Surface structured optical coatings with near-perfect broadband and wide-angle antireflective properties

Optical thin-film coatings are typically limited to designs where the refractive index varies in only a single dimension. However, additional control over the propagation of incoming light is possible by structuring the other two dimensions. In this work, we demonstrate a three-dimensional surface structured optical coating that combines the principles of thin-film optical design with bio-inspired nanostructures to yield near-perfect antireflection. Using this hybrid approach, we attain average reflection losses of 0.2% on sapphire and 0.6% on gallium nitride for 300-1800 nm light. This performance is maintained to very wide incidence angles, achieving less than 1% reflection at all measured wavelengths out to 45° for sapphire. This hybrid design has the potential to significantly enhance the broadband and wide-angle properties for a number of optical systems that require high transparency.

Design of antireflective nanostructures and optical coatings for next-generation multijunction photovoltaic devices

The successful development of multijunction photovoltaic devices with four or more subcells has placed additional importance on the design of high-quality broadband antireflection coatings. Antireflective nanostructures have shown promise for reducing reflection loss compared to the best thin-film interference coatings. However, material constraints make nanostructures difficult to integrate without introducing additional absorption or electrical losses. In this work, we compare the performance of various nanostructure configurations with that of an optimized multilayer antireflection coating. Transmission into a four-junction solar cell is computed for each antireflective design, and the corresponding cell efficiency is calculated. We find that the best performance is achieved with a hybrid configuration that combines nanostructures with a multilayer thin-film optical coating. This approach increases transmitted power into the top subcell by 1.3% over an optimal thin-film coating, corresponding to an increase of approximately 0.8% in the modeled cell efficiency.

Heterogeneously integrated III-V-on-silicon multibandgap superluminescent light-emitting diode with 290 nm optical bandwidth

A broadband superluminescent III-V-on-silicon light-emitting diode (LED) was realized. To achieve the large bandwidth, quantum well intermixing and multiple die bonding of InP on a silicon photonic waveguide circuit were combined for the first time, to the best of our knowledge. The device consists of four sections with different bandgaps, centered around 1300, 1380, 1460, and 1540 nm. The fabricated LEDs were connected on-chip in a serial way, where the light generated in the smaller bandgap sections travels through the larger bandgap sections. By balancing the pump current in the four LEDs, we achieved 292 nm of 3 dB bandwidth and an on-chip power of -8  dBm.

Athermal laser design

This paper discusses circuit based and waveguide based athermalization schemes and provides some design examples of athermalized lasers utilizing fully integrated athermal components as an alternative to power hungry thermo-electric controllers (TECs), off-chip wavelength lockers or monitors with lookup tables for tunable lasers. This class of solutions is important for uncooled transmitters on silicon.

Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map

Background

Lotus is a diploid plant with agricultural, medicinal, and ecological significance. Genetic linkage maps are fundamental resources for genome and genetic study, and also provide molecular markers for breeding in agriculturally important species. Genotyping by sequencing revolutionized genetic mapping, the restriction-site associated DNA sequencing (RADseq) allowed rapid discovery of thousands of SNPs markers, and a crucial aspect of the sequence based mapping strategy is the reference sequences used for marker identification.

Results

We assessed the effectiveness of linkage mapping using three types of references for scoring markers: the unmasked genome, repeat masked genome, and gene models. Overall, the repeat masked genome produced the optimal genetic maps. A high-density genetic map of American lotus was constructed using an F₁ population derived from a cross between Nelumbo nucifera ‘China Antique’ and N. lutea ‘AL1’. A total of 4,098 RADseq markers were used to construct the American lotus ‘AL1’ genetic map, and 147 markers were used to construct the Chinese lotus ‘China Antique’ genetic map. The American lotus map has 9 linkage groups, and spans 494.3 cM, with an average distance of 0.7 cM between adjacent markers. The American lotus map was used to anchor scaffold sequences in the N. nucifera ‘China Antique’ draft genome. 3,603 RADseq markers anchored 234 individual scaffold sequences into 9 megascaffolds spanning 67% of the 804 Mb draft genome.

Conclusions

Among the unmasked genome, repeat masked genome and gene models, the optimal reference sequences to call RADseq markers for map construction is repeat masked genome. This high density genetic map is a valuable resource for genomic research and crop improvement in lotus.

Low threshold and high speed short cavity distributed feedback hybrid silicon lasers

In this paper we investigate reducing threshold and improving the efficiency and speed of distributed feedback hybrid silicon lasers. A low threshold current of 8.8 mA was achieved for a 200 μm cavity at 20 °C. A 3 dB bandwidth of 9.5 GHz as well as 12.5 Gb/s direct modulation of DFB laser diode was achieved on the hybrid silicon platform for the first time.

