Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (17 results)

  • Article
  • Peer Reviewed
Faculty (2017)
We study two techniques to obtain new families of classical and general Dual-Feasible Functions: A conversion from minimal Gomory--Johnson functions; and computer-based search using polyhedral computation and an automatic maximality and extremality test.
    • Thesis
    • Peer Reviewed
    UC Santa Barbara Electronic Theses and Dissertations (2024)

    Modulation-based control and locking of lasers, filters, and other photonic components is a ubiquitous function across many applications that span the visible to infrared (IR) range, including atomic, molecular, and optical (AMO), quantum sciences, fiber communications, metrology, and microwave photonics. Today, modulators used to realize these control functions consist of high-power bulk-optic components for tuning, sideband modulation, and phase and frequency shifting while providing low optical insertion loss and moderate operation bandwidth. To enhance the power efficiency, scalability, and cost-effectiveness of these applications while reducing their size and weight, it is imperative to implement modulation control functions in a low-loss, wafer-scale complementary metal-oxide-semiconductor (CMOS)-compatible photonic integration platform. The silicon nitride integration platform has been successful in realizing extremely low waveguide losses across the visible to infrared range [1,2] and components including high-performance lasers [3], filters [4], resonators, stabilization cavities [5], and optical frequency combs [6]. However, the advancement in incorporating low-loss, low-power modulators into the silicon nitride platform while maintaining compatibility with wafer-scale processes has been constrained.This dissertation represents significant progress in the integration of a piezo-electric (PZT, lead zirconate titanate) actuated micro-ring modulator within a fully planar, wafer-scale silicon nitride platform, at both 1550 nm and 780 nm. This integration maintains low optical losses at infrared and visible wavelengths, accompanied by an order of magnitude increase in optical bandwidth (DC to 25 MHz 3-dB) and an order of magnitude lower power consumption of 20 nW improvement over prior PZT modulators [7,8]. This work demonstrated control applications utilizing the developed PZT modulator as sideband modulation in a Pound-Drever Hall (PDH) lock loop for laser stabilization and as a laser carrier tracking filter. Subsequently, an AOM/EOM-free laser stabilization scheme is demonstrated unifying both functions using a single PZT modulator. This approach has the potential to pave the way for photonic integrated stabilized lasers, given the compatibility of the PZT modulator with both the integrated reference cavity [9] and lasers [3,10]. The PZT modulator design can be extended to the visible region in the ultra-low loss silicon nitride platform with waveguide design changes. The integration of PZT modulation in the ultra-low loss silicon nitride waveguide platform enables modulator control functions in a wide range of visible to IR applications such as atomic and molecular transition locking for cooling, trapping and probing, controllable optical frequency combs, low-power external cavity tunable lasers, quantum computers, sensors and communications, atomic clocks, and tunable ultra-low linewidth lasers, and ultra-low phase noise microwave synthesizers. Finally, more complex photonic structures with PZT control are investigated, such as symmetrically coupled photonic molecules and their potential applications in optical isolators and high-order switchable filters. These results open the door to novel device designs and a wide range of applications including tunable lasers, high-order suppression ultra-narrow linewidth lasers, dispersion engineering, optical parametric oscillators, physics simulations, and atomic and quantum photonics.

