Mesoscale Optoelectronic Design of Wire-Based Photovoltaic and Photoelectrochemical Devices

The overarching theme of this thesis is mesoscale optical and optoelectronic design of photovoltaic and photoelectrochemical devices. In a photovoltaic device, light absorption and charge carrier transport are coupled together on the mesoscale, and in a photoelectrochemical device, light absorption, charge carrier transport, catalysis, and solution species transport are all coupled together on the mesoscale. The work discussed herein demonstrates that simulation-based mesoscale optical and optoelectronic modeling can lead to detailed understanding of the operation and performance of these complex mesostructured devices, serve as a powerful tool for device optimization, and efficiently guide device design and experimental fabrication efforts. In-depth studies of two mesoscale wire-based device designs illustrate these principles—(i) an optoelectronic study of a tandem Si|WO3 microwire photoelectrochemical device, and (ii) an optical study of III-V nanowire arrays.

The study of the monolithic, tandem, Si|WO3 microwire photoelectrochemical device begins with development and validation of an optoelectronic model with experiment. This study capitalizes on synergy between experiment and simulation to demonstrate the model’s predictive power for extractable device voltage and light-limited current density. The developed model is then used to understand the limiting factors of the device and optimize its optoelectronic performance. The results of this work reveal that high fidelity modeling can facilitate unequivocal identification of limiting phenomena, such as parasitic absorption via excitation of a surface plasmon-polariton mode, and quick design optimization, achieving over a 300% enhancement in optoelectronic performance over a nominal design for this device architecture, which would be time-consuming and challenging to do via experiment.

The work on III-V nanowire arrays also starts as a collaboration of experiment and simulation aimed at gaining understanding of unprecedented, experimentally observed absorption enhancements in sparse arrays of vertically-oriented GaAs nanowires. To explain this resonant absorption in periodic arrays of high index semiconductor nanowires, a unified framework that combines a leaky waveguide theory perspective and that of photonic crystals supporting Bloch modes is developed in the context of silicon, using both analytic theory and electromagnetic simulations. This detailed theoretical understanding is then applied to a simulation-based optimization of light absorption in sparse arrays of GaAs nanowires. Near-unity absorption in sparse, 5% fill fraction arrays is demonstrated via tapering of nanowires and multiple wire radii in a single array. Finally, experimental efforts are presented towards fabrication of the optimized array geometries. A hybrid self-catalyzed and selective area MOCVD growth method is used to establish morphology control of GaP nanowire arrays. Similarly, morphology and pattern control of nanowires is demonstrated with ICP-RIE of InP. Optical characterization of the InP nanowire arrays gives proof of principle that tapering and multiple wire radii can lead to near-unity absorption in sparse arrays of InP nanowires.

Aperiodic structures in optics and integrated optics and the transverse Bragg reflector laser

The first part of this work describes the uses of aperiodic structures in optics and integrated optics. In particular, devices are designed, fabricated, tested and analyzed which make use of a chirped grating corrugation on the surface of a dielectric waveguide. These structures can be used as input-output couplers, multiplexers and demultiplexers, and broad band filters.

Next, a theoretical analysis is made of the effects of a random statistical variation in the thicknesses of layers in a dielectric mirror on its reflectivity properties. Unlike the intentional aperiodicity introduced in the chirped gratings, the aperiodicity in the Bragg reflector mirrors is unintentional and is present to some extent in all devices made. The analysis involved in studying these problems relies heavily on the coupled mode formalism. The results are compared with computer experiments, as well as tests of actual mirrors.

The second part of this work describes a novel method for confining light in the transverse direction in an injection laser. These so-called transverse Bragg reflector lasers confine light normal to the junction plane in the active region, through reflection from an adjacent layered medium. Thus, in principle, it is possible to guide light in a dielectric layer whose index is lower than that of the surrounding material. The design, theory and testing of these diode lasers are discussed.

Quantum Electromechanics with Two Tone Drive

In the field of mechanics, it is a long standing goal to measure quantum behavior in ever larger and more massive objects. It may now seem like an obvious conclusion, but until recently it was not clear whether a macroscopic mechanical resonator -- built up from nearly 10¹³ atoms -- could be fully described as an ideal quantum harmonic oscillator. With recent advances in the fields of opto- and electro-mechanics, such systems offer a unique advantage in probing the quantum noise properties of macroscopic electrical and mechanical devices, properties that ultimately stem from Heisenberg's uncertainty relations. Given the rapid progress in device capabilities, landmark results of quantum optics are now being extended into the regime of macroscopic mechanics.