Fano resonances in a multimode waveguide coupled to a high-Q silicon nitride ring resonator

Silicon nitride (Si3N4) optical ring resonators provide exceptional opportunities for low-loss integrated optics. Here we study the transmission through a multimode waveguide coupled to a Si3N4 ring resonator. By coupling single-mode fibers to both input and output ports of the waveguide we selectively excite and probe combinations of modes in the waveguide. Strong asymmetric Fano resonances are observed and the degree of asymmetry can be tuned through the positions of the input and output fibers. The Fano resonance results from the interference between modes of the waveguide and light that couples resonantly to the ring resonator. We develop a theoretical model based on the coupled mode theory to describe the experimental results. The large extension of the optical modes out of the Si3N4 core makes this system promising for sensing applications.

Genetic analysis of safflower domestication

BACKGROUND

Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family.We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization.

RESULTS

We mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species.

CONCLUSIONS

As has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes.

Thermal stress implications in athermal TiO2 waveguides on a silicon substrate

Ring resonators with TiO2 core confinement factors from 0.07 to 0.42 are fabricated and measured for thermal sensitivity achieving -2.9 pm/K thermal drift in the best case. Materials used are CMOS compatible (TiO2, SiO2 and Si3N4) on a Si substrate. The under discussed role of stress in thermo-optic behavior is clearly observed when contrasting waveguides buried in SiO2 to those with etched sidewalls revealed to air. Multiphysics simulations are conducted to provide a theoretical explanation of this phenomenon in contrast to the more widely reported theories on thermo-optic behavior dominated by confinement factor.

InP-based waveguide photodiodes heterogeneously integrated on silicon-on-insulator for photonic microwave generation

High-linearity modified uni-traveling carrier photodiodes on silicon-on-insulator with low AM-to-PM conversion factor are demonstrated. The devices deliver more than 2.5 dBm RF output power up to 40 GHz and have an output third order intercept point of 30 dBm at 20 GHz. Photodiode arrays exceed a saturation current-bandwidth-product of 630 mA · GHz and reach unsaturated RF output power levels of 10 dBm at 20 GHz.

Field-effect modulation of thermoelectric properties in multigated silicon nanowires

Electric-field-induced charge carriers typically exhibit greater mobility over carriers contributed by chemical dopants and offer a powerful mechanism for thermoelectric power factor enhancement. We fabricate multigated silicon nanowires (Si NWs) and demonstrate significant modulation of electrical conductivity and the Seebeck coefficient with gate bias. Because of the higher mobility of field-effect charge carriers, we demonstrate that power factor for the gated Si NWs is similar to the highest values reported for n-type Si nanostructures despite charge transport only occurring at the NW surface. Field-effect doping is a promising strategy for optimizing power factor and may result in significant power factor enhancement in smaller diameter Si NWs where high average carrier densities can be obtained with induced surface charge.

Widely tunable Vernier ring laser on hybrid silicon

A hybrid silicon tunable Vernier ring laser is designed and fabricated by integration of two intra-cavity ring resonators, hybrid III-V-on-silicon gain elements, and resistive heaters for thermal tuning. Thermal tuning of more than 40 nm is demonstrated with side mode suppression ratio greater than 35 dB and linewidth of 338 kHz.

Nonlinear modeling of waveguide photodetectors

A new method of simulating photodiode nonlinearities is proposed. This model includes the effects of non-uniform absorption in three dimensions, self-heating, and is compatible with circuit components defined in the frequency domain, such as transmission lines. The saturated output power and third order output intercept points of two different waveguide photodiodes are simulated, with excellent agreement between measurement and theory. The technique is then used to provide guidance for the future design of linear waveguide-based photodetectors.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Background

Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.

Results

The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment.

Conclusions

The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.

Association mapping and the genomic consequences of selection in sunflower

The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval.

Integrated TE and TM optical circulators on ultra-low-loss silicon nitride platform

In this paper, we present two four-port optical circulators for TE and TM modes, respectively. Exploiting the recent technological development concerning Ce:YIG pulse laser deposition on silicon nitride platform, we design two integrated circulators, which can be used to implement several functions in integrated optics, such as de-interleavers, input/output amplifier isolators and output laser isolators. The proposed devices combine the benefit of low loss silicon nitride waveguides with the non-reciprocal properties of magneto-optical materials. The ring cross-section has been optimized in order to maximize the non-reciprocal phase shift and finally the scattering coefficients have been computed using the transfer matrix method. The material stability and refractive index regularity of silicon nitride, the small micro-ring footprint, and the high wavelength selectivity make these devices particularly attractive.

