic mass at m/z 44, increased continuously starting after 5 h of photooxidation.

The physical state and chemical composition of an organic aerosol affect the mixing of aerosol components and its interactions with condensing species. A laboratory chamber protocol was developed to evaluate the mixing of SOA produced sequentially from two different sources by heating the chamber to induce particle evaporation. Using this protocol, SOA produced from toluene was found to be less volatile than that produced from a-pinene. When the two types of SOA were formed sequentially, the evaporation behavior most closely represented that of SOA from the second parent hydrocarbon, suggesting that the structure of the mixed SOA particles resembles a core of SOA from the first precursor coated by a layer of SOA from the second precursor, indicative of limiting mixing.

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.

Detailed properties of high redshift galaxies

Galaxies evolve throughout the history of the universe from the first star-forming sources, through gas-rich asymmetric structures with rapid star formation rates, to the massive symmetrical stellar systems observed at the present day. Determining the physical processes which drive galaxy formation and evolution is one of the most important questions in observational astrophysics. This thesis presents four projects aimed at improving our understanding of galaxy evolution from detailed measurements of star forming galaxies at high redshift.

We use resolved spectroscopy of gravitationally lensed z ≃ 2 - 3 star forming galaxies to measure their kinematic and star formation properties. The combination of lensing with adaptive optics yields physical resolution of ≃ 100 pc, sufficient to resolve giant Hii regions. We find that ~ 70 % of galaxies in our sample display ordered rotation with high local velocity dispersion indicating turbulent thick disks. The rotating galaxies are gravitationally unstable and are expected to fragment into giant clumps. The size and dynamical mass of giant Hii regions are in agreement with predictions for such clumps indicating that gravitational instability drives the rapid star formation. The remainder of our sample is comprised of ongoing major mergers. Merging galaxies display similar star formation rate, morphology, and local velocity dispersion as isolated sources, but their velocity fields are more chaotic with no coherent rotation.

We measure resolved metallicity in four lensed galaxies at z = 2.0 − 2.4 from optical emission line diagnostics. Three rotating galaxies display radial gradients with higher metallicity at smaller radii, while the fourth is undergoing a merger and has an inverted gradient with lower metallicity at the center. Strong gradients in the rotating galaxies indicate that they are growing inside-out with star formation fueled by accretion of metal-poor gas at large radii. By comparing measured gradients with an appropriate comparison sample at z = 0, we demonstrate that metallicity gradients in isolated galaxies must flatten at later times. The amount of size growth inferred by the gradients is in rough agreement with direct measurements of massive galaxies. We develop a chemical evolution model to interpret these data and conclude that metallicity gradients are established by a gradient in the outflow mass loading factor, combined with radial inflow of metal-enriched gas.

We present the first rest-frame optical spectroscopic survey of a large sample of low-luminosity galaxies at high redshift (L < L*, 1.5 < z < 3.5). This population dominates the star formation density of the universe at high redshifts, yet such galaxies are normally too faint to be studied spectroscopically. We take advantage of strong gravitational lensing magnification to compile observations for a sample of 29 galaxies using modest integration times with the Keck and Palomar telescopes. Balmer emission lines confirm that the sample has a median SFR ∼ 10 M_sun yr^−1 and extends to lower SFR than has been probed by other surveys at similar redshift. We derive the metallicity, dust extinction, SFR, ionization parameter, and dynamical mass from the spectroscopic data, providing the first accurate characterization of the star-forming environment in low-luminosity galaxies at high redshift. For the first time, we directly test the proposal that the relation between galaxy stellar mass, star formation rate, and gas phase metallicity does not evolve. We find lower gas phase metallicity in the high redshift galaxies than in local sources with equivalent stellar mass and star formation rate, arguing against a time-invariant relation. While our result is preliminary and may be biased by measurement errors, this represents an important first measurement that will be further constrained by ongoing analysis of the full data set and by future observations.

We present a study of composite rest-frame ultraviolet spectra of Lyman break galaxies at z = 4 and discuss implications for the distribution of neutral outflowing gas in the circumgalactic medium. In general we find similar spectroscopic trends to those found at z = 3 by earlier surveys. In particular, absorption lines which trace neutral gas are weaker in less evolved galaxies with lower stellar masses, smaller radii, lower luminosity, less dust, and stronger Lyα emission. Typical galaxies are thus expected to have stronger Lyα emission and weaker low-ionization absorption at earlier times, and we indeed find somewhat weaker low-ionization absorption at higher redshifts. In conjunction with earlier results, we argue that the reduced low-ionization absorption is likely caused by lower covering fraction and/or velocity range of outflowing neutral gas at earlier epochs. This result has important implications for the hypothesis that early galaxies were responsible for cosmic reionization. We additionally show that fine structure emission lines are sensitive to the spatial extent of neutral gas, and demonstrate that neutral gas is concentrated at smaller galactocentric radii in higher redshift galaxies.

The results of this thesis present a coherent picture of galaxy evolution at high redshifts 2 ≲ z ≲ 4. Roughly 1/3 of massive star forming galaxies at this period are undergoing major mergers, while the rest are growing inside-out with star formation occurring in gravitationally unstable thick disks. Star formation, stellar mass, and metallicity are limited by outflows which create a circumgalactic medium of metal-enriched material. We conclude by describing some remaining open questions and prospects for improving our understanding of galaxy evolution with future observations of gravitationally lensed galaxies.

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.