The purpose of this dissertation is to describe three experiments -- motional sideband asymmetry, back-action evasion (BAE) detection, and mechanical squeezing -- that are directly related to the topic of measuring quantum noise with mechanical detection. These measurements all share three pertinent features: they explore quantum noise properties in a macroscopic electromechanical device driven by a minimum of two microwave drive tones, hence the title of this work: "Quantum electromechanics with two tone drive".

In the following, we will first introduce a quantum input-output framework that we use to model the electromechanical interaction and capture subtleties related to interpreting different microwave noise detection techniques. Next, we will discuss the fabrication and measurement details that we use to cool and probe these devices with coherent and incoherent microwave drive signals. Having developed our tools for signal modeling and detection, we explore the three-wave mixing interaction between the microwave and mechanical modes, whereby mechanical motion generates motional sidebands corresponding to up-down frequency conversions of microwave photons. Because of quantum vacuum noise, the rates of these processes are expected to be unequal. We will discuss the measurement and interpretation of this asymmetric motional noise in a electromechanical device cooled near the ground state of motion.

Next, we consider an overlapped two tone pump configuration that produces a time-modulated electromechanical interaction. By careful control of this drive field, we report a quantum non-demolition (QND) measurement of a single motional quadrature. Incorporating a second pair of drive tones, we directly measure the measurement back-action associated with both classical and quantum noise of the microwave cavity. Lastly, we slightly modify our drive scheme to generate quantum squeezing in a macroscopic mechanical resonator. Here, we will focus on data analysis techniques that we use to estimate the quadrature occupations. We incorporate Bayesian spectrum fitting and parameter estimation that serve as powerful tools for incorporating many known sources of measurement and fit error that are unavoidable in such work.

Fluorescence optofluidic microscopy and fluorescence microscopy based on the Talbot effect

Light microscopy has been one of the most common tools in biological research, because of its high resolution and non-invasive nature of the light. Due to its high sensitivity and specificity, fluorescence is one of the most important readout modes of light microscopy. This thesis presents two new fluorescence microscopic imaging techniques: fluorescence optofluidic microscopy and fluorescent Talbot microscopy. The designs of the two systems are fundamentally different from conventional microscopy, which makes compact and portable devices possible. The components of the devices are suitable for mass-production, making the microscopic imaging system more affordable for biological research and clinical diagnostics.

Fluorescence optofluidic microscopy (FOFM) is capable of imaging fluorescent samples in fluid media. The FOFM employs an array of Fresnel zone plates (FZP) to generate an array of focused light spots within a microfluidic channel. As a sample flows through the channel and across the array of focused light spots, a filter-coated CMOS sensor collects the fluorescence emissions. The collected data can then be processed to render a fluorescence microscopic image. The resolution, which is determined by the focused light spot size, is experimentally measured to be 0.65 μm.

Fluorescence Talbot microscopy (FTM) is a fluorescence chip-scale microscopy technique that enables large field-of-view (FOV) and high-resolution imaging. The FTM method utilizes the Talbot effect to project a grid of focused excitation light spots onto the sample. The sample is placed on a filter-coated CMOS sensor chip. The fluorescence emissions associated with each focal spot are collected by the sensor chip and are composed into a sparsely sampled fluorescence image. By raster scanning the Talbot focal spot grid across the sample and collecting a sequence of sparse images, a filled-in high-resolution fluorescence image can be reconstructed. In contrast to a conventional microscope, a collection efficiency, resolution, and FOV are not tied to each other for this technique. The FOV of FTM is directly scalable. Our FTM prototype has demonstrated a resolution of 1.2 μm, and the collection efficiency equivalent to a conventional microscope objective with a 0.70 N.A. The FOV is 3.9 mm × 3.5 mm, which is 100 times larger than that of a 20X/0.40 N.A. conventional microscope objective. Due to its large FOV, high collection efficiency, compactness, and its potential for integration with other on-chip devices, FTM is suitable for diverse applications, such as point-of-care diagnostics, large-scale functional screens, and long-term automated imaging.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Coupled plasmonic systems and devices : applications in visible metamaterials, nanophotonic circuits, and CMOS imaging