      Cover page: Integrated Stress-Optic Silicon Nitride Photonics for Communications and Atomic Applications
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2021)
      Stress is the response of an organism to demands for change, yet excessive or chronic stress contributes to nearly all psychiatric disorders. The advent of high-throughput transcriptomic methods such as single cell RNA sequencing poses new opportunities to understand the neurobiology of stress, yet substantial barriers to understanding stress remain. Stress adaptation is an organismal survival mechanism conserved across all organisms, yet there is an infinity of potential stressful experiences. Unraveling shared and separate transcriptional programs for adapting to stressful experience remains a challenge, despite methodological and analytic advances. Here we review the state of the field focusing on the technologies used to study the transcriptome for the stress neurobiologist, and also attempt to identify central questions about the heterogeneity of stress for those applying transcriptomic approaches. We further explore how postmortem transcriptome studies aided by preclinical animal models are converging on common molecular pathways for adaptation to aversive experience. Finally, we discuss approaches to integrate large genomic datasets with human neuroimaging and other datasets.
        Cover page: Transcriptomics of the depressed and PTSD brain.
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2017)
        We introduce the value of information obtained by comparing alternative crystal forms of the same sub-state (of outward open UlaA, our example protein), which is found in the same lattice configuration but different space groups. We compare instability estimates obtained using this new method (alternative crystal forms) with temperature factors. Using a transport assay result, we correlate observations for two homologous secondary structure elements, and show that the alternative states method for obtaining instability estimates provide differentiating information about an important and immobilized mid-TMS region. The data presented in this article are related to the article entitled "The V-motifs facilitate the substrate capturing step of the PTS elevator mechanism" (A. Vastermark, A. Driker, J. Weng, X. Li, J. Wang, M.H. Saier Jr., 2016).
          Cover page: Difference distance map data of alternative crystal forms of UlaA
          • Article
          • Peer Reviewed
          UC Santa Barbara Previously Published Works (2023)
          Cold atoms are important for precision atomic applications including timekeeping and sensing. The 3D magneto-optical trap (3D-MOT), used to produce cold atoms, will benefit from photonic integration to improve reliability and reduce size, weight, and cost. These traps require the delivery of multiple, large area, collimated laser beams to an atomic vacuum cell. Yet, to date, beam delivery using an integrated waveguide approach has remained elusive. Here we report the demonstration of a 87Rb 3D-MOT using a fiber-coupled photonic integrated circuit to deliver all beams to cool and trap > 1 ×106 atoms to near 200 μK. The silicon nitride photonic circuit transforms fiber-coupled 780 nm cooling and repump light via waveguides to three mm-width non-diverging free-space cooling and repump beams directly to the rubidium cell. This planar, CMOS foundry-compatible integrated beam delivery is compatible with other components, such as lasers and modulators, promising system-on-chip solutions for cold atom applications.
            Cover page: Photonic integrated beam delivery for a rubidium 3D magneto-optical trap.
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2016)
            We propose that the alternative crystal forms of outward open UlaA (which are experimental, not simulated, and contain the substrate in the cavity) can be used to interpret/validate the MD results from MalT (the substrate capture step, which involves the mobile second TMSs of the V-motifs, TMSs 2 and 7). Since the crystal contacts are the same between the two alternative crystal forms of outward open UlaA, the striking biological differences noted, including rearranged hydrogen bonds and salt bridge coordination, are not attributable to crystal packing differences. Using transport assays, we identified G58 and G286 as essential for normal vitamin C transport, but the comparison of alternative crystal forms revealed that these residues to unhinge TMS movements from substrate-binding side chains, rendering the mid-TMS regions of homologous TMSs 2 and 7 relatively immobile. While the TMS that is involved in substrate binding in MalT is part of the homologous bundle that holds the two separate halves of the transport assembly (two proteins) together, an unequal effect of the two knockouts was observed for UlaA where both V-motifs are free from such dimer interface interactions.
              Cover page: The V-motifs facilitate the substrate capturing step of the PTS elevator mechanism
              • Article
              • Peer Reviewed
              UC Santa Barbara Previously Published Works (2021)
              Photonic molecules can be used to realize complex optical energy states and modes, analogous to those found in molecules, with properties useful for applications like spectral engineering and quantum optics. It is desirable to implement photonic molecules using high quality factor photonic integrated ring resonators due to their narrow atom-like spectral resonance, tunability, and the ability to scale the number of resonators on a photonic circuit. However, to take full advantage of molecule spectral complexity and tuning degree of freedom, resonator structures should have full symmetry in terms of inter-resonator coupling and resonator-waveguide coupling as well as independent resonance tuning, and low power dissipation operation, in a scalable integration platform. To date, photonic molecule symmetry has been limited to dual- and triple-cavity geometries coupled to single- or dual-busses, and resonance tuning limited to dual resonator molecules. In this paper, we demonstrate a three-resonator photonic molecule, consisting of symmetrically coupled 8.11 million intrinsic Q silicon nitride rings, where each ring is coupled to the other two rings. The resonance of each ring, and that of the collective molecule, is controlled using low power dissipation, monolithically integrated thin-film lead zirconate titanate (PZT) actuators that are integrated with the ultra-low loss silicon nitride resonators. This performance is achieved without undercut waveguides, yielding the highest Q to date for a PZT controlled resonator. This advance leads to full control of complex photonic molecule resonance spectra and splitting in a wafer-scale integration platform. The resulting six tunable supermodes can be fully controlled, including degeneracy, location and splitting as well as designed by a model that can accurately predict the energy modes and transmission spectrum and tunable resonance splitting.
