Nanofabrication for On-Chip Optical Levitation, Atom-Trapping, and Superconducting Quantum Circuits

Researchers have spent decades refining and improving their methods for fabricating smaller, finer-tuned, higher-quality nanoscale optical elements with the goal of making more sensitive and accurate measurements of the world around them using optics. Quantum optics has been a well-established tool of choice in making these increasingly sensitive measurements which have repeatedly pushed the limits on the accuracy of measurement set forth by quantum mechanics. A recent development in quantum optics has been a creative integration of robust, high-quality, and well-established macroscopic experimental systems with highly-engineerable on-chip nanoscale oscillators fabricated in cleanrooms. However, merging large systems with nanoscale oscillators often require them to have extremely high aspect-ratios, which make them extremely delicate and difficult to fabricate with an "experimentally reasonable" repeatability, yield and high quality. In this work we give an overview of our research, which focused on microscopic oscillators which are coupled with macroscopic optical cavities towards the goal of cooling them to their motional ground state in room temperature environments. The quality factor of a mechanical resonator is an important figure of merit for various sensing applications and observing quantum behavior. We demonstrated a technique for pushing the quality factor of a micromechanical resonator beyond conventional material and fabrication limits by using an optical field to stiffen and trap a particular motional mode of a nanoscale oscillator. Optical forces increase the oscillation frequency by storing most of the mechanical energy in a nearly loss-less optical potential, thereby strongly diluting the effects of material dissipation. By placing a 130 nm thick SiO₂ pendulum in an optical standing wave, we achieve an increase in the pendulum center-of-mass frequency from 6.2 to 145 kHz. The corresponding quality factor increases 50-fold from its intrinsic value to a final value of Q_m = 5.8(1.1) x 10⁵, representing more than an order of magnitude improvement over the conventional limits of SiO₂ for a pendulum geometry. Our technique may enable new opportunities for mechanical sensing and facilitate observations of quantum behavior in this class of mechanical systems. We then give a detailed overview of the techniques used to produce high-aspect-ratio nanostructures with applications in a wide range of quantum optics experiments. The ability to fabricate such nanodevices with high precision opens the door to a vast array of experiments which integrate macroscopic optical setups with lithographically engineered nanodevices. Coupled with atom-trapping experiments in the Kimble Lab, we use these techniques to realize a new waveguide chip designed to address ultra-cold atoms along lithographically patterned nanobeams which have large atom-photon coupling and near 4π Steradian optical access for cooling and trapping atoms. We describe a fully integrated and scalable design where cold atoms are spatially overlapped with the nanostring cavities in order to observe a resonant optical depth of d₀ ≈ 0.15. The nanodevice illuminates new possibilities for integrating atoms into photonic circuits and engineering quantum states of atoms and light on a microscopic scale. We then describe our work with superconducting microwave resonators coupled to a phononic cavity towards the goal of building an integrated device for quantum-limited microwave-to-optical wavelength conversion. We give an overview of our characterizations of several types of substrates for fabricating a low-loss high-frequency electromechanical system. We describe our electromechanical system fabricated on a Si₃N₄ membrane which consists of a 12 GHz superconducting LC resonator coupled capacitively to the high frequency localized modes of a phononic nanobeam. Using our suspended membrane geometry we isolate our system from substrates with significant loss tangents, drastically reducing the parasitic capacitance of our superconducting circuit to ≈ 2.5$ fF. This opens up a number of possibilities in making a new class of low-loss high-frequency electromechanics with relatively large electromechanical coupling. We present our substrate studies, fabrication methods, and device characterization.

Injection Locked Clocking and Transmitter Equalization Techniques for Chip to Chip Interconnects

Semiconductor technology scaling has enabled drastic growth in the computational capacity of integrated circuits (ICs). This constant growth drives an increasing demand for high bandwidth communication between ICs. Electrical channel bandwidth has not been able to keep up with this demand, making I/O link design more challenging. Interconnects which employ optical channels have negligible frequency dependent loss and provide a potential solution to this I/O bandwidth problem. Apart from the type of channel, efficient high-speed communication also relies on generation and distribution of multi-phase, high-speed, and high-quality clock signals. In the multi-gigahertz frequency range, conventional clocking techniques have encountered several design challenges in terms of power consumption, skew and jitter. Injection-locking is a promising technique to address these design challenges for gigahertz clocking. However, its small locking range has been a major contributor in preventing its ubiquitous acceptance.

