Quantum confinement in Si and Ge nanostructures: Effect of crystallinity

We look at the relationship between the preparation method of Si and Ge nanostructures (NSs) and the structural, electronic, and optical properties in terms of quantum confinement (QC). QC in NSs causes a blue shift of the gap energy with decreasing NS dimension. Directly measuring the effect of QC is complicated by additional parameters, such as stress, interface and defect states. In addition, differences in NS preparation lead to differences in the relevant parameter set. A relatively simple model of QC, using a `particle-in-a-box'-type perturbation to the effective mass theory, was applied to Si and Ge quantum wells, wires and dots across a variety of preparation methods. The choice of the model was made in order to distinguish contributions that are solely due to the effects of QC, where the only varied experimental parameter was the crystallinity. It was found that the hole becomes de-localized in the case of amorphous materials, which leads to stronger confinement effects. The origin of this result was partly attributed to differences in the effective mass between the amorphous and crystalline NS as well as between the electron and hole. Corrections to our QC model take into account a position dependent effective mass. This term includes an inverse length scale dependent on the displacement from the origin. Thus, when the deBroglie wavelength or the Bohr radius of the carriers is on the order of the dimension of the NS the carriers `feel' the confinement potential altering their effective mass. Furthermore, it was found that certain interface states (Si-O-Si) act to pin the hole state, thus reducing the oscillator strength.Comment: arXiv admin note: substantial text overlap with arXiv:1111.201

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

Myaamiaataweenki eekincikoonihkiinki eeyoonki aapisaataweenki: A Miami Language Digital Tool for Language Reclamation

In 1988, a young graduate student at the University of California, Berkeley began searching for materials on a little-known Algonquian language called Miami, which had ceased to be spoken sometime in the mid-twentieth century. Prompted by curiosity to describe this little-known language, the search uncovered two and a half centuries of documentation. This archival record would serve as the basis for the grammatical reconstruction of what is known today as the Miami-Illinois language, a central Algonquian language of the southern Great Lakes region. These materials are crucial not only to the reconstruction of Miami-Illinois, but also for the growing interests of Myaamia (Miami) people to reclaim their language and cultural heritage. The next twenty years proved to be a struggle in locating, duplicating, organizing and building a physical corpus of data for linguistic analysis and use in community revitalization. Language reconstruction from documentation requires tools for archival interaction and access that linguistically-based software and database applications lacked at the time. This prompted Myaamia researchers and language educators to seek out support for the construction of a digital archival database that met the needs of both tribal linguists and community culture and language revitalizationists. The first version of the Miami-Illinois Digital Archive (MIDA) became a reality in 2012 after support from the National Endowment for the Humanities (NEH) was provided to Miami University’s Myaamia Center to develop this unique research tool. This paper describes the challenges of working with digitized archival materials and how MIDA has filled the software tool gap between archives, linguists and revitalizationists. The Miami-Illinois Digital Archive can be found at http://www.ilaatawaakani.org.National Foreign Language Resource Cente

Towards predictive modelling of near-edge structures in electron energy loss spectra of AlN based ternary alloys

Although electron energy loss near edge structure analysis provides a tool for experimentally probing unoccupied density of states, a detailed comparison with simulations is necessary in order to understand the origin of individual peaks. This paper presents a density functional theory based technique for predicting the N K-edge for ternary (quasi-binary) nitrogen alloys by adopting a core hole approach, a methodology that has been successful for binary nitride compounds. It is demonstrated that using the spectra of binary compounds for optimising the core hole charge ($0.35\,\mathrm{e}$ for cubic Ti$_{1-x}$Al$_x$N and $0.45\,\mathrm{e}$ for wurtzite Al$_x$Ga$_{1-x}$N), the predicted spectra evolutions of the ternary alloys agree well with the experiments. The spectral features are subsequently discussed in terms of the electronic structure and bonding of the alloys.Comment: 11 pages, 9 figures, 1 tabl

Chalk cliff retreat in East Sussex and Kent 1870s to 2001

The retreat of chalk cliffs fringing the eastern English Channel contributes shingle to the beaches which helps to protect the cliffs and slow down erosion. Conversely, cliff retreat endangers settlements and infrastructure on the clifftop. Rates of retreat have been calculated by a variety of methods over the past century, but no attempt has been made to provide a complete coverage that allows for a true comparison of retreat rates over the entire coastline. Using historic maps and recent orthophotos, cliff retreat rates have been calculated for consecutive 50 m sections of chalk cliff along the English side of the entire eastern English Channel for a period of 125 years. The chalk cliffs of East Sussex erode at an average rate of 0.25 - 0.3 m y−1 while those in Kent at a rate of 0.1 m y−1