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An in vitro Biomolecular Breadboard for Prototyping Synthetic Biological Circuits
Get PDFBiomolecular circuit engineering is critical for implementing complex functions in vivo, and is a baseline method in the synthetic biology space. However, current methods for conducting biomolecular circuit engineering are time-consuming and tedious. A complete design-build-test cycle typically takes weeks' to months' time due to the lack of an intermediary between design ex vivo and testing in vivo. In this work, we explore the development and application of a "biomolecular breadboard" composed of an in-vitro transcription-translation (TX-TL) lysate to rapidly speed up the engineering design-build-test cycle. We first developed protocols for creating and using lysates for conducting biological circuit design. By doing so we simplified the existing technology to an affordable ($0.03/uL) and easy to use three-tube reagent system. We then developed tools to accelerate circuit design by allowing for linear DNA use in lieu of plasmid DNA, and by utilizing principles of modular assembly. This allowed the design-build-test cycle to be reduced to under a business day. We then characterized protein degradation dynamics in the breadboard to aid to implementing complex circuits. Finally, we demonstrated that the breadboard could be applied to engineer complex synthetic circuits in vitro and in vivo. Specifically, we utilized our understanding of linear DNA prototyping, modular assembly, and protein degradation dynamics to characterize the repressilator oscillator and to prototype novel three- and five-node negative feedback oscillators both in vitro and in vivo. We therefore believe the biomolecular breadboard has wide application for acting as an intermediary for biological circuit engineering
Heteroepitaxy of Group IV and Group III-V semiconductor alloys for photovoltaic applications
Get PDFPhotovoltaic energy conversion represents a economically viable technology for realizing collection of the largest energy resource known to the Earth -- the sun. Energy conversion efficiency is the most leveraging factor in the price of energy derived from this process. This thesis focuses on two routes for high efficiency, low cost devices: first, to use Group IV semiconductor alloy wire array bottom cells and epitaxially grown Group III-V compound semiconductor alloy top cells in a tandem configuration, and second, GaP growth on planar Si for heterojunction and tandem cell applications.
Metal catalyzed vapor-liquid-solid grown microwire arrays are an intriguing alternative for wafer-free Si and SiGe materials which can be removed as flexible membranes. Selected area Cu-catalyzed vapor-liquid solid growth of SiGe microwires is achieved using chlorosilane and chlorogermane precursors. The composition can be tuned up to 12% Ge with a simultaneous decrease in the growth rate from 7 to 1 μm/min-1. Significant changes to the morphology were observed, including tapering and faceting on the sidewalls and along the lengths of the wires. Characterization of axial and radial cross sections with transmission electron microscopy revealed no evidence of defects at facet corners and edges, and the tapering is shown to be due to in-situ removal of catalyst material during growth. X-ray diffraction and transmission electron microscopy reveal a Ge-rich crystal at the tip of the wires, strongly suggesting that the Ge incorporation is limited by the crystallization rate.
Tandem Ga1-xInxP/Si microwire array solar cells are a route towards a high efficiency, low cost, flexible, wafer-free solar technology. Realizing tandem Group III-V compound semiconductor/Si wire array devices requires optimization of materials growth and device performance. GaP and Ga1-xInxP layers were grown heteroepitaxially with metalorganic chemical vapor deposition on Si microwire array substrates. The layer morphology and crystalline quality have been studied with scanning electron microscopy and transmission electron microscopy, and they provide a baseline for the growth and characterization of a full device stack. Ultimately, the complexity of the substrates and the prevalence of defects resulted in material without detectable photoluminescence, unsuitable for optoelectronic applications.
Coupled full-field optical and device physics simulations of a Ga0.51In0.49P/Si wire array tandem are used to predict device performance. A 500 nm thick, highly doped "buffer" layer between the bottom cell and tunnel junction is assumed to harbor a high density of lattice mismatch and heteroepitaxial defects. Under simulated AM1.5G illumination, the device structure explored in this work has a simulated efficiency of 23.84% with realistic top cell SRH lifetimes and surface recombination velocities. The relative insensitivity to surface recombination is likely due to optical generation further away from the free surfaces and interfaces of the device structure.
