Transitional disks and their origins: an infrared spectroscopic survey of Orion A

Transitional disks are protoplanetary disks around young stars, with inner holes or gaps which are surrounded by optically thick outer, and often inner, disks. Here we present observations of 62 new transitional disks in the Orion A star-forming region. These were identified using the \textit{Spitzer Space Telescope}'s Infrared Spectrograph and followed up with determinations of stellar and accretion parameters using the Infrared Telescope Facility's SpeX. We combine these new observations with our previous results on transitional disks in Taurus, Chamaeleon I, Ophiuchus and Perseus, and with archival X-ray observations. This produces a sample of 105 transitional disks of "cluster" age 3 Myr or less, by far the largest hitherto assembled. We use this sample to search for trends between the radial structure in the disks and many other system properties, in order to place constraints on the possible origins of transitional disks. We see a clear progression of host star accretion rate and the different disk morphologies. We confirm that transitional disks with complete central clearings have median accretion rates an order of magnitude smaller than radially continuous disks of the same population. Pre-transitional disks --- those objects with gaps that separate inner and outer disks --- have median accretion rates intermediate between the two. Our results from the search for statistically significant trends, especially related to $\dot{M}$, strongly support that in both cases the gaps are far more likely to be due to the gravitational influence of Jovian planets or brown dwarfs orbiting within the gaps, than to any of the photoevaporative, turbulent or grain-growth processes that can lead to disk dissipation. We also find that the fraction of Class II YSOs which are transitional disks is large, 0.1-0.2, especially in the youngest associations.Comment: 96 pages, 25 figures, resubmitted to Ap

Spitzer observations of HH54 and HH7-11: mapping the H2 ortho-to-para ratio in shocked molecular gas

We report the results of spectroscopic mapping observations carried out toward the Herbig-Haro objects HH7-11 and HH54 over the 5.2 - 37 micron region using the Infrared Spectrograph of the Spitzer Space Telescope. These observations have led to the detection and mapping of the S(0) - S(7) pure rotational lines of molecular hydrogen, together with emissions in fine structure transitions of Ne+, Si+, S, and Fe+. The H2 rotational emissions indicate the presence of warm gas with a mixture of temperatures in the range 400 - 1200 K, consistent with the expected temperature behind nondissociative shocks of velocity ~ 10 - 20 km/s, while the fine structure emissions originate in faster shocks of velocity 35 - 90 km/s that are dissociative and ionizing. Maps of the H2 line ratios reveal little spatial variation in the typical admixture of gas temperatures in the mapped regions, but show that the H2 ortho-to-para ratio is quite variable, typically falling substantially below the equilibrium value of 3 attained at the measured gas temperatures. The non-equilibrium ortho-to-para ratios are characteristic of temperatures as low as ~ 50 K, and are a remnant of an earlier epoch, before the gas temperature was elevated by the passage of a shock. Correlations between the gas temperature and H2 ortho-to-para ratio show that ortho-to-para ratios < 0.8 are attained only at gas temperatures below ~ 900 K; this behavior is consistent with theoretical models in which the conversion of para- to ortho-H2 behind the shock is driven by reactive collisions with atomic hydrogen, a process which possesses a substantial activation energy barrier (E_A/k ~ 4000 K) and is therefore very inefficient at low temperature.Comment: 45 pages, including 16 figures. Accepted for publication in Ap

Optical mapping discerns genome wide DNA methylation profiles

BACKGROUND: Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification. RESULTS: A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping. CONCLUSION: The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies

Optical nanofibers and spectroscopy

We review our recent progress in the production and characterization of tapered optical fibers with a sub-wavelength diameter waist. Such fibers exhibit a pronounced evanescent field and are therefore a useful tool for highly sensitive evanescent wave spectroscopy of adsorbates on the fiber waist or of the medium surrounding. We use a carefully designed flame pulling process that allows us to realize preset fiber diameter profiles. In order to determine the waist diameter and to verify the fiber profile, we employ scanning electron microscope measurements and a novel accurate in situ optical method based on harmonic generation. We use our fibers for linear and non-linear absorption and fluorescence spectroscopy of surface-adsorbed organic molecules and investigate their agglomeration dynamics. Furthermore, we apply our spectroscopic method to quantum dots on the surface of the fiber waist and to caesium vapor surrounding the fiber. Finally, towards dispersive measurements, we present our first results on building and testing a single-fiber bi-modal interferometer.Comment: 13 pages, 18 figures. Accepted for publication in Applied Physics B. Changes according to referee suggestions: changed title, clarification of some points in the text, added references, replacement of Figure 13

