Optical and ultraviolet spectroscopic analysis of SN 2011fe at late times

We present optical spectra of the nearby Type Ia supernova SN 2011fe at 100, 205, 311, 349, and 578 days post-maximum light, as well as an ultraviolet spectrum obtained with Hubble Space Telescope at 360 days post-maximum light. We compare these observations with synthetic spectra produced with the radiative transfer code PHOENIX. The day +100 spectrum can be well fit with models which neglect collisional and radiative data for forbidden lines. Curiously, including this data and recomputing the fit yields a quite similar spectrum, but with different combinations of lines forming some of the stronger features. At day +205 and later epochs, forbidden lines dominate much of the optical spectrum formation; however, our results indicate that recombination, not collisional excitation, is the most influential physical process driving spectrum formation at these late times. Consequently, our synthetic optical and UV spectra at all epochs presented here are formed almost exclusively through recombination-driven fluorescence. Furthermore, our models suggest that the ultraviolet spectrum even as late as day +360 is optically thick and consists of permitted lines from several iron-peak species. These results indicate that the transition to the "nebular" phase in Type Ia supernovae is complex and highly wavelength-dependent.Comment: 22 pages, 21 figuress, 1 table, submitted to MNRA

Extensive Spectroscopy and Photometry of the Type IIP Supernova 2013ej

We present extensive optical ($UBVRI$, $g'r'i'z'$, and open CCD) and near-infrared ($ZYJH$) photometry for the very nearby Type IIP SN ~2013ej extending from +1 to +461 days after shock breakout, estimated to be MJD $56496.9\pm0.3$. Substantial time series ultraviolet and optical spectroscopy obtained from +8 to +135 days are also presented. Considering well-observed SNe IIP from the literature, we derive $UBVRIJHK$ bolometric calibrations from $UBVRI$ and unfiltered measurements that potentially reach 2\% precision with a $B-V$ color-dependent correction. We observe moderately strong Si II $\lambda6355$ as early as +8 days. The photospheric velocity ($v_{\rm ph}$) is determined by modeling the spectra in the vicinity of Fe II $\lambda5169$ whenever observed, and interpolating at photometric epochs based on a semianalytic method. This gives $v_{\rm ph} = 4500\pm500$ km s$^{-1}$ at +50 days. We also observe spectral homogeneity of ultraviolet spectra at +10--12 days for SNe IIP, while variations are evident a week after explosion. Using the expanding photosphere method, from combined analysis of SN 2013ej and SN 2002ap, we estimate the distance to the host galaxy to be $9.0_{-0.6}^{+0.4}$ Mpc, consistent with distance estimates from other methods. Photometric and spectroscopic analysis during the plateau phase, which we estimated to be $94\pm7$ days long, yields an explosion energy of $0.9\pm0.3\times10^{51}$ ergs, a final pre-explosion progenitor mass of $15.2\pm4.2$~M$_\odot$ and a radius of $250\pm70$~R$_\odot$. We observe a broken exponential profile beyond +120 days, with a break point at +$183\pm16$ days. Measurements beyond this break time yield a $^{56}$Ni mass of $0.013\pm0.001$~M$_\odot$.Comment: 29 pages, 23 figures, 15 tables, Published in The Astrophisical Journa

The Lick AGN Monitoring Project 2011: Dynamical Modeling of the Broad-Line Region

We present models of the H$\beta$-emitting broad-line region (BLR) in seven Seyfert 1 galaxies from the Lick AGN (Active Galactic Nucleus) Monitoring Project 2011 sample, drawing inferences on the BLR structure and dynamics as well as the mass of the central supermassive black hole. We find that the BLR is generally a thick disk, viewed close to face-on, with preferential emission back toward the ionizing source. The dynamics in our sample range from near-circular elliptical orbits to inflowing or outflowing trajectories. We measure black hole masses of $\log_{10}(M_{\rm BH}/M_\odot) = 6.48^{+0.21}_{-0.18}$ for PG 1310$-$108, $7.50^{+0.25}_{-0.18}$ for Mrk 50, $7.46^{+0.15}_{-0.21}$ for Mrk 141, $7.58^{+0.08}_{-0.08}$ for Mrk 279, $7.11^{+0.20}_{-0.17}$ for Mrk 1511, $6.65^{+0.27}_{-0.15}$ for NGC 4593, and $6.94^{+0.14}_{-0.14}$ for Zw 229$-$015. We use these black hole mass measurements along with cross-correlation time lags and line widths to recover the scale factor $f$ used in traditional reverberation mapping measurements. Combining our results with other studies that use this modeling technique, bringing our sample size to 16, we calculate a scale factor that can be used for measuring black hole masses in other reverberation mapping campaigns. When using the root-mean-square (rms) spectrum and using the line dispersion to measure the line width, we find $\log_{10}(f_{{\rm rms},\sigma})_{\rm pred} = 0.57 \pm 0.19$. Finally, we search for correlations between $f$ and other AGN and BLR parameters and find marginal evidence that $f$ is correlated with $M_{\rm BH}$ and the BLR inclination angle, but no significant evidence of a correlation with the AGN luminosity or Eddington ratio.Comment: 26 pages, 14 figures. Accepted for publication in Ap