Finally, GaP has been grown free of antiphase domains on Si (112) oriented substrates using metalorganic chemical vapor deposition. Low temperature pulsed nucleation is followed by high temperature continuous growth, yielding smooth, specular thin films. Atomic force microscopy topography mapping showed very smooth surfaces (4-6 Å RMS roughness) with small depressions in the surface. Thin films (~ 50 nm) were pseudomorphic, as confirmed by high resolution x-ray diffraction reciprocal space mapping, and 200 nm thick films showed full relaxation. Transmission electron microscopy showed no evidence of antiphase domain formation, but there is a population of microtwin and stacking fault defects.</p
Cryogenic Silicon Optical Reference Cavities
Get PDFThermodynamical fluctuations in temperature and position exist in every physical system, and show up as a fundamental noise limit whenever we choose to measure some quantity in a laboratory environment. Thermodynamical fluctuations in the position of the atoms in the dielectric coatings on the mirrors for optical cavities at the forefront of precision metrology (e.g., LIGO, the cavities which probe atomic transitions to define the second) are a current limiting noise source for these experiments, and anything which involves locking a laser to an optical cavity. These thermodynamic noise sources scale physical geometry of experiment, material properties (such as mechanical loss in our dielectric coatings), and temperature. The temperature scaling provides a natural motivation to move to lower temperatures, with a potential huge benefit for redesigning a room temperature experiment which is limited by thermal noise for cryogenic operation.
We design, build, and characterize a pair of linear Fabry-Perot cavities to explore limitations to ultra low noise laser stabilization experiments at cryogenic temperatures. We use silicon as the primary material for the cavity and mirrors, due to a zero crossing in its linear coefficient of thermal expansion (CTE) at 123 K, and other desirable material properties. We use silica tantala coatings, which are currently the best for making high finesse low noise cavities at room temperature. The material properties of these coating materials (which set the thermal noise levels) are relatively unknown at cryogenic temperatures, which motivates us to study them at these temperatures. We were not able to measure any thermal noise source with our experiment due to excess noise. In this work we analyze the design and performance of the cavities, and recommend a design shift from mid length cavities to short cavities in order to facilitate a direct measurement of cryogenic coating noise.
In addition, we measure the cavities (frequency dependent) photo-thermal response. This can help characterize thermooptic noise in the coatings, which is poorly understood at cryogenic temperatures. We also explore the feasibility of using the cavity to do macroscopic quantum optomechanics such as ground state cooling.</p
Advancements in Jet Turbulence and Noise Modeling: Accurate One-Way Solutions and Empirical Evaluation of the Nonlinear Forcing of Wavepackets
Get PDFJet noise reduction is an important goal within both commercial and military aviation. Although large-scale numerical simulations are now able to simultaneously compute turbulent jets and their radiated sound, lost-cost, physically-motivated models are needed to guide noise-reduction efforts. A particularly promising modeling approach centers around certain large-scale coherent structures, called wavepackets, that are observed in jets and their radiated sound. The typical approach to modeling wavepackets is to approximate them as linear modal solutions of the Euler or Navier-Stokes equations linearized about the long-time mean of the turbulent flow field. The near-field wavepackets obtained from these models show compelling agreement with those educed from experimental and simulation data for both subsonic and supersonic jets, but the acoustic radiation is severely under-predicted in the subsonic case. This thesis contributes to two aspects of these models. First, two new solution methods are developed that can be used to efficiently compute wavepackets and their acoustic radiation, reducing the computational cost of the model by more than an order of magnitude. The new techniques are spatial integration methods and constitute a well-posed, convergent alternative to the frequently used parabolized stability equations. Using concepts related to well-posed boundary conditions, the methods are formulated for general hyperbolic equations and thus have potential applications in many fields of physics and engineering. Second, the nonlinear and stochastic forcing of wavepackets is investigated with the goal of identifying and characterizing the missing dynamics responsible for the under-prediction of acoustic radiation by linear wavepacket models for subsonic jets. Specifically, we use ensembles of large-eddy-simulation flow and force data along with two data decomposition techniques to educe the actual nonlinear forcing experienced by wavepackets in a Mach 0.9 turbulent jet. Modes with high energy are extracted using proper orthogonal decomposition, while high gain modes are identified using a novel technique called empirical resolvent-mode decomposition. In contrast to the flow and acoustic fields, the forcing field is characterized by a lack of energetic coherent structures. Furthermore, the structures that do exist are largely uncorrelated with the acoustic field. Instead, the forces that most efficiently excite an acoustic response appear to take the form of random turbulent fluctuations, implying that direct feedback from nonlinear interactions amongst wavepackets is not an essential noise source mechanism. This suggests that the essential ingredients of sound generation in high Reynolds number jets are contained within the linearized Navier-Stokes operator rather than in the nonlinear forcing terms, a conclusion that has important implications for jet noise modeling
