Tree-level electron-photon interactions in graphene

Graphene's low-energy electronic excitations obey a 2+1 dimensional Dirac Hamiltonian. After extending this Hamiltonian to include interactions with a quantized electromagnetic field, we calculate the amplitude associated with the simplest, tree-level Feynman diagram: the vertex connecting a photon with two electrons. This amplitude leads to analytic expressions for the 3D angular dependence of photon emission, the photon-mediated electron-hole recombination rate, and corrections to graphene's opacity $\pi \alpha$ and dynamic conductivity $\pi e^2/2 h$ for situations away from thermal equilibrium, as would occur in a graphene laser. We find that Ohmic dissipation in perfect graphene can be attributed to spontaneous emission.Comment: 5 pages, 3 figure

Measuring the Relational Aspects of Civic Engagement and Action

Civic leaders who are highly and effectively engaged often have strong relationships with key stakeholders across institutions and communities. The prevalence and nature of these relationships is not known among those with more typical levels of civic engagement. Via survey data of a random sample of residents of two neighboring French towns, we find that people perceive their neighbors to be, on average, more engaged than they perceive to be themselves, and that few individuals can provide specific action steps for how they would tackle social issues in their community. These results suggest that teaching civic action skills, including how to identify key decision makers as possible allies, is important for civic educators

Phylogeny based discovery of regulatory elements

BACKGROUND: Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. RESULTS: We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. CONCLUSION: The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs

Flow Dynamics And Plasma Heating Of Spheromaks In SSX

We report several new experimental results related to flow dynamics and heating from single dipole-trapped spheromaks and spheromak merging studies at SSX. Single spheromaks (stabilized with a pair of external coils, see Brown, Phys. Plasmas 13 102503 (2006)) and merged FRC-like configurations (see Brown, Phys. Plasmas 13, 056503 (2006)) are trapped in our prolate (R = 0.2 m, L = 0.6 m) copper flux conserver. Local spheromak flow is studied with two Mach probes (r(1) = rho(i) ) calibrated by time-of-flight with a fast set of magnetic probes at the edge of the device. Both Mach probes feature six ion collectors housed in a boron nitride sheath. The larger Mach probe will ultimately be used in the MST reversed field pinch. Line averaged flow is measured by ion Doppler spectroscopy (IDS) at the midplane. The SSX IDS instrument measures with 1 mu s or better time resolution the width and Doppler shift of the C-III impurity (H plasma) 229.7 nm line to determine the temperature and line-averaged flow velocity (see Cothran, RSI 77, 063504 (2006)). We find axial flows up to 100 km/s during formation of the dipole trapped spheromak. Flow returns at the wall to form a large vortex. Recent high-resolution IDS velocity measurements during spheromak merging show bi-directional outflow jets at +/- 40 km/s (nearly the Alfven speed). We also measure T-i \u3e= 80 eV and T-e \u3e= 20 eV during spheromak merging events after all plasma facing surfaces are cleaned with helium glow discharge conditioning. Transient electron heating is inferred from bursts on a four-channel soft x-ray array. The spheromaks are also characterized by a suite of magnetic probe arrays for magnetic structure B(r,t), and interferometry for n(e) . Finally, we are designing a new oblate, trapezoidal flux conserver for FRC studies. Equilibrium and dynamical simulations suggest that a tilt-stable, oblate FRC can be formed by spheromak merging in the new flux conserver