The Lick AGN Monitoring Project 2011: Reverberation Mapping of Markarian 50

The Lick AGN Monitoring Project 2011 observing campaign was carried out over the course of 11 weeks in Spring 2011. Here we present the first results from this program, a measurement of the broad-line reverberation lag in the Seyfert 1 galaxy Mrk 50. Combining our data with supplemental observations obtained prior to the start of the main observing campaign, our dataset covers a total duration of 4.5 months. During this time, Mrk 50 was highly variable, exhibiting a maximum variability amplitude of a factor of 4 in the U-band continuum and a factor of 2 in the H-beta line. Using standard cross-correlation techniques, we find that H-beta and H-gamma lag the V-band continuum by tau_cen = 10.64(-0.93,+0.82) and 8.43(-1.28,+1.30) days, respectively, while the lag of He II 4686 is unresolved. The H-beta line exhibits a symmetric velocity-resolved reverberation signature with shorter lags in the high-velocity wings than in the line core, consistent with an origin in a broad-line region dominated by orbital motion rather than infall or outflow. Assuming a virial normalization factor of f=5.25, the virial estimate of the black hole mass is (3.2+-0.5)*10^7 solar masses. These observations demonstrate that Mrk 50 is among the most promising nearby active galaxies for detailed investigations of broad-line region structure and dynamics.Comment: Accepted for publication in ApJ Letters. 6 pages, 4 figure

Kinetics and Optimization of the Lysine–Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriae

Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction conditions is of significant interest, but remains challenging. Recently, the lysine-isopeptide bond forming activity of the sortase enzyme that builds surface pili in Corynebacterium diphtheriae (CdSrtA) has been reconstituted in vitro. A mutationally activated form of CdSrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein (NSpaA), enabling the labeling of target proteins that are fused to NSpaA. Here we present a detailed analysis of the CdSrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the CdSrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in NSpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant (CdSrtAΔ) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage ("lid") that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the NSpaA substrate. Quantitative measurements reveal that CdSrtAΔ generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h-1 and that it has apparent KM values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its NSpaA and peptide substrates, respectively. CdSrtAΔ is 7-fold more active than previously studied variants, labeling >90% of NSpaA with peptide within 6 h. The results of this study further improve the utility of CdSrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis

The Lick AGN Monitoring Project 2011: Spectroscopic Campaign and Emission-Line Light Curves

In the Spring of 2011 we carried out a 2.5 month reverberation mapping campaign using the 3 m Shane telescope at Lick Observatory, monitoring 15 low-redshift Seyfert 1 galaxies. This paper describes the observations, reductions and measurements, and data products from the spectroscopic campaign. The reduced spectra were fitted with a multicomponent model in order to isolate the contributions of various continuum and emission-line components. We present light curves of broad emission lines and the AGN continuum, and measurements of the broad H-beta line widths in mean and root-mean square (rms) spectra. For the most highly variable AGNs we also measured broad H-beta line widths and velocity centroids from the nightly spectra. In four AGNs exhibiting the highest variability amplitudes, we detect anticorrelations between broad H-beta width and luminosity, demonstrating that the broad-line region "breathes" on short timescales of days to weeks in response to continuum variations. We also find that broad H-beta velocity centroids can undergo substantial changes in response to continuum variations; in NGC 4593 the broad H-beta velocity shifted by ~250 km/s over a one-month duration. This reverberation-induced velocity shift effect is likely to contribute a significant source of confusion noise to binary black hole searches that use multi-epoch quasar spectroscopy to detect binary orbital motion. We also present results from simulations that examine biases that can occur in measurement of broad-line widths from rms spectra due to the contributions of continuum variations and photon-counting noise.Comment: 33 pages, 28 figures, accepted for publication in ApJ Supplement Serie

