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Efficient Coupling of Tapered Optical Fibers to Silicon Nanophotonic Waveguides on Rare-Earth Doped Crystals
Get PDFQuantum networks are a rapidly developing field of quantum information processing that have the potential to enable long-range entanglement between future quantum computers as well as the implementation of secure communication through quantum key distribution. Two key components of such networks are quantum memories to store entangled photon pairs for use in the quantum repeater protocol and quantum light-matter interfaces to efficiently interconvert between stationary qubits and flying qubits in the form of photons. Rare-earth ion-doped crystals are a promising solid-state platform that show promise for both of these applications due to their long optical and spin coherence times. Due to their relatively weak optical transitions, rare-earth ions have been coupled with nanophotonic resonators to enhance their transition strengths, with past work in the Faraon group utilizing focused ion beam milled photonic crystal resonators with 45-degree angled couplers to couple light in and out. Such resonators have the disadvantage of requiring manual alignment to fabricate, and the couplers are also relatively inefficient which limits the performance of such devices. It is therefore desirable to move towards silicon photonics, where mature techniques such as electron-beam lithography can allow for scalable fabrication of nanophotonic cavities together with high coupling efficiencies.
In this thesis, we demonstrate significant progress towards the usage of acid-etched tapered optical fibers as an efficient interface for coupling light into tapered silicon nanophotonic waveguides. We show comprehensive simulations of the taper geometries required to achieve adiabatic coupling with theoretical efficiencies of more than 99%, and design a silicon photonic crystal mirror to be used in the measurement of the fiber-waveguide coupling efficiency. We then optimize the hydrofluoric acid fiber etching process and demonstrate the ability to make tapered fibers which are 200 microns long with a taper half-angle of 2 degrees and a tip diameter of 50 nm. Using these tapered fibers to couple light into tapered silicon waveguides fabricated using electron-beam lithography shows a moderately high coupling efficiency of 11.4% with the potential for improvement. This method of tapered fiber coupling shows promise to be integrated into silicon nanophotonic resonators on rare-earth ion doped crystals and allow for highly efficient quantum memories and quantum light-matter interfaces in the solid-state.</p
Unconventional Approaches to Structured Semiconductors
Get PDFThe function of semiconductor devices is intrinsically tied to their structure. While there are already myriad techniques in use today to fabricate an extreme diversity of devices, new processes are regularly developed to make the production of previously unrealizable structures, and consequently devices, possible.
This dissertation deals with several unconventional approaches to generating ordered semiconductor structures. One chapter discusses a novel technique to measure the various forces that impede the alignment of randomly dispersed microstructures. The technique made it possible to both determine the magnitude of the interactions that the particles must overcome in order to be organized into a useful structure and assess the functional form of the forces that the microstructure is experiencing, thereby giving insight into the physical origin of said forces.
The following chapter deal with the spontaneous structure formation seen in photoelectrodeposited semiconductor films. One chapter investigates how the natural tendency of these films to form oriented, high aspect ratio structures can be coupled to the geometry of the substrate on which they are grown. This work demonstrates that extremely straight, high aspect ratio structures can be grown over macroscopic areas by making simple modifications of the substrate.
