Enhancing the Radiative Rate in III-V Semiconductor Plasmonic Core-Shell Nanowire Resonators

We investigate the radiative properties of plasmonic core-shell nanowire resonators and, using boundary element method calculations, demonstrate enhanced radiative decay rate by up to 3500 times in nanoscale compound semi-conductor/metal cavities. Calculation of the local density of optical states enables identification of new types of modes in cavities with mode volumes on the order of 10^(-4)(λ/n)^3. These modes dramatically enhance the radiative decay rate and significantly modify the polarization of far-field emission

Size tunable visible and near-infrared photoluminescence from vertically etched silicon quantum dots

Corrugated etching techniques were used to fabricate size-tunable silicon quantum dots that luminesce under photoexcitation, tunable over the visible and near infrared. By using the fidelity of lithographic patterning and strain limited, self-terminating oxidation, uniform arrays of pillar containing stacked quantum dots as small as 2 nm were patterned. Furthermore, an array of pillars, with multiple similar sized quantum dots on each pillar, was fabricated and tested. The photoluminescence displayed a multiple, closely peaked emission spectra corresponding to quantum dots with a narrow size distribution. Similar structures can provide quantum confinement effects for future nanophotonic and nanoelectronic devices

An Iron-Based Ecosystem Model of the Central Equatorial Pacific

The central and eastern equatorial Pacific region is characterized by lower than expected phytoplankton biomass and primary production given the relatively high ambient nitrate concentrations. These unusual conditions have spawned several field programs and laboratory experiments to determine why this high nitrate-low chlorophyll pattern persists in this region. To synthesize the results from these field programs, as well as providing additional evidence in support of the iron hypothesis, we developed a one-dimensional, nine-component ecosystem model of 0 degrees N 140 degrees W. The model components include two phytoplankton size fractions, two zooplankton size fractions, two detrital size fractions, dissolved iron, nitrate, and ammonium. The model was run for 5 years (1990-1994) and was forced using an atmospheric radiative transfer model, an ocean general circulation model (GCM), and in situ data. To our knowledge, this is the first ecosystem model at 0 degrees N 140 degrees W to synthesize the Joint Global Ocean Flux Study Equatorial Pacific Process Study (JGOFS EqPac) data set, as well as to use both in situ and modeled physical data to drive the model. Modeled phytoplankton, zooplankton, and iron all varied on interannual timescales due to El Nino events. Total phytoplankton biomass increased by as much as 40% from early 1992 (El Nino warm) to 1993 (normal). The results also indicate that the biomass increase during a cool period is not constant for each phytoplankton component, but instead the increase is most evident in the netphytoplankton (\u3e10 mu m). Netphytoplankton increase from a low of 0.1% of the total chlorophyll in 1992 to a high of 30% of the total in 1993. Microzooplankton grazing rates fluctuated in response to changes in nanophytoplankton growth rates, whereas mesozooplankton grazing was unrelated to netphytoplankton growth rates. The magnitude and temporal variability of phytoplankton chlorophyll agreed well with in situ data collected during 1992. Modeled primary production was lower than measured during El Nino but agreed with observations during normal conditions. The low primary productivity was probably a result of downwelling produced by the physical model. New production was calculated from total and recycled iron rather than nitrate-based production and was more variable in general and almost 3 times the nitrate-based new production during non-El Nino conditions

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Tunable Visible and Near-IR Emission from Sub-10 nm Etched Single-Crystal Si Nanopillars

Visible and near-IR photoluminescence (PL) is reported from sub-10 nm silicon nanopillars. Pillars were plasma etched from single crystal Si wafers and thinned by utilizing strain-induced, self-terminating oxidation of cylindrical structures. PL, lifetime, and transmission electron microscopy were performed to measure the dimensions and emission characteristics of the pillars. The peak PL energy was found to blue shift with narrowing pillar diameter in accordance with a quantum confinement effect. The blue shift was quantified using a tight binding method simulation that incorporated the strain induced by the thermal oxidation process. These pillars show promise as possible complementary metal oxide semiconductor compatible silicon devices in the form of light-emitting diode or laser structures

Plasmonic Modes of Annular Nanoresonators Imaged by Spectrally Resolved Cathodoluminescence

We report the observation of plasmonic modes of annular resonators in nanofabricated Ag and Au surfaces that are imaged by spectrally resolved cathodoluminescence. A highly focused 30 keV electron beam is used to excite localized surface plasmons that couple to collective resonant modes of the nanoresonators. We demonstrate unprecedented resolution of plasmonic mode excitation and by combining these observations with full-field simulations find that cathodoluminescence in plasmonic nanostructures is most efficiently excited at positions corresponding to antinodes in the modal electric field intensity

Plasmonic Modes of Annular Nanoresonators Imaged by Spectrally Resolved Cathodoluminescence NANO LETTERS

We report the observation of plasmonic modes of annular resonators in nanofabricated Ag and Au surfaces that are imaged by spectrally resolved cathodoluminescence. A highly focused 30 keV electron beam is used to excite localized surface plasmons that couple to collective resonant modes of the nanoresonators. We demonstrate unprecedented resolution of plasmonic mode excitation and by combining these observations with full-field simulations find that cathodoluminescence in plasmonic nanostructures is most efficiently excited at positions corresponding to antinodes in the modal electric field intensity. Excitation and localization of surface plasmon polariton (SPP) modes in metallodielectric structures is currently a topic of intensive research motivated by the ability to achieve truly nanophotonic materials and devices with tunable optical dispersion. 1 In particular, nanoresonators are essential building blocks of future subwavelength-scale photonic systems as both active 2 and passive 3 device components. Nanostructures consisting of annular grooves and gratings in metal films exhibit exciting properties such as photon-to-plasmo