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Cu₂O Heterojunction Photovoltaics
Get PDFCuprous oxide (Cu2O) is an earth abundant semiconductor that has several promising photovoltaic properties, including high absorption in the visible range, high minority carrier diffusion length, and high majority carrier mobility. Cu2O can be easily synthesized by oxidation of copper foils in air. One important advantage that makes Cu2O highly relevant to today's solar cell markets dominated by crystalline silicon is its wide bandgap of 1.9 eV at room temperature, which makes it an ideal candidate for a top cell in tandem with a crystalline silicon bottom cell. The detailed balance efficiency of such a device exceeds 44%.
In this work we aim to understand and address several issues that have limited Cu2O solar cell efficiency. We address the intrinsic p-type nature and chemical instability of Cu2O by pairing it with an appropriate n-type heterojunction partner Zn(O,S), which allows us to achieve devices with open circuit voltages exceeding 1 V. We identify presence of a current blocking layer and reduce it, which results in more than doubling the short circuit current to exceed 5 mA/cm2. Light beam induced current measurements highlight some of the issues inherent to polycrystalline Cu2O solar cells, including grain dependent collection and current losses due to presence of grain boundaries.
In order to address the issues affecting Cu2O made by thermal oxidation we also develop thin film growth of Cu2O by molecular beam epitaxy on several substrates including MgO and heteroepitaxial noble metal templates that act as ohmic back contacts. These studies culminate in achievement of the first Cu2O/Zn(O,S) solar cells incorporating an absorber layer grown by molecular beam epitaxy
Mating at Advanced Age: How Old Nematodes Modulate Pheromone Production to Attract Young Males
Get PDFNematodes have been studied for centuries in their roles as pathogens of humans, crops, and livestock. In more recent times, the free-living nematode Caenorhabditis elegans and its close relatives have been heavily studied as genetic and developmental model organisms. Despite the extent of research into nematode biology and lifestyle, relatively little is known about communication between nematodes. In the last decade, there has been a burst of research into identifying the pheromones secreted by nematodes, as well as determining their effect on other nematodes in the population.
The bulk of pheromone research has focused on the chemical identification of olfactory signals, and studying the behavioral and physiological responses of worms exposed to these signals. We report the discovery of a new C. elegans mating pheromone, and an attempt to dissect the pathway that regulates its production. Instead of studying what a worm “hears” when this signal is received, we hope to understand what the worm that produces the signal is trying to “say”.
We also review the existing literature on nematode mating pheromones, highlighting the most stunning recent discoveries, and point out several questionable claims frequently made by authors in the field.</p
Blackbox Reconstruction of Depth Three Circuits with Top Fan-In Two
Get PDFReconstruction of arithmetic circuits has been heavily studied in the past few years and has connections to proving lower bounds and deterministic identity testing. In
this thesis we present a polynomial time randomized algorithm for reconstructing ΣΠΣ(2) circuits over characteristic zero fields F i.e. depth−3 circuits with fan-in 2 at the top addition gate and having coefficients from a field of characteristic zero.
The algorithm needs only a black-box query access to the polynomial f ∈ F[x1,...,xn] of degree d, computable by a ΣΠΣ(2) circuit C. In addition, we assume that the
"simple rank" of this polynomial (essential number of variables after removing the g.c.d. of the two multiplication gates) is bigger than a fixed constant. Our algorithm runs in time polynomial in n and d and with high probability returns an equivalent ΣΠΣ(2) circuit.
The problem of reconstructing ΣΠΣ(2) circuits over finite fields was first proposed by Shpilka [27]. The generalization to ΣΠΣ(k) circuits, k = O(1) (over finite
fields) was addressed by Karnin and Shpilka in [18]. The techniques in these previous involve iterating over all objects of certain kinds over the ambient field and thus
the running time depends on the size of the field F. Their reconstruction algorithm uses lower bounds on the lengths of linear locally decodable codes with 2 queries.
In our setting, such ideas immediately pose a problem and we need new techniques.