Environment-specific combinatorial cis-regulation in synthetic promoters

When a cell's environment changes, a large transcriptional response often takes place. The exquisite sensitivity and specificity of these responses are controlled in large part by the combinations of cis-regulatory elements that reside in gene promoters and adjacent control regions. Here, we present a study aimed at accurately modeling the relationship between combinations of cis-regulatory elements and the expression levels they drive in different environments. We constructed four libraries of synthetic promoters in yeast, consisting of combinations of transcription factor binding sites and assayed their expression in four different environments. Thermodynamic models relating promoter sequences to their corresponding four expression levels explained at least 56% of the variation in expression in each library through the different conditions. Analyses of these models suggested that a large fraction of regulated gene expression is explained by changes in the effective concentration of sequence-specific transcription factors, and we show that in most cases, the corresponding transcription factors are expressed in a pattern that is predicted by the thermodynamic models. Our analysis uncovered two binding sites that switch from activators to repressors in different environmental conditions. In both the cases, the switch was not the result of a single transcription factor changing regulatory modes, but most likely due to competition between multiple factors binding to the same site. Our analysis suggests that this mode of regulation allows for large and steep changes in expression in response to changing transcription factor concentrations. Our results demonstrate that many complex changes in gene expression are accurately explained by simple changes in the effective concentrations of transcription factors

A Survey of CN and CH Variations in Galactic Globular Clusters from SDSS Spectroscopy

We present a homogeneous survey of the CN and CH bandstrengths in eight Galactic globular clusters observed during the course of the Sloan Extension for Galactic Understanding and Exploration (SEGUE) sub-survey of the SDSS. We confirm the existence of a bimodal CN distribution among RGB stars in all of the clusters with metallicity greater than [Fe/H] = -1.7; the lowest metallicity cluster with an observed CN bimodality is M53, with [Fe/H] ~ -2.1. There is also some evidence for individual CN groups on the subgiant branches of M92, M2, and M13, and on the red giant branches of M92 and NGC 5053. Finally, we quantify the correlation between overall cluster metallicity and the slope of the CN bandstrength-luminosity plot as a means of further demonstrating the level of CN-enrichment in cluster giants. Our results agree well with previous studies reported in the literature.Comment: AJ submitted; 80 pages, 22 figure

3D Reconnection And Flow Dynamics In The SSX Experiment

Several new experimental results are reported from plasma merging studies at the Swarthmore Spheromak Experiment (SSX) with relevance to collisionless three-dimensional magnetic reconnection in laboratory and space plasmas. First, recent high-resolution velocity measurements of impurity ions using ion Doppler spectroscopy (IDS) show bi-directional outflow jets at 40 km/s (nearly the Alfven speed). The SSX IDS instrument measures with 1 mu s or better time resolution the width and Doppler shift of the C-III impurity (H plasma) 229.7 nm line to determine the temperature and line-averaged flow velocity during spheromak merging events. High flow speeds are corroborated using an in situ Mach probe. Second, ion heating to nearly 10(6) K is observed after reconnection events in a low-density kinetic regime. Transient electron heating is inferred from bursts on a 4-channel soft x-ray array as well as vacuum ultraviolet spectroscopy. Third, the out-of-plane magnetic field and the in-plane Lorentz force in a reconnection volume both show a quadrupolar structure at the ion inertial scale (c/omega(pi)). Time resolved vector magnetic field measurements on a 3D lattice B(r, t)) enables this measurement. Earlier work at SSX has shown that fori-nation of three-dimensional structure at the ion inertial scale is temporally and spatially correlated with the observation of superthermal, super-Alfvenic ions accelerated along the X-line normal to the local 2D plane of reconnection. Each of these measurements will be related to and compared with similar observations in a solar or space context