Causes and Correlates of Calf Mortality in Captive Asian Elephants (Elephas maximus)

Juvenile mortality is a key factor influencing population growth rate in density-independent, predation-free, well-managed captive populations. Currently at least a quarter of all Asian elephants live in captivity, but both the wild and captive populations are unsustainable with the present fertility and calf mortality rates. Despite the need for detailed data on calf mortality to manage effectively populations and to minimize the need for capture from the wild, very little is known of the causes and correlates of calf mortality in Asian elephants. Here we use the world's largest multigenerational demographic dataset on a semi-captive population of Asian elephants compiled from timber camps in Myanmar to investigate the survival of calves (n = 1020) to age five born to captive-born mothers (n = 391) between 1960 and 1999. Mortality risk varied significantly across different ages and was higher for males at any age. Maternal reproductive history was associated with large differences in both stillbirth and liveborn mortality risk: first-time mothers had a higher risk of calf loss as did mothers producing another calf soon (<3.7 years) after a previous birth, and when giving birth at older age. Stillbirth (4%) and pre-weaning mortality (25.6%) were considerably lower than those reported for zoo elephants and used in published population viability analyses. A large proportion of deaths were caused by accidents and lack of maternal milk/calf weakness which both might be partly preventable by supplementary feeding of mothers and calves and work reduction of high-risk mothers. Our results on Myanmar timber elephants with an extensive keeping system provide an important comparison to compromised survivorship reported in zoo elephants. They have implications for improving captive working elephant management systems in range countries and for refining population viability analyses with realistic parameter values in order to predict future population size of the Asian elephant

PTF11eon/SN2011dh: Discovery of a Type IIb Supernova From a Compact Progenitor in the Nearby Galaxy M51

On May 31, 2011 UT a supernova (SN) exploded in the nearby galaxy M51 (the Whirlpool Galaxy). We discovered this event using small telescopes equipped with CCD cameras, as well as by the Palomar Transient Factory (PTF) survey, and rapidly confirmed it to be a Type II supernova. Our early light curve and spectroscopy indicates that PTF11eon resulted from the explosion of a relatively compact progenitor star as evidenced by the rapid shock-breakout cooling seen in the light curve, the relatively low temperature in early-time spectra and the prompt appearance of low-ionization spectral features. The spectra of PTF11eon are dominated by H lines out to day 10 after explosion, but initial signs of He appear to be present. Assuming that He lines continue to develop in the near future, this SN is likely a member of the cIIb (compact IIb; Chevalier and Soderberg 2010) class, with progenitor radius larger than that of SN 2008ax and smaller than the eIIb (extended IIb) SN 1993J progenitor. Our data imply that the object identified in pre-explosion Hubble Space Telescope images at the SN location is possibly a companion to the progenitor or a blended source, and not the progenitor star itself, as its radius (~10^13 cm) would be highly inconsistent with constraints from our post-explosion photometric and spectroscopic data

Space Telescope and Optical Reverberation Mapping Project. VII. Understanding the Ultraviolet Anomaly in NGC 5548 with X-Ray Spectroscopy

During the Space Telescope and Optical Reverberation Mapping Project observations of NGC 5548, the continuum and emission-line variability became decorrelated during the second half of the six-month-long observing campaign. Here we present Swift and Chandra X-ray spectra of NGC 5548 obtained as part of the campaign. The Swift spectra show that excess flux (relative to a power-law continuum) in the soft X-ray band appears before the start of the anomalous emission-line behavior, peaks during the period of the anomaly, and then declines. This is a model-independent result suggesting that the soft excess is related to the anomaly. We divide the Swift data into on- and off-anomaly spectra to characterize the soft excess via spectral fitting. The cause of the spectral differences is likely due to a change in the intrinsic spectrum rather than to variable obscuration or partial covering. The Chandra spectra have lower signal-to-noise ratios, but are consistent with the Swift data. Our preferred model of the soft excess is emission from an optically thick, warm Comptonizing corona, the effective optical depth of which increases during the anomaly. This model simultaneously explains all three observations: the UV emission-line flux decrease, the soft-excess increase, and the emission-line anomaly