Our main techniques are based on the use of quantitative Sylvester Gallai theorems from the work of Barak et.al. [3] to find a small collection of "nice" subspaces to
project onto. The heart of this work lies in subtle applications of the quantitative Sylvester Gallai theorems to prove why projections w.r.t. the "nice" subspaces can
be ”glued”. We also use Brill’s equations from [9] to construct a small set of candidate linear forms (containing linear forms from both gates). Another important
technique which comes very handy is the polynomial time randomized algorithm for factoring multivariate polynomials given by Kaltofen [17].</p
Mapping mRNA and Protein Expression with High Signal-to-Background in Diverse Organisms
Get PDFIn situ hybridization (ISH) techniques allow for the study of the nucleic acid expression within whole biological samples. The quality of probes for ISH dictates how accurate and bright the signal is for the experiment; however, there is currently not a systematic way to determine what the best probe set would be. In response to this, we have developed a framework to optimize an ISH probe set to achieve the greatest signal-to-background ratio. As methods like ISH help obtain more information about biological processes, there is a growing desire to simultaneously analyze various targets within the same sample to examine these complex genetic interactions. To facilitate this, a novel amplification technique called hybridization chain reaction (HCR) has allowed for the in situ detection of multiple target mRNAs concurrently in zebrafish embryos. We have now expanded this technology further by adapting HCR amplification for ISH to other model organisms, particularly, whole mount Drosophila melanogaster embryos and formalin-fixed parafin-embedded human tissue sections. Beyond looking at mRNA, immunohistochemistry (IHC) provides another tool to understand biological systems by analyzing protein expression patterns. The ability to easily look at both mRNAs and proteins in the same sample offers significant advantages as each provides unique information, but current methods are technically difficult and labor intensive. In response, we have engineered a scheme to use HCR to amplify signal for IHC. We then used this advancement to develop a straightforward protocol using HCR amplification for simultaneous detection of multiple proteins and mRNAs with a high signal-to-background ratio
Development of Chemoenzymatic Labeling Approaches for the Detection of Fucosylated Biomarkers
Get PDFProtein fucosylation regulates a diverse set of physiological functions such as memory and learning, development, and disease pathogenesis. However, our current understanding of these processes is far behind that of other post-translational modifications, such as phosphorylation. This is, in part, due to the lack of tools available for the study of this important protein modification. To address this need, I have developed novel chemoenzymatic methods that enable the labeling and detection of unique forms of fucosylation, specifically fucose-α(1-2)-galactose (Fucα(1-2)Gal) and core fucose. Additionally, novel glycosyltransferase assays were developed in-house to aid in the future development of both new and existing chemoenzymatic approaches.
I have demonstrated that the approach to detect Fucα(1-2)Gal is highly selective for this disaccharide motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of this motif on live cells, discriminating malignant from normal cells. I have also shown that the chemoenzymatic detection of core fucose exhibits superior specificity towards this glycan on a variety of complex N-glycans and when compared to current fucose-specific lectins. Further, the approach is amenable to detection of core fucosylated glycans from multiple biological settings, can be exploited as an antibody-conjugation method, and can be integrated into a diagnostic platform for the profiling of protein specific core fucosylation levels. These approaches represent new potential strategies for biomarker identification and expand the technologies available for understanding the role of these important fucosylated glycans in physiology and disease.</p
Mechanisms of Regulation and Fidelity in Tail-Anchored Membrane Protein Targeting
Get PDFAccurate protein localization is crucial to generate and to maintain cellular organization. Achieving accuracy is challenging, as the molecular signals that dictate a protein’s destination are often promiscuous. The localization of tail-anchored (TA) proteins, whose transmembrane domain resides at its extreme C-terminus, presents major challenges to protein targeting machineries. This dissertation explores how TA capture and release are spatially and temporally regulated in the Guided Entry of Tail Anchored proteins (GET) pathway and how endoplasmic reticulum (ER) destined TAs are targeted with high fidelity.
A quantitative framework of the Get3 ATPase cycle reveals that ATP and GET pathway effector proteins specifically induce multiple conformational changes in Get3, which culminate in the ATPase activation that drives unidirectional targeting in the pathway. The Get4/5 TA loading complex locks Get3 in the ATP-bound state that is primed for TA protein capture, whereas the TA substrate induces tetramerization of Get3 and activates its ATPase reaction.