Tracing the Orphan Stream to 55 kpc with RR Lyrae Stars

We report positions, velocities and metallicities of 50 ab-type RR Lyrae (RRab) stars observed in the vicinity of the Orphan stellar stream. Using about 30 RRab stars classified as being likely members of the Orphan stream, we study the metallicity and the spatial extent of the stream. We find that RRab stars in the Orphan stream have a wide range of metallicities, from -1.5 dex to -2.7 dex. The average metallicity of the stream is -2.1 dex, identical to the value obtained by Newberg et al. (2010) using blue horizontal branch stars. We find that the most distant parts of the stream (40-50 kpc from the Sun) are about 0.3 dex more metal-poor than the closer parts (within ~30 kpc), suggesting a possible metallicity gradient along the stream's length. We have extended the previous studies and have mapped the stream up to 55 kpc from the Sun. Even after a careful search, we did not identify any more distant RRab stars that could plausibly be members of the Orphan stream. If confirmed with other tracers, this result would indicate a detection of the end of the leading arm of the stream. We have compared the distances of Orphan stream RRab stars with the best-fit orbits obtained by Newberg et al. (2010). We find that model 6 of Newberg et al. (2010) cannot explain the distances of the most remote Orphan stream RRab stars, and conclude that the best fit to distances of Orphan stream RRab stars and to the local circular velocity is provided by potentials where the total mass of the Galaxy within 60 kpc is M_{60}~2.7x10^{11} Msun, or about 60% of the mass found by previous studies. More extensive modelling that would consider non-spherical potentials and the possibility of misalignment between the stream and the orbit, is highly encouraged.Comment: Submitted to ApJ, 15 pages in emulateapj format, three tables in machine-readable format (download "Source" from "Other formats"

At risk of being risky: The relationship between "brain age" under emotional states and risk preference.

Developmental differences regarding decision making are often reported in the absence of emotional stimuli and without context, failing to explain why some individuals are more likely to have a greater inclination toward risk. The current study (N=212; 10-25y) examined the influence of emotional context on underlying functional brain connectivity over development and its impact on risk preference. Using functional imaging data in a neutral brain-state we first identify the "brain age" of a given individual then validate it with an independent measure of cortical thickness. We then show, on average, that "brain age" across the group during the teen years has the propensity to look younger in emotional contexts. Further, we show this phenotype (i.e. a younger brain age in emotional contexts) relates to a group mean difference in risk perception - a pattern exemplified greatest in young-adults (ages 18-21). The results are suggestive of a specified functional brain phenotype that relates to being at "risk to be risky.

Why do models overestimate surface ozone in the Southeast United States

Ozone pollution in the Southeast US involves complex chemistry driven by emissions of anthropogenic nitrogen oxide radicals (NOx  ≡  NO + NO2) and biogenic isoprene. Model estimates of surface ozone concentrations tend to be biased high in the region and this is of concern for designing effective emission control strategies to meet air quality standards. We use detailed chemical observations from the SEAC4RS aircraft campaign in August and September 2013, interpreted with the GEOS-Chem chemical transport model at 0.25°  ×  0.3125° horizontal resolution, to better understand the factors controlling surface ozone in the Southeast US. We find that the National Emission Inventory (NEI) for NOx from the US Environmental Protection Agency (EPA) is too high. This finding is based on SEAC4RS observations of NOx and its oxidation products, surface network observations of nitrate wet deposition fluxes, and OMI satellite observations of tropospheric NO2 columns. Our results indicate that NEI NOx emissions from mobile and industrial sources must be reduced by 30–60 %, dependent on the assumption of the contribution by soil NOx emissions. Upper-tropospheric NO2 from lightning makes a large contribution to satellite observations of tropospheric NO2 that must be accounted for when using these data to estimate surface NOx emissions. We find that only half of isoprene oxidation proceeds by the high-NOx pathway to produce ozone; this fraction is only moderately sensitive to changes in NOx emissions because isoprene and NOx emissions are spatially segregated. GEOS-Chem with reduced NOx emissions provides an unbiased simulation of ozone observations from the aircraft and reproduces the observed ozone production efficiency in the boundary layer as derived from a regression of ozone and NOx oxidation products. However, the model is still biased high by 6 ± 14 ppb relative to observed surface ozone in the Southeast US. Ozonesondes launched during midday hours show a 7 ppb ozone decrease from 1.5 km to the surface that GEOS-Chem does not capture. This bias may reflect a combination of excessive vertical mixing and net ozone production in the model boundary layer