                Cover page: Fully symmetric controllable integrated three-resonator photonic moleculeCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Santa Barbara Previously Published Works (2024)
                Heterogeneous and monolithic integration of the versatile low-loss silicon nitride platform with low-temperature materials such as silicon electronics and photonics, III-V compound semiconductors, lithium niobate, organics, and glasses has been inhibited by the need for high-temperature annealing as well as the need for different process flows for thin and thick waveguides. New techniques are needed to maintain the state-of-the-art losses, nonlinear properties, and CMOS-compatible processes while enabling this next generation of 3D silicon nitride integration. We report a significant advance in silicon nitride integrated photonics, demonstrating the lowest losses to date for an anneal-free process at a maximum temperature 250 °C, with the same deuterated silane based fabrication flow, for nitride and oxide, for an order of magnitude range in nitride thickness without requiring stress mitigation or polishing. We report record low anneal-free losses for both nitride core and oxide cladding, enabling 1.77 dB m-1 loss and 14.9 million Q for 80 nm nitride core waveguides, more than half an order magnitude lower loss than previously reported sub 300 °C process. For 800 nm-thick nitride, we achieve as good as 8.66 dB m-1 loss and 4.03 million Q, the highest reported Q for a low temperature processed resonator with equivalent device area, with a median of loss and Q of 13.9 dB m-1 and 2.59 million each respectively. We demonstrate laser stabilization with over 4 orders of magnitude frequency noise reduction using a thin nitride reference cavity, and using a thick nitride micro-resonator we demonstrate OPO, over two octave supercontinuum generation, and four-wave mixing and parametric gain with the lowest reported optical parametric oscillation threshold per unit resonator length. These results represent a significant step towards a uniform ultra-low loss silicon nitride homogeneous and heterogeneous platform for both thin and thick waveguides capable of linear and nonlinear photonic circuits and integration with low-temperature materials and processes.
                  Cover page: Anneal-free ultra-low loss silicon nitride integrated photonics.
                  • Article
                  • Peer Reviewed
                  UC Santa Barbara Previously Published Works (2022)
                  Atomic, molecular and optical (AMO) visible light systems are the heart of precision applications including quantum, atomic clocks and precision metrology. As these systems scale in terms of number of lasers, wavelengths, and optical components, their reliability, space occupied, and power consumption will push the limits of using traditional laboratory-scale lasers and optics. Visible light photonic integration is critical to advancing AMO based sciences and applications, yet key performance aspects remain to be addressed, most notably waveguide losses and laser phase noise and stability. Additionally, a visible light integrated solution needs to be wafer-scale CMOS compatible and capable of supporting a wide array of photonic components. While the regime of ultra-low loss has been achieved at telecommunication wavelengths, progress at visible wavelengths has been limited. Here, we report the lowest waveguide losses and highest resonator Qs to date in the visible range, to the best of our knowledge. We report waveguide losses at wavelengths associated with strontium transitions in the 461 nm to 802 nm wavelength range, of 0.01 dB/cm to 0.09 dB/cm and associated intrinsic resonator Q of 60 Million to 9.5 Million, a decrease in loss by factors of 6x to 2x and increase in Q by factors of 10x to 1.5x over this visible wavelength range. Additionally, we measure an absorption limited loss and Q of 0.17 dB/m and 340 million at 674 nm. This level of performance is achieved in a wafer-scale foundry compatible Si3N4 platform with a 20 nm thick core and TEOS-PECVD deposited upper cladding oxide, and enables waveguides for different wavelengths to be fabricated on the same wafer with mask-only changes per wavelength. These results represent a significant step forward in waveguide platforms that operate in the visible, opening up a wide range of integrated applications that utilize atoms, ions and molecules including sensing, navigation, metrology and clocks.
                    Cover page: Ultra-low loss visible light waveguides for integrated atomic, molecular, and quantum photonics.
                    • Article
                    • Peer Reviewed
                    UC Riverside Previously Published Works (2011)

                    Background

                    Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study.

                    Results

                    We comprehensively compared three platforms: NimbleGen's Sequence Capture Array and SeqCap EZ, and Agilent's SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the three platforms achieved a similar accuracy of genotype assignment and SNP detection. Importantly, all three platforms showed similar levels of reproducibility, GC bias and reference allele bias.

                    Conclusions

                    We demonstrate key differences between the three platforms, particularly advantages of solutions over array capture and the importance of a large gene target set.
                      Cover page: Comprehensive comparison of three commercial human whole-exome capture platforms
                      Top