The final chapter characterizes the iridescence that these films exhibit. A simple physical explanation for the origin of the coloration is posited and verified. Then the information gleaned about the optical response of these films is used to generate vibrant, colorful patterns on electrode using consumer electronics.</p
From Single-Cell to Whole-Body: Developing a Molecular Neuroscience Toolkit
Get PDFThroughout my Ph.D. I have worked on technology development, at first to answer basic scientific questions and eventually for therapeutic applications. This technology development applied to a variety of fields, from neuroscience to development to gene therapy, and acted upon biological systems in a wide range of scale, from the single-cell monitoring to organism-wide gene-transfer. My graduate research began with the engineering of microbial rhodopsin spectral properties and fluorescence. By making use of their ability to absorb light and emit fluorescence in a voltage-dependent manner, I aimed to interrogate neuronal activity during behavior at the single-cell level. That line of research ended with publication of the voltage-sensor Archer, which I used to track activity of a single cell in vivo in awake, behaving worms. I then shifted from tracking activity at the single cell level, to visualizing entire organisms, by developing clearing techniques that enable a high-resolution, three-dimensional analysis of a diverse range of tissues. I began by optimizing tissue-clearing parameters for various tissue types and a wide variety of experimental needs. I then took that knowledge and applied it to visualizing and tracking the developing neural crest in cleared, whole-mount chicken embryos, discovering some unexpected derivates. Finally, I became interested not only in visualizing entire organisms, but in developing technologies to facilitate gene transfer throughout the body. The rapidly growing field of gene therapy is in constant need of new tools that target specific tissues, avoiding off-target effects. The end of my Ph.D. has been spent engineering viruses that can be delivered body-wide, but target only specific areas of therapeutic interest, like the brain and lungs.</p
Light Management in Photovoltaics and Photoelectrochemical Cells using Tapered Micro and Nano Structures
Get PDFEnhancing the efficiency and reducing the cost of solar photovoltaic (PV) systems is critical for increasing their penetration into energy generation market. The intermittency of energy generation from such systems due to diurnal, seasonal, and weather-related variation of sunlight limits them to low capacity factors (typically ~ 25%). Therefore, despite the cost of electricity from solar PV systems being cost competitive, further reductions are necessary to incorporate storage and increase the fraction of solar energy in total energy generation. An integrated photoelectrochemical (PEC) system that can generate fuel directly from sunlight could potentially reduce the balance of systems cost that dominates current PV systems, and provide an alternative way for energy storage. PEC systems are currently in research stage.
In this work conical and triangular micro-nano structures are utilized to explore optical solutions for maximizing the light absorption and therefore enhancing the efficiencies of both PV and PEC systems. Silicon (Si) based micro conical arrays demonstrate < 1 % Spectrum-and-Angle-Averaged reflection, and absorption nearing ray optic light trapping limit in a 20 µm effectively thick Si substrates. Si microcone based photocathodes prepared for performing hydrogen evolution reaction (HER) show that thick layers of light blocking Pt and Co-P catalysts can be incorporated with only a 6 % photocurrent loss. The light trapping properties of Si micro-cones are a result of efficient coupling of light to available waveguide modes in a conical geometry. Alternatively, TiO2 based dielectric nano-conical arrays are shown to couple the light to waveguide modes and transmit the light into a planar Si substrate despite covering 54 % of the planar front surface with a light blocking Ni catalyst as an alternative way of light trapping without texturing the light absorber.
Triangular silver (Ag) front contacts in place of conventional flat contacts over PV cells are shown as another alternative for reducing front contact reflection losses and enhancing the efficiency by ~ 1% in Si heterojunction solar cells. These structures are implemented using a polymer stamp prepared from a Si master with triangular groves, and by flowing Ag ink through them. A Si master fabrication method is shown for fabrication of multiple configurations of triangular Ag contacts which can potentially be applied to other PV and PEC systems to enhance their efficiency.</p
Engineering Heme Proteins for Olefin and Carbon−Hydrogen Bond Functionalization Reactions