Sidewall gratings in ultra-low-loss Si3N4 planar waveguides

We demonstrate sidewall gratings in an ultra-low-loss Si3N4 planar waveguide platform. Through proper geometrical design we can achieve coupling constant values between 13 and 310 cm(-1). The TE waveguide propagation loss over the range of 1540 to 1570 nm is below 5.5 dB/m.

Silicon on ultra-low-loss waveguide photonic integration platform

We demonstrate a novel integrated silicon and ultra-low-loss Si3N4 waveguide platform. Coupling between layers is achieved with (0.4 ± 0.2) dB of loss per transition and a 20 nm 3-dB bandwidth for one tapered coupler design and with (0.8 ± 0.2) dB of loss per transition and a 100 nm 3-dB bandwidth for another. The minimum propagation loss measured in the ultra-low-loss waveguides is 1.2 dB/m in the 1590 nm wavelength regime.

Realization of an ultra-short silicon polarization beam splitter with an asymmetrical bent directional coupler

An ultra-short (~10 μm long) polarization beam splitter (PBS) based on an asymmetrical bent directional coupler (DC) is demonstrated experimentally by using silicon-on-insulator nanowires. The bent DC is designed to cross-couple TM polarized light completely while there is almost no coupling for TE polarization. Grating couplers are introduced at both ends of the PBS for efficient coupling to single-mode fibers. The measurement results show that the extinction ratios of the fabricated ultra-short PBS are higher than 10 dB for both polarizations in a broad wavelength range. It is also shown that the present PBS has a large fabrication tolerance.

A "2-omega" technique for measuring anisotropy of thermal conductivity

A popular method of measuring the thermal conductivity of thin films and substrates, the "3-omega" method, is modified to yield a new technique for measuring the anisotropy in thermal transport in bulk materials. The validity of the proposed technique is established by measuring the thermal conductivity of strontium titanate, which is expected to be isotropic because of its cubic unit cell. The technique is then applied to rutile TiO(2). The analysis of experimental results on (100) and (001) TiO(2) reveals that the anisotropy is a function of the crystalline quality, as quantified by the effective thermal conductivity obtained through conventional "3-omega" measurements. The advantages of the proposed technique are similar to those of the standard "3-omega" method, namely the simplicity of sample preparation and measurement, and negligible errors due to radiation because of the small volume of material being heated. For anisotropy determination, the proposed technique has the additional advantage that a single sample is sufficient to determine both components of the thermal conductivity, namely the values in and perpendicular to the plane of cleavage. This is significant for materials in which there is a large variation in the crystalline quality from sample to sample. For such materials, it is unreliable to use two different samples, one for measuring the thermal conductivity in each direction. Experimental data are analyzed using a 3D Fourier-series based method developed in this work. The proposed method determines each component of the thermal conductivity with an estimated accuracy of about 10%.

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

BACKGROUND

Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut.

RESULTS

A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution.

CONCLUSIONS

Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.

Hybrid III/V silicon photonic source with integrated 1D free-space beam steering

A chip-scale optical source with integrated beam steering is demonstrated. The chip was fabricated using the hybrid silicon platform and incorporates an on-chip laser, waveguide splitter, amplifiers, phase modulators, and surface gratings to comprise an optical phased array with beam steering across a 12° field of view in one axis. Tuning of the phased array is used to achieve 1.8°(steered axis)×0.6°(nonsteered axis) beam width with 7 dB background suppression for arbitrary beam direction within the field of view.

Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.)

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

Background

Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea.

Results

More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago.

Conclusions

The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.

Design and demonstration of ultra-fast W-band photonic transmitter-mixer and detectors for 25 Gbits/sec error-free wireless linking

A 25 Gbits/s error-free on-off-keying (OOK) wireless link between an ultra high-speed W-band photonic transmitter-mixer (PTM) and a fast W-band envelope detector is demonstrated. At the transmission end, the high-speed PTM is developed with an active near-ballistic uni-traveling carrier photodiode (NBUTC-PD) integrated with broadband front-end circuitry via the flip-chip bonding technique. Compared to our previous work, the wireless data rate is significantly increased through the improvement on the bandwidth of the front-end circuitry together with the reduction of the intermediate-frequency (IF) driving voltage of the active NBUTC-PD. The demonstrated PTM has a record-wide IF modulation (DC-25 GHz) and optical-to-electrical fractional bandwidths (68-128 GHz, ~67%). At the receiver end, the demodulation is realized with an ultra-fast W-band envelope detector built with a zero-bias Schottky barrier diode with a record wide video bandwidth (37 GHz) and excellent sensitivity. The demonstrated PTM is expected to find applications in multi-gigabit short-range wireless communication.