In the first part of this dissertation we describe a wideband injection locking scheme in an LC oscillator. Phase locked loop (PLL) and injection locking elements are combined symbiotically to achieve wide locking range while retaining the simplicity of the latter. This method does not require a phase frequency detector or a loop filter to achieve phase lock. A mathematical analysis of the system is presented and the expression for new locking range is derived. A locking range of 13.4 GHz–17.2 GHz (25%) and an average jitter tracking bandwidth of up to 400 MHz are measured in a high-Q LC oscillator. This architecture is used to generate quadrature phases from a single clock without any frequency division. It also provides high frequency jitter filtering while retaining the low frequency correlated jitter essential for forwarded clock receivers.

To improve the locking range of an injection locked ring oscillator; QLL (Quadrature locked loop) is introduced. The inherent dynamics of injection locked quadrature ring oscillator are used to improve its locking range from 5% (7-7.4GHz) to 90% (4-11GHz). The QLL is used to generate accurate clock phases for a four channel optical receiver using a forwarded clock at quarter-rate. The QLL drives an injection locked oscillator (ILO) at each channel without any repeaters for local quadrature clock generation. Each local ILO has deskew capability for phase alignment. The optical-receiver uses the inherent frequency to voltage conversion provided by the QLL to dynamically body bias its devices. A wide locking range of the QLL helps to achieve a reliable data-rate of 16-32Gb/s and adaptive body biasing aids in maintaining an ultra-low power consumption of 153pJ/bit.

From the optical receiver we move on to discussing a non-linear equalization technique for a vertical-cavity surface-emitting laser (VCSEL) based optical transmitter, to enable low-power, high-speed optical transmission. A non-linear time domain optical model of the VCSEL is built and evaluated for accuracy. The modelling shows that, while conventional FIR-based pre-emphasis works well for LTI electrical channels, it is not optimum for the non-linear optical frequency response of the VCSEL. Based on the simulations of the model an optimum equalization methodology is derived. The equalization technique is used to achieve a data-rate of 20Gb/s with power efficiency of 0.77pJ/bit.

A single-layer magnetic atom chip for trapping an array of Bose-Einstein condensate

We propose a simple single-layer magnetic microtrap configuration which can trap an array of magnetically-trapped Bose-Einstein condensate. The configuration consists of two series of parallel wires perpendicular to each other and all of the crossing points are cut off for maintaining the uniformity of the current. We analyse the trapping potential, the position of trapping centres and the uniformity of the array of the traps. The trapping depth and trapping frequency with different parameters are also calculated. Lastly, the effect of the cut-off crossing points, dissipate power, chip production are introduced concisely.

Guiding neutral atoms with two current-carrying wires and a vertical bias field on the atom chip

We demonstrate the guiding of neutral atoms with two parallel microfabricated current-carrying wires on the atom chip and a vertical magnetic bias field. The atoms are guided along a magnetic field minimum parallel to the current-carrying wires and confined in the other two directions. We describe in detail how the precooled atoms are efficiently loaded into the two-wire guide. We present a detailed experimental study of the motional properties of the atoms in the guide and the relationship between the location of the guide and the vertical bias field. This two-wire guide with vertical bias field can be used to realize large area atom interferometer.

TWO-DIMENSIONAL ARRAY OF ION TRAPS ON A PLANAR CHIP

We investigate a planar ion chip design with a two-dimensional array of linear ion traps for the scalable quantum information processor. The segmented electrodes reside in a single plane on a substrate and a grounded metal plate, a combination of appropriate rf and DC potentials are applied to them for stable ion confinement, and the trap axes are located above the surface at a distance controlled by the electrodes' lateral extent and the substrate's height as discussed. The potential distributions are calculated using static electric field qualitatively. This architecture is conceptually simple and many current microfabrication techniques are feasible for the basic structure. It may provide a promising route for scalable quantum computers.

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.

DNA-mediated oxidation of transcription factor p53

Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs with a shallow distance dependence over long distances through the π-stacked DNA bases, leading to the oxidation and dissociation of DNA-bound p53. The extent of p53 dissociation depends upon the redox potential of the response element DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using radiolabeled oligonucleotides containing both synthetic and human p53 response elements with an appended anthraquinone photooxidant. Greater p53 dissociation is observed from DNA sequences containing low redox potential purine regions, particularly guanine triplets, within the p53 response element. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites, which correspond to locations of preferred electron hole localization, were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets within the response element. Oxidative DNA damage is inhibited in the presence of p53, however, only at DNA sites within the response element, and therefore in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress, as well as possible biological implications, have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA-mediated oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.

