Light Scattering and Electron Microscopy Study of the Surface Morphology of GaAs Films Grown by Molecular Beam Epitaxy

The surface morphology of thermally quenched GaAs films grown by molecular beam epitaxy on GaAs substrates has been studied by elastic light scattering, by scanning electron microscopy and by scanning tunneling microscopy (STM) in air. STM shows that the oxide-desorbed surface of GaAs is pitted, but smooths after deposition of a few hundred nanometers of material. Light scattering shows that, after the surface has smoothed, the power spectral density of the surface approaches a q-2 dependence on spatial frequency over the spatial frequency range 0.2 μm-1 \u3c q \u3c 20 μm-1 that is accessible to the light scattering measurements at 488 nm. This result is in agreement with the predictions of dynamical scaling theory in the case where the time evolution of the surface morphology is described by an Edwards-Wilkinson type equation

Dispersive photoluminescence decay by geminate recombination in amorphous semiconductors

The photoluminescence decay in amorphous semiconductors is described by power law $t^{-delta}$ at long times. The power-law decay of photoluminescence at long times is commonly observed but recent experiments have revealed that the exponent, $delta sim 1.2-1.3$, is smaller than the value 1.5 predicted from a geminate recombination model assuming normal diffusion. Transient currents observed in the time-of-flight experiments are highly dispersive characterized by the disorder parameter $alpha$ smaller than 1. Geminate recombination rate should be influenced by the dispersive transport of charge carriers. In this paper we derive the simple relation, $delta = 1+ alpha/2$. Not only the exponent but also the amplitude of the decay calculated in this study is consistent with measured photoluminescence in a-Si:H.Comment: 18pages. Submitted for the publication in Phys. Rev.

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for {\em de novo} assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly

In situ synchrotron investigation of degenerate graphite nodule evolution in ductile cast iron

Ductile cast irons (DCIs) are of increasing importance in the renewable energy and transportation sectors. The distribution and morphology of the graphite nodules, in particular the formation of degenerate features during solidification, dictate the mechanical performance of DCIs. In situ high-speed synchrotron X-ray tomography was used to capture the evolution of graphite nodules during solidification of DCI, including degenerate features and the effect of the carbon concentration field. The degeneration of nodules is observed to increase with re-melting cycles, which is attributed to Mg-loss. The dendritic primary austenite and carbon concentration gradients in the surrounding liquid phase were found to control nodule morphology by locally restricting and promoting growth. A coupled diffusion-mechanical model was developed, confirming the experimentally informed hypothesis that protrusions form through liquation cracking of the austenite shell and subsequent localised growth. These results provide valuable insights into the solidification kinetics of cast irons, supporting the design of advanced alloys

A Coupled Equations Model for Epitaxial Growth on Textured Surfaces

We have developed a continuum model that explains the complex surface shapes observed in epitaxial regrowth on micron scale gratings. This model describes the dependence of the surface morphology on film thickness and growth temperature in terms of a few simple atomic scale processes including adatom diffusion, step-edge attachment and detachment, and a net downhill migration of surface adatoms. The continuum model reduces to the linear part of the Kardar-Parisi-Zhang equation with a flux dependent smoothing coefficient in the long wavelength limit.Comment: 11 pages, 4 figures. Submitted to the Journal of Crystal Growt

Measuring Charge Transport in an Amorphous Semiconductor Using Charge Sensing

We measure charge transport in hydrogenated amorphous silicon (a-Si:H) using a nanometer scale silicon MOSFET as a charge sensor. This charge detection technique makes possible the measurement of extremely large resistances. At high temperatures, where the a-Si:H resistance is not too large, the charge detection measurement agrees with a direct measurement of current. The device geometry allows us to probe both the field effect and dispersive transport in the a-Si:H using charge sensing and to extract the density of states near the Fermi energy.Comment: 4 pages, 4 figure

Divergence in Gene Regulation Contributes to Sympatric Speciation of \u3ci\u3eShewanella baltica\u3c/i\u3e Strains

Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185—the strain isolated from a nitrate-rich environment—upregulated nearly twice the number of shared genes upregulated by OS195—the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations

Auger recombination suppression and band alignment in GaAsBi/GaAs heterostructures

Using a combination of experimental and theoretical techniques we present the dependence of the bandgap Eg and the spin orbit splitting energy so, with Bi concentration in GaAsBi/GaAs samples. We find that the concentration at which so,> Eg occurs at 9%. Both spectroscopic as well as first device results indicate a type I alignment

Unraveling compacted graphite evolution during solidification of cast iron using in-situ synchrotron X-ray tomography

In spite of many years of research, the physical phenomena leading to the evolution of compacted graphite (CG) during solidification is still not fully understood. In particular, it is unknown how highly branched CG aggregates form and evolve in the semi-solid, and how local microstructural variations at micrometer length scale affect this growth process. We present here the first time-resolved synchrotron tomography combined with a bespoke high-temperature environmental cell that allows direct observation of the evolution of CG and relates this dynamic process to the local surrounding microstructures in a cast iron sample during repeated melting and solidification. Distinct processes are identified for the formation of CG involving the nucleation, growth, development of branches and interconnection of graphite particles, ultimately evolving into highly branched graphite aggregates with large sizes and low sphericities. CG is found to nucleate with a spheroidal or a plate-like shape, developing branches induced by high carbon concentration, e.g. thin melt channels. Additionally, CG grows much faster than spheroidal graphite during subsequent cooling in solid state. The direct visualization of the dynamic solidification process provides unprecedented new insights into formation mechanisms of CG and correlating factors such as local microstructural variations, and guides the development of CG iron solidification models

Simple transfer functions for calculating benthic fixed nitrogen losses and C:N:P regeneration ratios in global biogeochemical models

Empirical transfer functions are derived for predicting the total benthic nitrate loss(LNO3) and the net loss of dissolved inorganic nitrogen (LDIN) in marine sediments,equivalent to sedimentary denitrification. The functions are dynamic vertically integratedsediment models which require the rain rate of particulate organic carbon to the seafloor(RRPOC) and a proposed new variable(O2-NO3)bw (bottom water O2 concentration minus NO3-concentration) as the only input parameters. Applied globally to maps of RRPOC and(O2-NO3)bw on a 1° x 1° spatial resolution, the models predict a NO3- drawdown of 196 Tg yr-1 (LNO3)of which 153 – 155 Tg yr-1 is denitrified to N2 (LDIN). This is in good agreement with previous estimates using very different methods. Our approach implicitly accounts for fixed N loss via anammox, such that our findings do not support the idea that the relatively recent discovery of anammox in marine sediments might require current estimates of the global benthic marine N budget to be revised. The continental shelf (0 – 200 m) accounts for >50% of global LNO3 and LDIN, with slope (200 – 2000 m) and deep-sea (>2000 m) sediments contributing ca. 30% and 20%, respectively. Denitrification in high-nitrate/low-oxygen regions such as oxygen minimum zones is significant (ca. 15 Tg N yr-1; 10% of global) despite covering only 1% of the seafloor. The data are used to estimate the net fluxes of nitrate (18 Tg N yr-1) and phosphate(27 Tg P yr-1) across the sediment-water interface. The benthic fluxes strongly deviate from Redfield composition, with globally averaged N:P, N:C and C:P values of 8.3, 0.067 and 122, respectively, indicating world-wide fixed N losses (by denitrification) relative to C and P. The transfer functions are designed to be coupled dynamically to general circulation models to better predict the feedback of sediments on pelagic nutrient cycling and dissolved O2 distributions