Best practices for measuring emerging light-emitting diode technologies

The arrival of light-emitting diodes based on new materials is posing challenges for the characterization and comparison of devices in a trusted and consistent manner. Here we provide some advice and guidelines that we hope will benefit the community

Dust Processing and Grain Growth in Protoplanetary Disks in the Taurus-Auriga Star-Forming Region

Mid-infrared spectra of 65 T Tauri stars (TTS) taken with the Infrared Spectrograph (IRS) on board the Spitzer Space Telescope are modeled using dust at two temperatures to probe the radial variation in dust composition in the uppermost layers of protoplanetary disks. Most spectra indicating crystalline silicates require Mg-rich minerals and silica, but a few suggest otherwise. Spectra indicating abundant enstatite at higher temperatures also require crystalline silicates at temperatures lower than those required for spectra showing high abundance of other crystalline silicates. A few spectra show 10 micron complexes of very small equivalent width. They are fit well using abundant crystalline silicates but very few large grains, inconsistent with the expectation that low peak-to-continuum ratio of the 10 micron complex always indicates grain growth. Most spectra in our sample are fit well without using the opacities of large crystalline silicate grains. If large grains grow by agglomeration of submicron grains of all dust types, the amorphous silicate components of these aggregates must typically be more abundant than the crystalline silicate components. Crystalline silicate abundances correlate positively with other such abundances, suggesting that crystalline silicates are processed directly from amorphous silicates and that neither forsterite, enstatite, nor silica are intermediate steps when producing either of the other two. Disks with more dust settling typically have greater crystalline abundances. Large-grain abundance is somewhat correlated with greater settling of disks. The lack of strong correlation is interpreted to mean that settling of large grains is sensitive to individual disk properties. Lower-mass stars have higher abundances of large grains in their inner regions.Comment: 84 pages, 27 figures, submitted to the Astrophysical Journal on 7 November, 200

A Spitzer IRS Survey of NGC 1333: Insights into disk evolution from a very young cluster

We report on the {\lambda} = 5-36{\mu}m Spitzer Infrared Spectrograph spectra of 79 young stellar objects in the very young nearby cluster NGC 1333. NGC 1333's youth enables the study of early protoplanetary disk properties, such as the degree of settling as well as the formation of gaps and clearings. We construct spectral energy distributions (SEDs) using our IRS data as well as published photometry and classify our sample into SED classes. Using "extinction-free" spectral indices, we determine whether the disk, envelope, or photosphere dominates the spectrum. We analyze the dereddened spectra of objects which show disk dominated emission using spectral indices and properties of silicate features in order to study the vertical and radial structure of protoplanetary disks in NGC 1333. At least nine objects in our sample of NGC 1333 show signs of large (several AU) radial gaps or clearings in their inner disk. Disks with radial gaps in NGC 1333 show more-nearly pristine silicate dust than their radially continuous counterparts. We compare properties of disks in NGC 1333 to those in three other well studied regions, Taurus-Auriga, Ophiuchus and Chamaeleon I, and find no difference in their degree of sedimentation and dust processing.Comment: 67 pages, 20 figures, accepted to The Astrophysical Journal Supplement Serie

Disk Evolution in the three Nearby Star-Forming Regions of Taurus, Chamaeleon, and Ophiuchus

We analyze samples of Spitzer Infrared Spectrograph (IRS) spectra of T Tauri stars in the Ophiuchus, Taurus, and Chamaeleon I star-forming regions, whose median ages lie in the <1 to 2 Myr range. The median mid-infrared spectra of objects in these three regions are similar in shape, suggesting, on average, similar disk structures. When normalized to the same stellar luminosity, the medians follow each other closely, implying comparable mid-infrared excess emission from the circumstellar disks. We use the spectral index between 13 and 31 micron and the equivalent width of the 10 micron silicate emission feature to identify objects whose disk configuration departs from that of a continuous, optically thick accretion disk. Transitional disks, whose steep 13-31 micron spectral slope and near-IR flux deficit reveal inner disk clearing, occur with about the same frequency of a few percent in all three regions. Objects with unusually large 10 micron equivalent widths are more common (20-30%); they could reveal the presence of disk gaps filled with optically thin dust. Based on their medians and fraction of evolved disks, T Tauri stars in Taurus and Chamaeleon I are very alike. Disk evolution sets in early, since already the youngest region, the Ophiuchus core (L1688), has more settled disks with larger grains. Our results indicate that protoplanetary disks show clear signs of dust evolution at an age of a few Myr, even as early as ~1 Myr, but age is not the only factor determining the degree of evolution during the first few million years of a disk's lifetime.Comment: 23 pages, 20 figures; accepted for publication in Ap