We present results from a model of the chemical evolution of protoplanetary disks. In our models we directly calculate the changing propagation and penetration of a high energy radiation field with Lyman α radiation included. We also explore the effect on our models of including dust grain settling. We find that, in agreement with earlier studies, the evolution of dust grains plays a large role in determining how deep the UV radiation penetrates into the disk. Significant grain settling at the midplane leads to much smaller freeze-out regions and a correspondingly larger molecular layer, which leads to an increase in column density for molecular species such as CO, CN and SO. The inclusion of Lyman α radiation impacts the disk chemistry through specific species that have large photodissociation cross sections at 1216Å. These include HCN, NH 3 and CH 4 , for which the column densities are decreased by an order of magnitude or more due to the presence of Lyman α radiation in the UV spectrum. A few species, such as CO 2 and SO, are enhanced by the presence of Lyman α radiation, but rarely by more than a factor of a few.

We observed three molecular clouds and four isolated cores at wavelengths from 3.6− 24 µm. The clouds we observed were Ophiuchus, Perseus, and Serpens and the cores were L204C-2, L1152, L1155C-2, and L1228. Our goal was to use these deep infrared data to map changes in the extinction law and the dust properties throughout the observed regions. In our clouds, we found the lowest density regions have an IRAC extinction law similar to the one observed in the diffuse ISM. At higher extinctions, there is evidence for grain growth because the extinction law flattens compared to the diffuse ISM law and becomes more consistent with a model utilizing larger dust grains. In the densest regions of Serpens and Perseus, A K s ≥ 2, it appears icy mantles are forming on the dust grains. We detected one low extinction region in Perseus with an anomalous extinction law that is not explained by current ideas about grain growth or the formation of ices onto dust grains. The extinction law in the cores shows only a slight flattening of the extinction law with increased extinction. Even at the lowest extinctions, the extinction law is more consistent with a dust model containing grain growth, rather than with the diffuse ISM. Two of the four cores have evidence for ices forming the densest regions. Molecular outflows appear to have an impact on the dust grains in two of our cores: L1152 and L1228. In both our clouds and cores, the extinction law at 24 µm is almost always higher than the value predicted by current dust models, but is consistent with other observations. We find some evidence for the 24 µm extinction law decreasing as the extinction increases. Overall, there are relatively few stars with detections ≥ 3σ at 24 µm. More observations are needed to understand the nature of the extinction law at this wavelength.

Recent astronomical observations have revealed what may prove to be the ubiquity of water vapor during the early stages of planet formation. We present here a simple mechanism showing how water vapor forms in situ and is capable of shielding itself from molecule-destroying stellar radiation. The absorption of this radiation by water can control the thermodynamics of the terrestrial planet-forming zone. Similar to Earth's ozone layer, which shelters the chemistry of life, the water layer protects other water molecules and allows for a rich organic chemistry. The total abundance of water vapor in the natal habitable zone is equal to that of several thousand oceans.

For Classical T Tauri Stars (CTTSs), the resonance doublets of N v, Si iv, and C iv, as well as the He ii 1640Å line, trace hot gas flows and act as diagnostics of the accretion process. In this paper we assemble a large high-resolution, high-sensitivity dataset of these lines in CTTSs and Weak T Tauri Stars (WTTSs). The sample comprises 35 stars: one Herbig Ae star, 28 CTTSs, and 6 WTTSs. We find that the C iv, Si iv, and N v lines in CTTSs all have similar shapes. We decompose the C iv and He ii lines into broad and narrow Gaussian components (BC & NC). The most common (50 %) C iv line morphology in CTTSs is that of a low-velocity NC together with a redshifted BC. For CTTSs, a strong BC is the result of the accretion process. The contribution fraction of the NC to the C iv line flux in CTTSs increases with accretion rate, from ∼20% to up to ∼80%. The velocity centroids of the BCs and NCs are such that V BC 4 V N C , consistent with the predictions of the accretion shock model, in at most 12 out of 22 CTTSs. We do not find evidence of the post-shock becoming buried in the stellar photosphere due to the pressure of the accretion flow. The He ii CTTSs lines are generally symmetric and narrow, with FWHM and redshifts comparable to those of WTTSs. They are less redshifted than the CTTSs C iv lines, by ∼10 km s −1 . The amount of flux in the BC of the He ii line is small compared to that of the C iv line, and we show that this is consistent with models of the pre-shock column emission. Overall, the observations are consistent with the presence of multiple accretion columns with different densities or with accretion models that predict a slow-moving, lowdensity region in the periphery of the accretion column. For HN Tau A and RW Aur A, most of the C iv line is blueshifted suggesting that the C iv emission is produced by shocks within outflow jets. In our sample, the Herbig Ae star DX Cha is the only object for which we find a P-Cygni profile in the C iv line, which argues for the presence of a hot (10 5 K) wind. For the overall sample, the Si iv and N v line luminosities are correlated with the C iv line luminosities, although the relationship between Si iv and C iv shows large scatter about a linear relationship and suggests that TW Hya, V4046 Sgr, AA Tau, DF Tau, GM Aur, and V1190 Sco are silicon-poor, while CV Cha, DX Cha, RU Lup, and RW Aur may be silicon-rich.