With the size of transistors approaching the sub-nanometer scale and Si-based photonics pinned at the micrometer scale due to the diffraction limit of light, we are unable to easily integrate the high transfer speeds of this comparably bulky technology with the increasingly smaller architecture of state-of-the-art processors. However, we find that we can bridge the gap between these two technologies by directly coupling electrons to photons through the use of dispersive metals in optics. Doing so allows us to access the surface electromagnetic wave excitations that arise at a metal/dielectric interface, a feature which both confines and enhances light in subwavelength dimensions - two promising characteristics for the development of integrated chip technology. This platform is known as plasmonics, and it allows us to design a broad range of complex metal/dielectric systems, all having different nanophotonic responses, but all originating from our ability to engineer the system surface plasmon resonances and interactions. In this thesis, we demonstrate how plasmonics can be used to develop coupled metal-dielectric systems to function as tunable plasmonic hole array color filters for CMOS image sensing, visible metamaterials composed of coupled negative-index plasmonic coaxial waveguides, and programmable plasmonic waveguide network systems to serve as color routers and logic devices at telecommunication wavelengths.

Signal transduction with hybridization chain reactions

Some of the most exciting developments in the field of nucleic acid engineering include the utilization of synthetic nucleic acid molecular devices as gene regulators, as disease marker detectors, and most recently, as therapeutic agents. The common thread between these technologies is their reliance on the detection of specific nucleic acid input markers to generate some desirable output, such as a change in the copy number of an mRNA (for gene regulation), a change in the emitted light intensity (for some diagnostics), and a change in cell state within an organism (for therapeutics). The research presented in this thesis likewise focuses on engineering molecular tools that detect specific nucleic acid inputs, and respond with useful outputs.

Four contributions to the field of nucleic acid engineering are presented: (1) the construction of a single nucleotide polymorphism (SNP) detector based on the mechanism of hybridization chain reaction (HCR); (2) the utilization of a single-stranded oligonucleotide molecular Scavenger as a means of enhancing HCR selectivity; (3) the implementation of Quenched HCR, a technique that facilitates transduction of a nucleic acid chemical input into an optical (light) output, and (4) the engineering of conditional probes that function as sequence transducers, receiving target signal as input and providing a sequence of choice as output. These programmable molecular systems are conceptually well-suited for performing wash-free, highly selective rapid genotyping and expression profiling in vitro, in situ, and potentially in living cells.

Experimental and theoretical studies of Notch signaling-mediated spatial pattern

Notch signaling acts in many diverse developmental spatial patterning processes. To better understand why this particular pathway is employed where it is and how downstream feedbacks interact with the signaling system to drive patterning, we have pursued three aims: (i) to quantitatively measure the Notch system's signal input/output (I/O) relationship in cell culture, (ii) to use the quantitative I/O relationship to computationally predict patterning outcomes of downstream feedbacks, and (iii) to reconstitute a Notch-mediated lateral induction feedback (in which Notch signaling upregulates the expression of Delta) in cell culture. The quantitative Notch I/O relationship revealed that in addition to the trans-activation between Notch and Delta on neighboring cells there is also a strong, mutual cis-inactivation between Notch and Delta on the same cell. This feature tends to amplify small differences between cells. Incorporating our improved understanding of the signaling system into simulations of different types of downstream feedbacks and boundary conditions lent us several insights into their function. The Notch system converts a shallow gradient of Delta expression into a sharp band of Notch signaling without any sort of feedback at all, in a system motivated by the Drosophila wing vein. It also improves the robustness of lateral inhibition patterning, where signal downregulates ligand expression, by removing the requirement for explicit cooperativity in the feedback and permitting an exceptionally simple mechanism for the pattern. When coupled to a downstream lateral induction feedback, the Notch system supports the propagation of a signaling front across a tissue to convert a large area from one state to another with only a local source of initial stimulation. It is also capable of converting a slowly-varying gradient in parameters into a sharp delineation between high- and low-ligand populations of cells, a pattern reminiscent of smooth muscle specification around artery walls. Finally, by implementing a version of the lateral induction feedback architecture modified with the addition of an autoregulatory positive feedback loop, we were able to generate cells that produce enough cis ligand when stimulated by trans ligand to themselves transmit signal to neighboring cells, which is the hallmark of lateral induction.