Design, Synthesis, and Study of Novel Platforms for Iron-N2 Chemistry and Photoinduced, Copper-mediated C-N Bond Formation
Get PDFSeveral new ligand platforms designed to support iron dinitrogen chemistry have been developed. First, we report Fe complexes of a tris(phosphino)alkyl (CPiPr3) ligand featuring an axial carbon donor intended to conceptually model the interstitial carbide atom of the nitrogenase iron-molybdenum cofactor (FeMoco). It is established that in this scaffold, the iron center binds dinitrogen trans to the Calkyl anchor in three structurally characterized oxidation states. Fe-Calkyl lengthening is observed upon reduction, reflective of significant ionic character in the Fe-Calkyl interaction. The anionic (CPiPr3)FeN2- species can be functionalized by a silyl electrophile to generate (CPiPr3)Fe-N2SiR3. This species also functions as a modest catalyst for the reduction of N2 to NH3. Next, we introduce a new binucleating ligand scaffold that supports an Fe(μ-SAr)Fe diiron subunit that coordinates dinitrogen (N2-Fe(μ-SAr)Fe-N2) across at least three oxidation states (FeIIFeII, FeIIFeI, and FeIFeI). Despite the sulfur-rich coordination environment of iron in FeMoco, synthetic examples of transition metal model complexes that bind N2 and also feature sulfur donor ligands remain scarce; these complexes thus represent an unusual series of low-valent diiron complexes featuring thiolate and dinitrogen ligands. The (N2-Fe(μ-SAr)Fe-N2) system undergoes reduction of the bound N2 to produce NH3 (~50% yield) and can efficiently catalyze the disproportionation of N2H4 to NH3 and N2. The present scaffold also supports dinitrogen binding concomitant with hydride as a co-ligand. Next, inspired by the importance of secondary-sphere interactions in many metalloenzymes, we present complexes of iron in two new ligand scaffolds ([SiPNMe3] and [SiPiPr2PNMe]) that incorporate hydrogen-bond acceptors (tertiary amines) which engage in interactions with nitrogenous substrates bound to the iron center (NH3 and N2H4). Cation binding is also facilitated in anionic Fe(0)-N2 complexes. While Fe-N2 complexes of a related ligand ([SiPiPr3]) lacking hydrogen-bond acceptors produce a substantial amount of ammonia when treated with acid and reductant, the presence of the pendant amines instead facilitates the formation of metal hydride species.
Additionally, we present the development and mechanistic study of copper-mediated and copper-catalyzed photoinduced C-N bond forming reactions. Irradiation of a copper-amido complex, ((m-tol)3P)2Cu(carbazolide), in the presence of aryl halides furnishes N-phenylcarbazole under mild conditions. The mechanism likely proceeds via single-electron transfer from an excited state of the copper complex to the aryl halide, generating an aryl radical. An array of experimental data are consistent with a radical intermediate, including a cyclization/stereochemical investigation and a reactivity study, providing the first substantial experimental support for the viability of a radical pathway for Ullmann C-N bond formation. The copper complex can also be used as a precatalyst for Ullmann C-N couplings. We also disclose further study of catalytic Calkyl-N couplings using a CuI precatalyst, and discuss the likely role of [Cu(carbazolide)2]- and [Cu(carbazolide)3]- species as intermediates in these reactions.
Finally, we report a series of four-coordinate, pseudotetrahedral P3FeII-X complexes supported by tris(phosphine)borate ([PhBP3FeR]-) and phosphiniminato X-type ligands (-N=PR'3) that in combination tune the spin-crossover behavior of the system. Low-coordinate transition metal complexes such as these that undergo reversible spin-crossover remain rare, and the spin equilibria of these systems have been studied in detail by a suite of spectroscopic techniques.</p
Using Earth Deformation Caused by Surface Mass Loading to Constrain the Elastic Structure of the Crust and Mantle
Get PDFSurface mass loads come in many different varieties, including the oceans, atmosphere, rivers, lakes, glaciers, ice caps, and snow fields. The loads migrate over Earth's surface on time scales that range from less than a day to many thousand years. The weights of the shifting loads exert normal forces on Earth's surface. Since the Earth is not perfectly rigid, the applied pressure deforms the shape of the solid Earth in a manner controlled by the material properties of Earth's interior. One of the most prominent types of surface mass loading, ocean tidal loading (OTL), comes from the periodic rise and fall in sea-surface height due to the gravitational influence of celestial objects, such as the moon and sun. Depending on geographic location, the surface displacements induced by OTL typically range from millimeters to several centimeters in amplitude, which may be inferred from Global Navigation and Satellite System (GNSS) measurements with sub-millimeter precision. Spatiotemporal characteristics of observed OTL-induced surface displacements may therefore be exploited to probe Earth structure. In this thesis, I present descriptions of contemporary observational and modeling techniques used to explore Earth's deformation response to OTL and other varieties of surface mass loading. With the aim to extract information about Earth's density and elastic structure from observations of the response to OTL, I investigate the sensitivity of OTL-induced surface displacements to perturbations in the material structure. As a case study, I compute and compare the observed and predicted OTL-induced surface displacements for a network of GNSS receivers across South America. The residuals in three distinct and dominant tidal bands are sub-millimeter in amplitude, indicating that modern ocean-tide and elastic-Earth models well predict the observed displacement response in that region. Nevertheless, the sub-millimeter residuals exhibit regional spatial coherency that cannot be explained entirely by random observational uncertainties and that suggests deficiencies in the forward-model assumptions. In particular, the discrepancies may reveal sensitivities to deviations from spherically symmetric, non-rotating, elastic, and isotropic (SNREI) Earth structure due to the presence of the South American craton
Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry
Get PDFThis thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides
Dynamics of Granular Crystals with Elastic-Plastic Contacts
Get PDFWe study the behavior of granular crystals subjected to impact loading that creates plastic deformation at the contacts between constituent particles. Granular crystals are highly periodic arrangements of spherical particles, arranged into densely packed structures resembling crystals. This special class of granular materials has been shown to have unique dynamics with suggested applications in impact protection. However, previous work has focused on very low amplitude impacts where every contact point can be described using the Hertzian contact law, valid only for purely elastic deformation. In this thesis, we extend previous investigation of the dynamics of granular crystals to significantly higher impact energies more suitable for the majority of applications. Additionally, we demonstrate new properties specific to elastic-plastic granular crystals and discuss their potential applications as well. We first develop a new contact law to describe the interaction between particles for large amplitude compression of elastic-plastic spherical particles including a formulation for strain-rate dependent plasticity. We numerically and experimentally demonstrate the applicability of this contact law to a variety of materials typically used in granular crystals. We then extend our investigation to one-dimensional chains of elastic-plastic particles, including chains of alternating dissimilar materials. We show that, using the new elastic-plastic contact law, we can predict the speed at which impact waves with plastic dissipation propagate based on the material properties of the constituent particles. Finally, we experimentally and numerically investigate the dynamics of two-dimensional and three-dimensional granular crystals with elastic-plastic contacts. We first show that the predicted wave speeds for 1D granular crystals can be extended to 2D and 3D materials. We then investigate the behavior of waves propagating across oblique interfaces of dissimilar particles. We show that the character of the refracted wave can be predicted using an analog to Snell's law for elastic-plastic granular crystals and ultimately show how it can be used to design impact guiding "lenses" for mitigation applications
Two Roads to Planet Detection
Get PDFOne 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.</p
Tectonics of Central and Eastern California, Late Cretaceous to Modern
Get PDFThe Late Cretaceous to Modern tectonic evolution of central and eastern California has been studied for many decades, with published work generally focusing on specific geographic areas and time periods. The resulting literature leaves the reader, whether graduate student, faculty member, or layperson, wondering what a coherently integrated tectonic evolution might look like, or if it would be at all possible to undertake such a task. This question is the common thread weaving together the four studies presented in this work. Each of the individual chapters is targeted at a specific location and time period which I have identified as a critical yet missing link in piecing together a coherent regional tectonic story. In the first chapter, we re-discover a set of major west down normal faults running along the western slope of the southern Sierra, the western Sierra fault system (WSFS). We show that one of these faults was offset by roughly a kilometer in Eocene time, and that this activity directly resulted in the incision of much of the relief present in modern Kings Canyon. The second chapter is a basement landscape and thermochronometric study of the hanging wall of the WSFS. New data from this study area provide a significant westward expansion of basement thermochronometric data from the southern Sierra Nevada batholith. Thermal modeling results of these data provide critical new constraints on the early exhumation of the Sierra Nevada batholith, and in the context of the results from Chapter I, allow us to piece together a coherent chronology of tectonic forcings and landscape evolution for the southern Sierra Nevada. In the third chapter, I present a study of the surface rupture of the 1999 Hector Mine earthquake, a dextral strike slip event on a fault in the Eastern California Shear Zone (ECSZ). New constraints on the active tectonics in ECSZ will help future studies better resolve the enigmatic mismatch between geologic slip rates and geodetically determined regional rates. Chapter IV is a magnetostratigraphic pilot study of the Paleocene Goler Formation. This study provides strong evidence that continued investigation will yield new constraints on the depositional age of the only fossil-bearing Paleocene terrestrial deposit on the west coast of North America. Each of these studies aims to provide important new data at critical missing links in the tectonic evolution of central and eastern California