Get PDFOne of the most important challenges in chemistry is the creation of new catalysts. Nature excels at this: constructed from biologically available elements, enzymes are versatile catalysts which adapt quickly to changing environments in order to sustain life. The combination of adaptable proteins with abiological reagents from synthetic chemistry affords a new direction for catalyst development. This thesis describes new enzymes, derived from a cytochrome P450 monooxygenase, which catalyze nitrogen and carbon atom transfer reactions to olefins and carbon−hydrogen bonds. Chapter 1 introduces directed evolution, a strategy for the laboratory optimization of proteins, in the context of improving metalloproteins for their native catalysis or for new reactions. Chapter 2 details the development of an enzyme-catalyzed transformation of olefins to aziridines, a valuable motif which is both present in bioactive molecules and used as a versatile building block for synthesis. This study establishes that when provided the appropriate reagents (e.g. styrenes and tosyl azide), heme proteins can adopt a nitrene transfer catalytic cycle to form aziridine products and that the turnover and selectivity of the catalyst can be optimized through mutation of its amino acid sequence. The activity of heme protein catalysts is extended to the functionalization of sp3 hybridized C−H bonds for carbon–nitrogen and carbon–carbon bond formation through nitrene and carbene insertion respectively (Chapters 3 and 4). With the exception of C−H oxygenation chemistry, iron complexes are under-utilized for sp3 C−H functionalization reactions, despite iron being readily available and non-toxic. Combining previously engineered heme proteins with suitable substrates led to initial reaction discovery. Directed evolution of these enzymes significantly improved their C−H functionalization activity (by 140-fold in Chapter 4). Characterization of evolved enzymes, including the attainment of an X-ray crystal structure (Chapter 3) and substrate scope studies (Chapters 3 and 4), were pursued. In sum, the thesis work addresses both the biological question of expanding the catalytic capabilities of existing enzymes through mutation and expands the chemistry of iron-porphyrin catalysts
Numerical Relativity Beyond General Relativity
Get PDFEinstein’s theory of general relativity has passed all precision tests to date. At some length scale, however, general relativity (GR) must break down and be reconciled with quantum mechanics in a quantum theory of gravity (a beyond-GR theory). Binary black hole mergers probe the non-linear, highly dynamical regime of gravity, and gravitational waves from these systems may contain signatures of such a theory. In this thesis, we seek to make gravitational wave predictions for binary black hole mergers in a beyond-GR theory. These predictions can then be used to perform model-dependent tests of GR with gravitational wave detections.
We make predictions using numerical relativity, the practice of precisely numerically solving the equations governing spacetime. This allows us to probe the behavior of a binary black hole system through full inspiral, merger, and ringdown. We choose to work in dynamical Chern-Simons gravity (dCS), a higher-curvature beyond-GR effective field theory that couples spacetime curvature to a scalar field, and has motivations in string theory and loop quantum gravity. In order to obtain a well-posed initial value formalism, we perturb this theory around GR. We compute the leading-order behavior of the dCS scalar field in a binary black hole merger, as well as the leading-order dCS correction to the spacetime metric and hence gravitational radiation. We produce the first numerical relativity beyond-GR waveforms in a higher-curvature theory of gravity.
This thesis contains additional results, all of which harness the power of numerical relativity to test GR. We compute black hole shadows in dCS gravity, numerically prove the leading-order stability of rotating black holes in dCS gravity, and lay out a formalism for determining the start time of binary black hole ringdown using information from the strong-field region of a binary black hole simulation.</p
Stereoselective Synthesis of Diazaheterocycles by Decarboxylative Asymmetric Allylic Alkylation
Get PDFThe Stoltz group has developed transition-metal catalyzed methods to synthesize quaternary and tetrasubstituted stereocenters over the past fourteen years. Using iridium, palladium, copper, and nickel, the group has synthesized a myriad cyclic and acylic quaternary motifs of incredible synthetic and medicinal utility. This thesis presents several projects that further expand the scope of Pd-catalyzed decarboxylative allylic alkylation and examine its applications to the synthesis of medicinally important small molecules. The synthesis of chiral gem-disubstituted five-, six-, and seven-membered diazaheterocycles is presented. Their utility as building blocks for complex medicinal compounds is highlighted. Then, we explore the utility of gem-disubstituted heterocycles in the context of medicinal chemistry.</p
Noncovalent Interactions of Silent Agonists Binding to the Nicotinic Acetylcholine Receptor -and- Investigation into Expanding the Substrate Scope and Improving the Efficiency of Organic Photochemical Protecting Groups
Get PDFThis dissertation describes two very different projects. The first project focuses on the binding of a silent agonist to a ligand gated ion channel. The second project focuses on the study of development of new longer wavelength photolabile protecting groups for use in a biological setting to enable the spatially and temporally controlled release of biologically active small molecules.