Topics in LIGO-related physics: interferometric speed meters and tidal work

In the quest to develop viable designs for third-generation optical interferometric gravitational-wave detectors, one strategy is to monitor the relative momentum or speed of the test-mass mirrors, rather than monitoring their relative position. The most straightforward design for a speed-meter interferometer that accomplishes this is described and analyzed in Chapter 2. This design (due to Braginsky, Gorodetsky, Khalili, and Thorne) is analogous to a microwave-cavity speed meter conceived by Braginsky and Khalili. A mathematical mapping between the microwave speed meter and the optical interferometric speed meter is developed and used to show (in accord with the speed being a quantum nondemolition observable) that in principle the interferometric speed meter can beat the gravitational-wave standard quantum limit (SQL) by an arbitrarily large amount, over an arbitrarily wide range of frequencies . However, in practice, to reach or beat the SQL, this specific speed meter requires exorbitantly high input light power. The physical reason for this is explored, along with other issues such as constraints on performance due to optical dissipation.

Chapter 3 proposes a more sophisticated version of a speed meter. This new design requires only a modest input power and appears to be a fully practical candidate for third-generation LIGO. It can beat the SQL (the approximate sensitivity of second-generation LIGO interferometers) over a broad range of frequencies (~ 10 to 100 Hz in practice) by a factor h/h_SQL ~ √W^(SQL)_(circ)/W_circ. Here W_circ is the light power circulating in the interferometer arms and W_SQL ≃ 800 kW is the circulating power required to beat the SQL at 100 Hz (the LIGO-II power). If squeezed vacuum (with a power-squeeze factor e^-2R) is injected into the interferometer's output port, the SQL can be beat with a much reduced laser power: h/h_SQL ~ √W^(SQL)_(circ)/W_circe^-2R. For realistic parameters (e^-2R ≃ 10 and W_circ ≃ 800 to 2000 kW), the SQL can be beat by a factor ~ 3 to 4 from 10 to 100 Hz. [However, as the power increases in these expressions, the speed meter becomes more narrow band; additional power and re-optimization of some parameters are required to maintain the wide band.] By performing frequency-dependent homodyne detection on the output (with the aid of two kilometer-scale filter cavities), one can markedly improve the interferometer's sensitivity at frequencies above 100 Hz.

Chapters 2 and 3 are part of an ongoing effort to develop a practical variant of an interferometric speed meter and to combine the speed meter concept with other ideas to yield a promising third- generation interferometric gravitational-wave detector that entails low laser power.

Chapter 4 is a contribution to the foundations for analyzing sources of gravitational waves for LIGO. Specifically, it presents an analysis of the tidal work done on a self-gravitating body (e.g., a neutron star or black hole) in an external tidal field (e.g., that of a binary companion). The change in the mass-energy of the body as a result of the tidal work, or "tidal heating," is analyzed using the Landau-Lifshitz pseudotensor and the local asymptotic rest frame of the body. It is shown that the work done on the body is gauge invariant, while the body-tidal-field interaction energy contained within the body's local asymptotic rest frame is gauge dependent. This is analogous to Newtonian theory, where the interaction energy is shown to depend on how one localizes gravitational energy, but the work done on the body is independent of that localization. These conclusions play a role in analyses, by others, of the dynamics and stability of the inspiraling neutron-star binaries whose gravitational waves are likely to be seen and studied by LIGO.

Selective data gathering in community sensor networks

Smartphones and other powerful sensor-equipped consumer devices make it possible to sense the physical world at an unprecedented scale. Nearly 2 million Android and iOS devices are activated every day, each carrying numerous sensors and a high-speed internet connection. Whereas traditional sensor networks have typically deployed a fixed number of devices to sense a particular phenomena, community networks can grow as additional participants choose to install apps and join the network. In principle, this allows networks of thousands or millions of sensors to be created quickly and at low cost. However, making reliable inferences about the world using so many community sensors involves several challenges, including scalability, data quality, mobility, and user privacy.

This thesis focuses on how learning at both the sensor- and network-level can provide scalable techniques for data collection and event detection. First, this thesis considers the abstract problem of distributed algorithms for data collection, and proposes a distributed, online approach to selecting which set of sensors should be queried. In addition to providing theoretical guarantees for submodular objective functions, the approach is also compatible with local rules or heuristics for detecting and transmitting potentially valuable observations. Next, the thesis presents a decentralized algorithm for spatial event detection, and describes its use detecting strong earthquakes within the Caltech Community Seismic Network. Despite the fact that strong earthquakes are rare and complex events, and that community sensors can be very noisy, our decentralized anomaly detection approach obtains theoretical guarantees for event detection performance while simultaneously limiting the rate of false alarms.

Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.