To determine whether the change in p53 response element occupancy observed in vitro also correlates in cellulo, chromatin immunoprecipition (ChIP) and quantitative PCR (qPCR) were used to directly quantify p53 binding to certain response elements in HCT116N cells. The HCT116N cells containing a wild type p53 were treated with the photooxidant [Rh(phi)2bpy]³⁺, Nutlin-3 to upregulate p53, and subsequently irradiated to induce oxidative genomic stress. To covalently tether p53 interacting with DNA, the cells were fixed with disuccinimidyl glutarate and formaldehyde. The nuclei of the harvested cells were isolated, sonicated, and immunoprecipitated using magnetic beads conjugated with a monoclonal p53 antibody. The purified immounoprecipiated DNA was then quantified via qPCR and genomic sequencing. Overall, the ChIP results were significantly varied over ten experimental trials, but one trend is observed overall: greater variation of p53 occupancy is observed in response elements from which oxidative dissociation would be expected, while significantly less change in p53 occupancy occurs for response elements from which oxidative dissociation would not be anticipated.

The chemical oxidation of transcription factor p53 via DNA CT was also investigated with respect to the protein at the amino acid level. Transcription factor p53 plays a critical role in the cellular response to stress stimuli, which may be modulated through the redox modulation of conserved cysteine residues within the DNA-binding domain. Residues within p53 that enable oxidative dissociation are herein investigated. Of the 8 mutants studied by electrophoretic mobility shift assay (EMSA), only the C275S mutation significantly decreased the protein affinity (KD) for the Gadd45 response element. EMSA assays of p53 oxidative dissociation promoted by photoexcitation of anthraquinone-tethered Gadd45 oligonucleotides were used to determine the influence of p53 mutations on oxidative dissociation; mutation to C275S severely attenuates oxidative dissociation while C277S substantially attenuates dissociation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide labeled, while oxidized cysteines participating in disulfide bonds were ¹³C₂D₂-iodoacetamide labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed using a QTRAP 6500 LC-MS/MS system, quantified with Skyline, and directly compared. A distinct shift in peptide labeling toward ¹³C₂D₂-iodoacetamide labeled cysteines is observed in oxidized samples as compared to the respective controls. All of the observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds potentially among the C124, C135, C141, C182, C275, and C277. Based on these data it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.

Investigation of Fundamental Processes Governing Secondary Organic Aerosol Formation in Laboratory Chambers

Our understanding of the processes and mechanisms by which secondary organic aerosol (SOA) is formed is derived from laboratory chamber studies. In the atmosphere, SOA formation is primarily driven by progressive photooxidation of SOA precursors, coupled with their gas-particle partitioning. In the chamber environment, SOA-forming vapors undergo multiple chemical and physical processes that involve production and removal via gas-phase reactions; partitioning onto suspended particles vs. particles deposited on the chamber wall; and direct deposition on the chamber wall. The main focus of this dissertation is to characterize the interactions of organic vapors with suspended particles and the chamber wall and explore how these intertwined processes in laboratory chambers govern SOA formation and evolution.

A Functional Group Oxidation Model (FGOM) that represents SOA formation and evolution in terms of the competition between functionalization and fragmentation, the extent of oxygen atom addition, and the change of volatility, is developed. The FGOM contains a set of parameters that are to be determined by fitting of the model to laboratory chamber data. The sensitivity of the model prediction to variation of the adjustable parameters allows one to assess the relative importance of various pathways involved in SOA formation.

A critical aspect of the environmental chamber is the presence of the wall, which can induce deposition of SOA-forming vapors and promote heterogeneous reactions. An experimental protocol and model framework are first developed to constrain the vapor-wall interactions. By optimal fitting the model predictions to the observed wall-induced decay profiles of 25 oxidized organic compounds, the dominant parameter governing the extent of wall deposition of a compound is identified, i.e., wall accommodation coefficient. By correlating this parameter with the molecular properties of a compound via its volatility, the wall-induced deposition rate of an organic compound can be predicted based on its carbon and oxygen numbers in the molecule.

