We report, for the first time, bandgap guidance above 3 mum in a silica based air-core photonic crystal fiber. The peak of the bandgap is at 3.14mum with a typical attenuation of ~ 2.6 dB m-1. By further optimization of the structure, modeling suggests that a loss below 1 dB m-1 should be achievable, greatly extending the useful operating range of silica-based single-mode fibers. Such fibers have many potential applications in the mid-IR, offering an alternative to fluoride, tellurite or chalcogenide glass based optical fibers for chemical and biological sensing applications.
Populus species are widely distributed across the Northern Hemisphere. The genetic diversity makes the genus an ideal study system for traits of ecological or agronomic significance. However, sequence variation between the genome-sequenced Populus trichocarpa Nisqually-1 and many other Populus species and hybrids poses significant challenges for research that employs sequence-sensitive approaches, such as next-generation sequencing and sitespecific genome editing. Using the routinely transformed genotype Populus tremula×alba 717-1B4 as a test case, we utilized established variant-calling pipelines with affordable re-sequencing (~20×) and publicly available transcriptome data to generate a variant-substituted custom genome (sPta717). The sPta717 genome harbors over 10 million SNPs or small indels relative to the P. trichocarpa v3 reference genome. When applied to RNA-Seq analysis, the fraction of uniquely mapped reads increased by 13-28 % relative to that obtained with the P. trichocarpa reference genome, depending on read length and sequence type. The enhanced mapping rates enabled detection of several hundred more expressed genes and improved the differential expression analysis. Similar improvements were observed for DNA-Seq and ChIP-Seq data mapping. The sPta717 genome is also instrumental in guide RNA (gRNA) design for CRISPR-mediated genome editing. We showed that a majority of gRNAs designed from the P. trichocarpa reference genome contain mismatches with the corresponding target sequences of sPta717, likely rendering those gRNAs ineffective in transgenic 717. A website is provided for querying the sPta717 genome by gene model or homology search. The same approach should be applicable to other outcrossing species with a closely related reference genome.
A 250-microm-bore size and 50-cm-length hollow-glass waveguide (HGW) coated with a thin film of silver has been used to transport laser pulses at 800 nm from a Ti:sapphire oscillator. The silver film is deposited by a liquid-phase process. The measured transmission of this silver-coated HGW is 95%, which is considerably higher than the transmission of HGWs with no coating, as reported by other groups. The image of the output beam taken at different distances from the fiber output shows that a single HE11 mode couples to free-space modes from the exit of the fiber. Considerable spectral broadening can be obtained with high-intensity femtosecond pulse when this waveguide is filled with argon. This HGW can be used for such applications as beam transport and optical-pulse compression.
Abstract. Silicon photonic crystal sensors have become very attractive for various optical sensing applications. Using silicon as a material platform provides the ability to fabricate sensors with other photonic devices on a single chip. In this paper, a new optical sensor based on optical resonance in a one-dimensional silicon photonic crystal with an air defect is theoretically studied for refractive index sensing in the infrared wavelength region. The air defect introduces a cavity into the photonic crystal, making it suitable for probing the properties of a gas found within the cavity. This photonic crystal nanocavity is designed to oscillate at a single mode with a high quality factor, allowing for refractive index sensing of gases with a high sensitivity. A method is presented to maximize the sensitivity of the sensor and to obtain a very narrow bandwidth cavity mode for good sensor resolution. We change the thickness of the air layers linearly in the photonic crystals on both sides of the nanocavity and show that a sensitivity of 1200 nm RIU −1 can be achieved. We present a detailed analysis of the sensor and variations of the layer thicknesses, the cavity length, and the number of periodic layers in the photonic crystal are investigated. This optical sensor has a much simpler design and higher sensitivity compared to other photonic crystal sensors reported previously.
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