Evolutionary approach for finding the atomic structure of steps on stable crystal surfaces

The problem addressed here can be concisely formulated as follows: Given a stable surface orientation with a known reconstruction and given a direction in the plane of this surface, find the atomic structure of the steps oriented along that direction. We report a robust and generally applicable variable-number genetic algorithm for determining the atomic configuration of crystallographic steps, and exemplify it by finding structures for several types of monatomic steps on Si(114)-2×1. We show that the location of the step edge with respect to the terrace reconstructions, the step width (number of atoms), and the positions of the atoms in the step region can all be simultaneously determined

The stability of strained H:Si(105) and H:Ge(105) surfaces

We report atomic scale studies of the effect of applied strain and hydrogen environment on the reconstructions of the (105) Si and Ge surfaces. Surface energy calculations for monohydride-terminated (001) and (105) reconstructions reveal that the recently established single-height rebonded model is unstable not only with respect to (001), but also in comparison to other monohydride (105) structures. This finding persists for both Si and Ge, for applied biaxial strains from -4% to 4%, and for nearly the entire relevant domain of the chemical potential of hydrogen, thus providing an explanation for the recently observed H-induced destabilization of the Ge(105) surface

Compact silicon photonic waveguide modulator based on the vanadium dioxide metal-insulator phase transition

We have integrated lithographically patterned VO2 thin films grown by pulsed laser deposition with silicon-on-insulator photonic waveguides to demonstrate a compact in-line absorption modulator for use in photonic circuits. Using single-mode waveguides at λ = 1550 nm, we show optical modulation of the guided transverse-electric mode of more than 6.5 dB with 2 dB insertion loss over a 2-µm active device length. Loss is determined for devices fabricated on waveguide ring resonators by measuring the resonator spectral response, and a sharp decrease in resonator quality factor is observed above 70 °C, consistent with switching of VO_2 to its metallic phase. A computational study of device geometry is also presented, and we show that it is possible to more than double the modulation depth with modified device structures

Wafer-bonded single-crystal silicon slot waveguides and ring resonators

We fabricated horizontal Si slot waveguides with a 25 nm SiO2 slot layer by bonding thin Si-on-insulator wafers. After removing the Si substrate and buried oxide from one side of the bonded structure, grating-coupled waveguides and ring resonators were partially etched into the Si/SiO2/Si device layers. The gratings exhibit efficiencies of up to 23% at 1550 nm and the ring resonators were measured to have loaded quality factors near 42 000 for the lowest-order transverse-electric mode, corresponding to a propagation loss of 15 dB/cm. The leaky lowest-order transverse-magnetic mode was also observed with a propagation loss of 44 dB/cm

Identification of the expressome by machine learning on omics data.

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes

Highly Strained Compliant Optical Metamaterials with Large Frequency Tunability

Metamaterial designs are typically limited to operation over a narrow bandwidth dictated by the resonant line width. Here we report a compliant metamaterial with tunability of Δλ ~ 400 nm, greater than the resonant line width at optical frequencies, using high-strain mechanical deformation of an elastomeric substrate to controllably modify the distance between the resonant elements. Using this compliant platform, we demonstrate dynamic surface-enhanced infrared absorption by tuning the metamaterial resonant frequency through a CH stretch vibrational mode, enhancing the reflection signal by a factor of 180. Manipulation of resonator components is also used to tune and modulate the Fano resonance of a coupled system

Efficient Coupling between Dielectric-Loaded Plasmonic and Silicon Photonic Waveguides

The realization of practical on-chip plasmonic devices will require efficient coupling of light into and out of surface plasmon waveguides over short length scales. In this letter, we report on low insertion loss for polymer-on-gold dielectric-loaded plasmonic waveguides end-coupled to silicon-on-insulator waveguides with a coupling efficiency of 79 ± 2% per transition at telecommunication wavelengths. Propagation loss is determined independently of insertion loss by measuring the transmission through plasmonic waveguides of varying length, and we find a characteristic surface-plasmon propagation length of 51 ± 4 μm at a free-space wavelength of λ = 1550 nm. We also demonstrate efficient coupling to whispering-gallery modes in plasmonic ring resonators with an average bending-loss-limited quality factor of 180 ± 8

Modifying the radiative quantum efficiency of erbium-doped glass in silicon slot waveguides

We have modulated the radiative emission rate of Er In SI slot waveguides with Er-doped glass slots by varying the waveguide layer dimensions. The corresponding quantum efficiency of 1537-nm emission varies between 0.37 and 0.51

Index-Coupled Distributed-Feedback Semiconductor Quantum Cascade Lasers Fabricated Without Epitaxial Regrowth

Quantum cascade (QC) lasers and methods of fabricating such QC lasers are provided. The QC lasers incorporate a DFB grating without requiring the use of relying on epitaxial regrowth processes. The DFB gratings are formed as sidewall gratings along the lateral length of the QC active region, or the DFB gratings are formed atop the lateral length of the QC active region, and wherein the top DFB grating is planarized with a polymeric material