Heterogeneous transformation of δ-hydroxycarbonyl, a major first-generation product from long-chain alkane photochemistry, is observed on the surface of particles and walls. The uniqueness of this reaction scheme is the production of substituted dihydrofuran, which is highly reactive towards ozone, OH, and NO3, thereby opening a reaction pathway that is not usually accessible to alkanes. A spectrum of highly-oxygenated products with carboxylic acid, ester, and ether functional groups is produced from the substituted dihydrofuran chemistry, thereby affecting the average oxidation state of the alkane-derived SOA.

The vapor wall loss correction is applied to several chamber-derived SOA systems generated from both anthropogenic and biogenic sources. Experimental and modeling approaches are employed to constrain the partitioning behavior of SOA-forming vapors onto suspended particles vs. chamber walls. It is demonstrated that deposition of SOA-forming vapors to the chamber wall during photooxidation experiments can lead to substantial and systematic underestimation of SOA. Therefore, it is likely that a lack of proper accounting for vapor wall losses that suppress chamber-derived SOA yields contribute substantially to the underprediction of ambient SOA concentrations in atmospheric models.

Conserved quantities and the formation of black holes in the Brans-Dicke theory of gravitation

In Part I, we construct a symmetric stress-energy-momentum pseudo-tensor for the gravitational fields of Brans-Dicke theory, and use this to establish rigorously conserved integral expressions for energy-momentum Pⁱ and angular momentum J^ik. Application of the two-dimensional surface integrals to the exact static spherical vacuum solution of Brans leads to an identification of our conserved mass with the active gravitational mass. Application to the distant fields of an arbitrary stationary source reveals that Pⁱ and J^ik have the same physical interpretation as in general relativity. For gravitational waves whose wavelength is small on the scale of the background radius of curvature, averaging over several wavelengths in the Brill-Hartle-Isaacson manner produces a stress-energy-momentum tensor for gravitational radiation which may be used to calculate the changes in Pⁱ and J^ik of their source.

In Part II, we develop strong evidence in favor of a conjecture by Penrose--that, in the Brans-Dicke theory, relativistic gravitational collapse in three dimensions produce black holes identical to those of general relativity. After pointing out that any black hole solution of general relativity also satisfies Brans-Dicke theory, we establish the Schwarzschild and Kerr geometries as the only possible spherical and axially symmetric black hole exteriors, respectively. Also, we show that a Schwarzschild geometry is necessarily formed in the collapse of an uncharged sphere.

Appendices discuss relationships among relativistic gravity theories and an example of a theory in which black holes do not exist.

On the formation of ephippia in some Cladocera (Crustacea) [Translation from: Zoologicheskie Zhurnal 61, 1425-1427, 1982]

The determination of relative connections between families and genera of Cladocera, necessary for the construction of their natural systems, must be based on various criteria, among them on the structure of the ephippia. Of particular interest is the study of the process of formation and structure of the ephippium in Macrothricidae, different representatives of which differ significantly among themselves according to this criterion. In this article are presented the results of an investigation of the features of formation of the ephippium in seven species of Macrothricidae and in the moinid Moina weismanni Ishikawa (Moinidae).

Studies on the complex formation of iron with humic substances [Translation from: Vom Wasser 53, 243-247, 1979]

Most of the humic substances which occur in natural waters have an iron content of a few percent, indicated by the mg/1 content of organically-bonded carbon. This iron is apparently bound in a complex with the humic substances, for it quite plainly differs in its chemical and physico-chemical properties from what one would expect from the purely inorganic iron-water system. The deviations range from the solubility to the redox behaviour, and thus are frequently the basis of analytical and technical difficulties. The key to the solution of most of this problem lies in a better understanding of the aforementioned bonds between the iron and the humic substances. This paper studies the iron content of the humic substance concentration from a bog lake sample and the complexing of iron by humic substances from the surface of the bog lake.

Mechanism of mass transfer in the formation of hydrothermal deposits of sulphides [Translation from: Trudy Inst.Geol.rudn.Mesterozh. 16, 80 [pages 44-46 ”Solubility of sulphides of iron” only], 1958]

This partial translation of the original paper provides the summary of this study of the mechanism of mass transfer in the formation of hydrothermal deposits of sulphides. For determining the solubility of sulphides of iron, the radioactive isotope Fe59 was used. The solubility of two sulphides was determined.