High-fidelity view of the structure and fragmentation of the high-mass, filamentary IRDC G11.11-0.12

Star formation in molecular clouds is intimately linked to their internal mass distribution. We present an unprecedentedly detailed analysis of the column density structure of a high-mass, filamentary molecular cloud, namely IRDC G11.11-0.12 (G11). We use two novel column density mapping techniques: high-resolution (FWHM=2", or ~0.035 pc) dust extinction mapping in near- and mid-infrared, and dust emission mapping with the Herschel satellite. These two completely independent techniques yield a strikingly good agreement, highlighting their complementarity and robustness. We first analyze the dense gas mass fraction and linear mass density of G11. We show that G11 has a top heavy mass distribution and has a linear mass density (M_l ~ 600 Msun pc^{-1}) that greatly exceeds the critical value of a self-gravitating, non-turbulent cylinder. These properties make G11 analogous to the Orion A cloud, despite its low star-forming activity. This suggests that the amount of dense gas in molecular clouds is more closely connected to environmental parameters or global processes than to the star-forming efficiency of the cloud. We then examine hierarchical fragmentation in G11 over a wide range of size-scales and densities. We show that at scales 0.5 pc > l > 8 pc, the fragmentation of G11 is in agreement with that of a self-gravitating cylinder. At scales smaller than l < 0.5 pc, the results agree better with spherical Jeans' fragmentation. One possible explanation for the change in fragmentation characteristics is the size-scale-dependent collapse time-scale that results from the finite size of real molecular clouds: at scales l < 0.5 pc, fragmentation becomes sufficiently rapid to be unaffected by global instabilities.Comment: 8 pages, 8 figures, accepted to A&

Line Profiles of Cores within Clusters. III. What is the most reliable tracer of core collapse in dense clusters?

Recent observational and theoretical investigations have emphasised the importance of filamentary networks within molecular clouds as sites of star formation. Since such environments are more complex than those of isolated cores, it is essential to understand how the observed line profiles from collapsing cores with non-spherical geometry are affected by filaments. In this study, we investigate line profile asymmetries by performing radiative transfer calculations on hydrodynamic models of three collapsing cores that are embedded in filaments. We compare the results to those that are expected for isolated cores. We model the five lowest rotational transition line (J = 1-0, 2-1, 3-2, 4-3, and 5-4) of both optically thick (HCN, HCO$^+$) as well as optically thin (N$_2$H$^+$, H$^{13}$CO$^+$) molecules using constant abundance laws. We find that less than 50% of simulated (1-0) transition lines show blue infall asymmetries due to obscuration by the surrounding filament. However, the fraction of collapsing cores that have a blue asymmetric emission line profile rises to 90% when observed in the (4-3) transition. Since the densest gas towards the collapsing core can excite higher rotational states, upper level transitions are more likely to produce blue asymmetric emission profiles. We conclude that even in irregular, embedded cores one can trace infalling gas motions with blue asymmetric line profiles of optically thick lines by observing higher transitions. The best tracer of collapse motions of our sample is the (4-3) transition of HCN, but the (3-2) and (5-4) transitions of both HCN and HCO$^+$ are also good tracers.Comment: accepted by MNRAS; 13 pages, 16 figures, 6 table