Additional analyses define multiple physicochemical features that distinguish TA proteins destined to different organelles. The GET pathway selects for these features at distinct stages using mechanisms such as differential binding, induced fit, and kinetic proofreading after ATP hydrolysis by Get3. These results reveal new roles for the cochaperone Sgt2 in providing key selection filters, and provide a biological logic for the complex cascade of substrate relay events during post-translational membrane protein targeting.</p
Numerical Simulations of Droplet Aerobreakup
Get PDFThe work presented in this thesis aims to bridge an existing gap in the state of droplet aerobreakup knowledge associated with the fundamental flow physics that govern the experimentally observable droplet morphologies. Using direct numerical simulations of the aerobreakup of water cylinders and droplets in the flow behind shock waves in air, we investigate the behavior of the surrounding gas flow to gain insight into the droplet’s deformation and evolution in the stripping breakup regime. The compressible multicomponent Navier-Stokes equations are solved using the Multicomponent Flow Code — a high-order accurate structured finite-volume flow solver with shock- and interface-capturing. Following qualitative descriptions of the aerobreakup process, comparisons are made with available experimental data. In 2D, accurate measurements of the cylinder’s center-of-mass acceleration across a range of incident shock Mach numbers allow characterization of the unsteady drag coefficient. Additionally, mass loss measurements from viscous simulations refute a well-known boundary layer stripping theory. The results of a 3D nonaxisymmetric aerobreakup simulation are presented with an emphasis on describing the intricate flow phenomena observable in the wake region. Subsequent analyses of the surface instabilities and a Fourier decomposition of the flow field reveal asymmetrical azimuthal modulations and broadband instability growth that result in the devolution of the wake region into chaotic flow
Optical Phase Conjugation and Its Applications in Biology
Get PDFOptical phase conjugation is a process where an incoming electromagnetic wave is reflected with a reversed phase. The propagation direction of an incoming beam (equivalently, local phase gradient) can thereby be precisely reversed by the phase conjugate beam. This intriguing effect, so called "time-reversal of electromagnetic waves," allows cancellation of spatial distortion introduced into the incoming beam. Recently, this concept has provided a new avenue to overcome or utilize random scattering in the field of biophotonics.
This thesis discusses a number of interrelated topics regarding optical phase conjugation and its applications in biology. First, two examples of exploiting optical phase conjugation for light focusing are presented. The first example shows that the axial resolution can be improved based on the counter-propagating property of the phase-conjugate beam, and the second example demonstrates how the random scattering media can be used to enhance the flexibility in focusing range. We then discuss a new class of techniques that involves the use of guidestars in the phase conjugation process for deep tissue (> 1mm) light focusing and imaging. In the context of in vivo application, we model and estimate the penetration depth limit of one prominent example of this approach, time-reversed ultrasonically encoded (TRUE) optical focusing. Based on the analysis, we show that the iteration of phase conjugation operation can improve the contrast and resolution of the focal spot created inside deep tissue. We also present a new kind of guidestar-assisted method, time-reversed ultrasound microbubble encoded (TRUME) light focusing, which can focus light with sub-ultrasound wavelength resolution. At last, the effect of dynamic scatterers on time-reversal fidelity is studied to explore the possibility of applying the optical phase conjugation techniques in living tissue.</p
Carbonate-Associated Microbial Ecology at Methane Seeps: Assemblage Composition, Response to Changing Environmental Conditions, and Implications for Biomarker Longevity
Get PDFMethane seeps are globally distributed geologic features in which reduced fluid from below the seafloor is advected upward and meets the oxidized bottom waters of Earth’s oceans. This redox gradient fuels chemosynthetic communities anchored by the microbially-mediated anaerobic oxidation of methane (AOM). Both today and in Earth’s past, methane seeps have supported diverse biological communities extending from microorgansisms to macrofauna and adding to the diversity of life on Earth. Simultaneously, the carbon cycling associated with methane seeps may have played a significant role in modulating ancient Earth’s climate, particularly by acting as a control on methane emissions.
The AOM metabolism generates alkalinity and dissolved inorganic carbon (DIC) and at a 2:1 ratio, promoting the abiogenic, or authigenic, precipitation of carbonate minerals. Over time, these precipitates can grow into pavements covering hundreds of square meters on the seafloor and dominating the volumetric habitat space available in seep ecosystems. Importantly, carbonates are incorporated into the geologic record and therefore preserve an inorganic (i.e., d13C) and organic (i.e., lipid biomarker) history of methane seepage. However, the extent to which preserved biomarkers represent a snapshot of microorganisms present at the time of primary precipitation, a time-integrated history of microbial assemblages across the life cycle of a methane seep, or a view of the final microorganisms inhabiting a carbonate prior to incorporation in the sedimentary record is unresolved.