Chapter I introduces ligand gated ion channels and in particular a model of agonist binding at the nicotinic acetylcholine receptor. In addition, the nonsense suppression methodology used to incorporate the non-canonical amino acids required to probe non-covalent binding interactions is detailed. The second chapter details the use of non-canonical amino acids to study the binding of silent agonist NS6740 at the nicotinic acetylcholine receptor α7 subunit and the discovery of a novel hydrogen bond that modulates silent agonist activity.
Chapters III, IV and V focus on efforts to expand the scope of photolabile protecting groups towards designing longer wavelength derivatives. Chapter III introduces the topic of photoremovable protecting groups and details the mechanist background of a quinone methide based photochemical protecting group.
The fourth chapter investigates the use of quinoline and quinolinium derivatives as photochemical quinone methide precursors. Two quinoline derivatives were found to form a quinone methide transient when irradiated. Quinolinium derivatives proved photostable, most likely due to the electron withdrawing nature of the quinolinium.
The final chapter details efforts to improve the photochemical reaction efficiency of quinone photoreduction by using a radical decarboxylation strategy to trap the charge transfer state. Synthesis of two glycine containing quinone compounds is detailed and their photochemistry is evaluated. Both proved to be photostable.</p
Mechanisms of Co-Translational Protein Targeting by Mammalian SRP
Get PDFProper biogenesis of nascent protein is essential for cell survival. Signal recognition particle (SRP) is an essential and universally conserved factor involved in biogenesis of ~30% of the proteome through co-translational targeting of nascent proteins to Endoplasmic Reticulum (ER). Despite its importance, the mechanisms by which eukaryotic SRP ensure selective and efficient delivery of substrates to ER is poorly understood. Here, we reconstituted human SRP and SRP receptor (SR) to study the interaction between human SRP and SR, and conformational dynamics of SRP and SRP-SR targeting complex through biochemical and biophysical methods. We find that signal sequence and ribosomal components of the substrate sequentially activate human SRP. Especially, presence of signal sequence pre-organizes SRP conformation for efficient recruitment of SR, allowing specific and efficient targeting. In addition, we discover two essential roles of a conformational change in SR, where it is required not only for brining targeting complex near the ER membrane, but also for inducing subsequent conformational changes of SRP-SR complex that ensures proper delivery of substrates to Sec61 translocon on ER membrane.</p
Structural and Biochemical Studies of Enzymes in Bacterial Glycobiology
Get PDFThe speed that bacterial pathogens gain resistance to antibiotics is alarming. Designing new antibacterial agents is urgent, but it requires understanding their bacterial targets at the molecular level to achieve high specificity and potency. In this thesis, I discuss the structural and biochemical investigations of three potential protein targets for antibiotics. The first is a UDP-Glc/GlcNAc 4-epimerase, called Gne, from the human pathogen Campylobacter jejuni. This enzyme is the sole source of N-acetylgalactosamine (GalNAc) in C. jejuni, which is a common component in three major glycoconjugates decorating the cell surface and is critical for pathogenesis. The second target protein is an integral membrane protein, called MraY, which catalyzes the transfer of phospho-N-acetylmuramyl (MurNAc) pentapeptide to a lipid carrier, undecaprenyl phosphate (C55-P), producing Lipid I in the peptidoglycan biosynthesis pathway. In the following step, a peripheral protein called MurG catalyzes transferring N-acetylglucosamine (GlcNAc) to Lipid I and produces Lipid II, which provides the first building block of the peptidoglycan layer. Peptidoglycan is uniquely bacterial, with MraY and MurG both being essential for cell viability; therefore, they are attractive targets for the development of antibacterial agents and work toward their structures is presented. Finally, MraY from Escherichia coli is the target for the lysis protein E from phage ΦX174.Efforts toward elucidating the EcMraY-E complexstructure are demonstrated here. In total, this thesis provides important data toward a full mechanistic understanding of these important antibacterial targets