Young stars surrounded by disks with very low mass accretion rates are likely in the final stages of inner disk evolution and therefore particularly interesting to study. We present ultraviolet (UV) observations of the ∼5-9 Myr old stars RECX-1 and RECX-11, obtained with the Cosmic Origins Spectrograph and Space Telescope Imaging Spectrograph on the Hubble Space Telescope, as well as optical and near-infrared spectroscopic observations. The two stars have similar levels of near-UV emission, although spectroscopic evidence indicates that RECX-11 is accreting and RECX-1 is not. The line profiles of Hα and He i λ10830 in RECX-11 show both broad and narrow redshifted absorption components that vary with time, revealing the complexity of the accretion flows. We show that accretion indicators commonly used to measure mass accretion rates, e.g., U-band excess luminosity or the Ca ii triplet line luminosity, are unreliable for low accretors, at least in the middle K spectral range. Using RECX-1 as a template for the intrinsic level of photospheric and chromospheric emission, we determine an upper limit of 3 × 10 −10 M yr −1 for RECX-11. At this low accretion rate, recent photoevaporation models predict that an inner hole should have developed in the disk. However, the spectral energy distribution of RECX-11 shows fluxes comparable to the median of Taurus in the near-infrared, indicating that substantial dust remains. Fluorescent H 2 emission lines formed in the innermost disk are observed in RECX-11, showing that gas is present in the inner disk, along with the dust.

We study the role resonant scattering plays in the transport of Lyα photons in accreting protoplanetary disk systems subject to varying degrees of dust settling. While the intrinsic stellar far-UV (FUV) spectrum of accreting T Tauri systems may already be dominated by a strong, broad Lyα line (∼80% of the FUV luminosity), we find that resonant scattering further enhances the Lyα density in the deep molecular layers of the disk. Lyα is scattered downward efficiently by the photodissociated atomic hydrogen layer that exists above the molecular disk. In contrast, FUV-continuum photons pass unimpeded through the photodissociation layer and (forward-)scatter inefficiently off dust grains. Using detailed, adaptive grid Monte Carlo radiative transfer simulations we show that the resulting Lyα/FUV-continuum photon density ratio is strongly stratified; FUV-continuum-dominated in the photodissociation layer and Lyα-dominated field in the molecular disk. The enhancement is greatest in the interior of the disk (r ∼ 1 AU) but is also observed in the outer disk (r ∼ 100 AU). The majority of the total disk mass is shown to be increasingly Lyα dominated as dust settles toward the midplane.

We explore the chemical structure of a disk that contains a large central gap of R ∼ 45 AU, as is commonly seen in transitional disk systems. In our chemical model of a disk with a cleared inner void, the midplane becomes revealed to the central star so that it is directly irradiated. The midplane material at the truncation radius is permissive to reprocessed optical heating radiation, but opaque to the photo-dissociating ultraviolet, creating an environment abundant in gas-phase molecules. Thus the disk midplane, which would otherwise for a full disk be dominated by near complete heavy element freeze-out, should become observable in molecular emission. If this prediction is correct this has exciting prospects for observations with the Atacama Large Millimeter/Submillimeter Array (ALMA), as the inner transition region should thus be readily detected and resolved, especially using high-J rotational transitions excited in the high density midplane gas. Therefore such observations will potentially provide us with a direct probe of the physics and chemistry at this actively evolving interface.

We provide simple polynomial fits to the X-ray photoelectric cross-sections (0.03 keV < E < 10 keV) for mixtures of gas and dust found in protoplanetary disks. Using the solar elemental abundances of Asplund et al., we treat the gas and dust components separately, facilitating the further exploration of evolutionary processes such as grain settling and gain growth. We find that blanketing due to advanced grain growth (a max > 1 μm) can reduce the X-ray opacity of dust appreciably at E X ∼ 1 keV, coincident with the peak of typical T Tauri X-ray spectra. However, the reduction of dust opacity by dust settling, which is known to occur in protoplanetary disks, is probably a more significant effect. The absorption of 1-10 keV X-rays is dominated by gas opacity once the dust abundance has been reduced to about 1% of its diffuse interstellar value. The gas disk establishes a floor to the opacity at which point X-ray transport becomes insensitive to further dust evolution. Our choice of fitting function follows that of Morrison & McCammon, providing a degree of backward compatibility.