Dual slot-mode NOEM phase shifter.

Photonic system component counts are increasing rapidly, particularly in CMOS-compatible silicon photonics processes. Large numbers of cascaded active photonic devices are difficult to implement when accounting for constraints on area, power dissipation, and response time. Plasma dispersion and the thermo-optic effect, both available in CMOS-compatible silicon processes, address a subset of these criteria. With the addition of a few back-end-of-line etch processing steps, silicon photonics platforms can support nano-opto-electro-mechanical (NOEM) phase shifters. Realizing NOEM phase shifters that operate at CMOS-compatible voltages (≤ 1.2 V) and with low insertion loss remains a challenge. Here, we introduce a novel NOEM phase shifter fabricated alongside 90 nanometer transistors that imparts 5.63 radians phase shift at 1.08 volts bias over an actuation length of 25µm with an insertion loss of less than 0.04 dB and 3 dB bandwidth of 0.26 MHz.

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Despite intensive study for 50 years, the biochemical and genetic links between lysine metabolism and central metabolism in Pseudomonas putida remain unresolved. To establish these biochemical links, we leveraged random barcode transposon sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both l- and d-lysine metabolism. We first describe three pathway enzymes that catabolize l-2-aminoadipate (l-2AA) to 2-ketoglutarate (2KG), connecting d-lysine to the TCA cycle. One of these enzymes, P. putida 5260 (PP_5260), contains a DUF1338 domain, representing a family with no previously described biological function. Our work also identified the recently described coenzyme A (CoA)-independent route of l-lysine degradation that results in metabolization to succinate. We expanded on previous findings by demonstrating that glutarate hydroxylase CsiD is promiscuous in its 2-oxoacid selectivity. Proteomics of selected pathway enzymes revealed that expression of catabolic genes is highly sensitive to the presence of particular pathway metabolites, implying intensive local and global regulation. This work demonstrated the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria, as well as its utility a powerful tool for validating previous research.IMPORTANCEP. putida lysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, the connection of lysine catabolism to central metabolism in P. putida remained undefined. Here, we used random barcode transposon sequencing to fill the gaps of lysine metabolism in P. putida We describe a route of 2-oxoadipate (2OA) catabolism, which utilizes DUF1338-containing protein P. putida 5260 (PP_5260) in bacteria. Despite its prevalence in many domains of life, DUF1338-containing proteins have had no known biochemical function. We demonstrate that PP_5260 is a metalloenzyme which catalyzes an unusual route of decarboxylation of 2OA to d-2-hydroxyglutarate (d-2HG). Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results and expand the understanding of glutarate hydroxylase CsiD by showing that can it use either 2OA or 2KG as a cosubstrate. Our work demonstrated that biological novelty can be rapidly identified using unbiased experimental genetics and that RB-TnSeq can be used to rapidly validate previous results.

Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase.

The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.

Nonlinear characterization of a silicon integrated Bragg waveguide filter.

Bragg waveguides are promising optical filters for pump suppression in spontaneous four-wave mixing (FWM) photon sources. In this work, we investigate the generation of unwanted photon pairs in the filter itself. We do this by taking advantage of the relation between spontaneous and classical FWM, which allows for the precise characterization of the nonlinear response of the device. The pair generation rate estimated from the classical measurement is compared with the theoretical value calculated by means of a full quantum model of the filter, which also allows investigation of the spectral properties of the generated pairs. We find a good agreement between theory and experiment, confirming that stimulated FWM is a valuable approach to characterize the nonlinear response of an integrated filter, and that the pairs generated in a Bragg waveguide are not a serious issue for the operation of a fully integrated nonclassical source.

Bioproduction of a betalain color palette in Saccharomyces cerevisiae.

Betalains are a family of natural pigments found exclusively in the plant order Caryophyllales. All members of this chemical family are biosynthesized through the common intermediate betalamic acid, which is capable of spontaneously condensing with various primary and secondary amines to produce betalains. Of particular interest is the red-violet betanin, most commonly obtained from Beta vulgaris (beet) as a natural food dye. We demonstrate the first complete microbial production of betanin in Saccharomyces cerevisiae from glucose, an early step towards a fermentation process enabling rapid, on-demand production of this natural dye. A titer of 17mg/L was achieved, corresponding to a color intensity obtained from 10g/L of beetroot extract. Further, we expanded the spectrum of betalain colors by condensing betalamic acid with various amines fed to an engineered strain of S. cerevisiae. Our work establishes a platform for microbial production of betalains of various colors as a potential alternative to land- and resource-intensive agricultural production.

Programmable dispersion on a photonic integrated circuit for classical and quantum applications.

We demonstrate a large-scale tunable-coupling ring resonator array, suitable for high-dimensional classical and quantum transforms, in a CMOS-compatible silicon photonics platform. The device consists of a waveguide coupled to 15 ring-based dispersive elements with programmable linewidths and resonance frequencies. The ability to control both quality factor and frequency of each ring provides an unprecedented 30 degrees of freedom in dispersion control on a single spatial channel. This programmable dispersion control system has a range of applications, including mode-locked lasers, quantum key distribution, and photon-pair generation. We also propose a novel application enabled by this circuit - high-speed quantum communications using temporal-mode-based quantum data locking - and discuss the utility of the system for performing the high-dimensional unitary optical transformations necessary for a quantum data locking demonstration.

Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria.