This thesis addresses the ecology of carbonate-associated seep microorganisms. Chapters One and Two contextualize the extant microbial diversity on seep carbonates versus within seep sediments, as determined through 16S rRNA gene biomarkers. Small, protolithic carbonate “nodules” recovered from within seep sediments are observed to be capable of capturing surrounding sediment-hosted microbial diversity, but in some cases also diverge from sediments. Meanwhile, lithified carbonate blocks recovered from the seafloor host microbial assemblages demonstrably distinct from seep sediments (and seep nodules). Microbial 16S rRNA gene diversity within carbonate samples is well-differentiated by the extent of contemporary seepage. In situ seafloor transplantation experiments further demonstrated the microbial assemblages associated with seep carbonates to be sensitive to seep quiescence and activation on short (13-month) timescales. This was particularly true for organisms whose 16S rRNA genes imply physiologies dependent on methane or sulfur oxidation. With an improved understanding of the modern ecology of carbonate-associated microorganisms, Chapter Three applies intact polar lipid (IPL) and core lipid analyses to begin describing whether, and to what extent, geologically relevant biomarkers mimic short-term dynamics observed in 16S rRNA gene profiles versus archive a record of historic microbial diversity. Biomarker longevity is determined to increase from 16S rRNA genes to IPLs to core lipids, with IPLs preserving microbial diversity history on timescales more similar to 16S rRNA genes than core lipids. Ultimately, individual IPL biomarkers are identified which may be robust proxies for determining whether the biomarker profile recorded in a seep carbonate represents vestiges of active seepage processes, or the profile of a microbial community persisting after seep quiescence.</p
Shock Wave Propagation in Composites and Electro-Thermomechanical Coupling of Ferroelectric Materials
Get PDFHow is material behavior at the macro scale influenced by its properties and structure at the micro and meso-scales? How do heterogeneities influence the properties and the response of a material? How does nonlinear coupling of electro-thermo-mechanical properties influence the behavior of a ferroelectric material? How can design at the micro-scale be exploited to obtain selective response? These questions have been topics of significant interest in the materials and mechanics community. Recently, new materials like multifunctional composites and metamaterials have been developed, targeted at selective applications. These materials find applications in areas like energy harvesting, damage mitigation, biomedical devices, and various aerospace applications. The current thesis explores these questions with two major thrusts: (i) internal reflects of shocks in composite media and (ii) shocks in ferroelectric media.
Under the application of high-pressure, high strain rate loading, such as during high velocity impact, shock waves are generated in the material. They can cause the material to achieve very high stress states, and if transmitted without mitigation, can lead to failure of key components. An important question here is 'Can we design materials which can successfully mitigate damage due to shocks?' In a heterogeneous material, like a layered composite, the traveling waves undergo scattering due to internal reflections. In order to understand internal reflections, an idealized problem that focuses on nonlinear shocks and ignores less important elastic waves was formulated and studied in detail. The problem is studied by classifying all possible interactions in the material and then solving corresponding Riemann problems. Using dynamic programming tools, a new algorithm is designed that uses these solutions to generate a complete picture of the impact process. Different laminate designs are explored to study optimal design, by varying individual layer properties and their arrangement. Phenomena like spallation and delamination are also investigated.
Upon high strain rate loading, ferroelectric materials like lead zirconate titanate (PZT) undergo ferroelectric to anti-ferroelectric phase transition leading to large pulsed current output. These materials have thus found applications as pulsed power generators. The problem of shock induced depolarization and the associated electro-thermo-mechanical coupling of ferroelectric materials is studied in this thesis using theoretical and numerical methods. A large deformation dynamic analysis of such materials is conducted to study phase boundary propagation in the medium. The presence of high electrical fields can lead to formation of charges in the material, such as surface charge on the phase boundary. Using conservation laws and the second law of thermodynamics, a set of governing equations are formulated that dictate the phase boundary propagation in isothermal and adiabatic environments. Due to the possibility of surface charges on the phase boundary, the curvature of the phase boundary starts to play a role in the driving force acting on the phase boundary. The equations of motion and driving force see the contribution of nonlinear electro-thermomechanical coupling in the material. Using the equations derived, a canonical problem of impact on a ferroelectric material is studied. A new finite-volume, front-tracking method is developed to solve these equations. Finally, results from numerical simulations are compared to the experimental results.</p