A putative lipopeptide biosynthetic gene cluster is conserved in many species of Actinobacteria, including Mycobacterium tuberculosis and M. marinum, but the specific function of the encoding proteins has been elusive. Using both in vivo heterologous reconstitution and in vitro biochemical analyses, we have revealed that the five encoding biosynthetic enzymes are capable of synthesizing a family of isonitrile lipopeptides (INLPs) through a thio-template mechanism. The biosynthesis features the generation of isonitrile from a single precursor Gly promoted by a thioesterase and a nonheme iron(II)-dependent oxidase homolog and the acylation of both amino groups of Lys by the same isonitrile acyl chain facilitated by a single condensation domain of a nonribosomal peptide synthetase. In addition, the deletion of INLP biosynthetic genes in M. marinum has decreased the intracellular metal concentration, suggesting the role of this biosynthetic gene cluster in metal transport.

Energy correlations of photon pairs generated by a silicon microring resonator probed by Stimulated Four Wave Mixing.

Compact silicon integrated devices, such as micro-ring resonators, have recently been demonstrated as efficient sources of quantum correlated photon pairs. The mass production of integrated devices demands the implementation of fast and reliable techniques to monitor the device performances. In the case of time-energy correlations, this is particularly challenging, as it requires high spectral resolution that is not currently achievable in coincidence measurements. Here we reconstruct the joint spectral density of photons pairs generated by spontaneous four-wave mixing in a silicon ring resonator by studying the corresponding stimulated process, namely stimulated four wave mixing. We show that this approach, featuring high spectral resolution and short measurement times, allows one to discriminate between nearly-uncorrelated and highly-correlated photon pairs.

On-chip detection of non-classical light by scalable integration of single-photon detectors.

Photonic-integrated circuits have emerged as a scalable platform for complex quantum systems. A central goal is to integrate single-photon detectors to reduce optical losses, latency and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps jitter and nanosecond-scale reset time. However, while single detectors have been incorporated into individual waveguides, the system detection efficiency of multiple SNSPDs in one photonic circuit-required for scalable quantum photonic circuits-has been limited to <0.2%. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of photonic circuits. Ten low-jitter detectors are integrated on one circuit with 100% device yield. With an average system detection efficiency beyond 10%, and estimated on-chip detection efficiency of 14-52% for four detectors operated simultaneously, we demonstrate, to the best of our knowledge, the first on-chip photon correlation measurements of non-classical light.

Nanofabrication on unconventional substrates using transferred hard masks.

A major challenge in nanofabrication is to pattern unconventional substrates that cannot be processed for a variety of reasons, such as incompatibility with spin coating, electron beam lithography, optical lithography, or wet chemical steps. Here, we present a versatile nanofabrication method based on re-usable silicon membrane hard masks, patterned using standard lithography and mature silicon processing technology. These masks, transferred precisely onto targeted regions, can be in the millimetre scale. They allow for fabrication on a wide range of substrates, including rough, soft, and non-conductive materials, enabling feature linewidths down to 10 nm. Plasma etching, lift-off, and ion implantation are realized without the need for scanning electron/ion beam processing, UV exposure, or wet etching on target substrates.

Efficient, compact and low loss thermo-optic phase shifter in silicon.

We design a resistive heater optimized for efficient and low-loss optical phase modulation in a silicon-on-insulator (SOI) waveguide and characterize the fabricated devices. Modulation is achieved by flowing current perpendicular to a new ridge waveguide geometry. The resistance profile is engineered using different dopant concentrations to obtain localized heat generation and maximize the overlap between the optical mode and the high temperature regions of the structure, while simultaneously minimizing optical loss due to free-carrier absorption. A 61.6 µm long phase shifter was fabricated in a CMOS process with oxide cladding and two metal layers. The device features a phase-shifting efficiency of 24.77 ± 0.43 mW/π and a -3 dB modulation bandwidth of 130.0 ± 5.59 kHz; the insertion loss measured for 21 devices across an 8-inch wafer was only 0.23 ± 0.13 dB. Considering the prospect of densely integrated photonic circuits, we also quantify the separation necessary to isolate thermo-optic devices in the standard 220 nm SOI platform.

Broadband on-chip optical non-reciprocity using phase modulators.

Breaking the reciprocity of light propagation in a nanoscale photonic integrated circuit (PIC) is a topic of intense research, fostered by the promises of this technology in areas ranging from experimental research in classical and quantum optics to high-rate telecommunications and data interconnects. In particular, silicon PICs fabricated in processes compatible with the existing complementary metal-oxide-semiconductor (CMOS) infrastructure have attracted remarkable attention. However, a practical solution for integrating optical isolators and circulators within the current CMOS technology remains elusive. Here, we introduce a new non-reciprocal photonic circuit operating with standard single-mode waveguides or optical fibers. Our design exploits a time-dependent index modulation obtained with conventional phase modulators such as the one widely available in silicon photonics platforms. Because it is based on fully balanced interferometers and does not involve resonant structures, our scheme is also intrinsically broadband. Using realistic parameters we calculate an extinction ratio superior to 20dB and insertion loss below 3dB.

Ultralow drive voltage silicon traveling-wave modulator.

There has been great interest in the silicon platform as a material system for integrated photonics. A key challenge is the development of a low-power, low drive voltage, broadband modulator. Drive voltages at or below 1 Vpp are desirable for compatibility with CMOS processes. Here we demonstrate a CMOS-compatible broadband traveling-wave modulator based on a reverse-biased pn junction. We demonstrate operation with a drive voltage of 0.63 Vpp at 20 Gb/s, a significant improvement in the state of the art, with an RF energy consumption of only 200 fJ/bit.