The fate of xylem-transported CO2 in plants

The concentration of carbon dioxide in tree stems can be ~30-750 times higher than current atmospheric [CO2]. Dissolved inorganic carbon enters the xylem from root and stem respiration and travels with water through the plant. However, the fate of much of this xylem-transported CO2 is unknown. In these studies I examined the fate of xylem-transported CO2 traveling through the petiole and leaf. This was accomplished by placing cut leaves from a woody and herbaceous C3 species, and a Kranz-type C4 species, in a solution of dissolved NaH13CO3 at concentrations similar to those measured in nature. This allowed me to track the efflux of 13CO2 using tunable diode laser absorption spectroscopy and compare this with 12CO2 fluxes derived from plant metabolism. The objective of the first study was to measure the efflux of xylem-transported CO2 out of the woody species Populus deltoides and the herbaceous C3 species Brassica napus in the dark by testing the relationship among the concertation of bicarbonate in the xylem, the rate of transpiration, and the rate of gross CO2 efflux. I found when the concentration of CO2 in the xylem is high and when the rate of transpiration is also high, the magnitude of 13CO2 efflux can approach half of the rate of respiration in the dark. The second study extends measurements of the fate of xylem-transported CO2 into lighted conditions where photosynthesis is active. I measured 12CO2 and 13CO2 fluxes across light- and CO2-response curves with the objectives of: 1) determining how much and under what conditions xylem-transported CO2 exited cut leaves in the light, and 2) determining how much xylem-transported CO2 was used for photosynthesis and when the overall contribution to photosynthesis was most important. I found that in the light the contribution of xylem-transported CO2 is most important when intercellular [CO2] is low which occurs under high irradiance and low [CO2]. The last study focused on the efflux and use of xylem-transported CO2 in the Kranz-type C4 species, Amaranthus hypochondriacus. Species with Kranz anatomy have highly active photosynthetic cells surrounding the vascular bundle, which is where xylem-transported CO2 would first interact with photosynthetic cells. The objectives of this study were to determine: 1) the rate and total efflux of xylem-transported CO2 exiting a cut leaf of the Kranz-type C4 species, A. hypochondriacus, in the dark and 2) the rate and contribution of xylem-transported CO2 to total assimilation in the light for A. hypochondriacus. Rates of dark efflux of xylem-transported CO2 out of A. hypochondriacus leaves were lower in the dark compared to rates observed in B. napus across the same rates of transpiration and bicarbonate concentrations. In the light a higher portion of xylem-transported CO2 was used for photosynthesis in A. hypochondriacus compared to B. napus suggesting that Kranz anatomy influences how C4 plants use xylem-transported CO2 for photosynthesis

BioSimulator.jl: Stochastic simulation in Julia

Biological systems with intertwined feedback loops pose a challenge to mathematical modeling efforts. Moreover, rare events, such as mutation and extinction, complicate system dynamics. Stochastic simulation algorithms are useful in generating time-evolution trajectories for these systems because they can adequately capture the influence of random fluctuations and quantify rare events. We present a simple and flexible package, BioSimulator.jl, for implementing the Gillespie algorithm, $\tau$-leaping, and related stochastic simulation algorithms. The objective of this work is to provide scientists across domains with fast, user-friendly simulation tools. We used the high-performance programming language Julia because of its emphasis on scientific computing. Our software package implements a suite of stochastic simulation algorithms based on Markov chain theory. We provide the ability to (a) diagram Petri Nets describing interactions, (b) plot average trajectories and attached standard deviations of each participating species over time, and (c) generate frequency distributions of each species at a specified time. BioSimulator.jl's interface allows users to build models programmatically within Julia. A model is then passed to the simulate routine to generate simulation data. The built-in tools allow one to visualize results and compute summary statistics. Our examples highlight the broad applicability of our software to systems of varying complexity from ecology, systems biology, chemistry, and genetics. The user-friendly nature of BioSimulator.jl encourages the use of stochastic simulation, minimizes tedious programming efforts, and reduces errors during model specification.Comment: 27 pages, 5 figures, 3 table

Hier ist wahrhaftig ein Loch im Himmel - The NGC 1999 dark globule is not a globule

The NGC 1999 reflection nebula features a dark patch with a size of ~10,000 AU, which has been interpreted as a small, dense foreground globule and possible site of imminent star formation. We present Herschel PACS far-infrared 70 and 160mum maps, which reveal a flux deficit at the location of the globule. We estimate the globule mass needed to produce such an absorption feature to be a few tenths to a few Msun. Inspired by this Herschel observation, we obtained APEX LABOCA and SABOCA submillimeter continuum maps, and Magellan PANIC near-infrared images of the region. We do not detect a submillimer source at the location of the Herschel flux decrement; furthermore our observations place an upper limit on the mass of the globule of ~2.4x10^-2 Msun. Indeed, the submillimeter maps appear to show a flux depression as well. Furthermore, the near-infrared images detect faint background stars that are less affected by extinction inside the dark patch than in its surroundings. We suggest that the dark patch is in fact a hole or cavity in the material producing the NGC 1999 reflection nebula, excavated by protostellar jets from the V 380 Ori multiple system.Comment: accepted for the A&A Herschel issue; 7 page

On the nature of the deeply embedded protostar OMC-2 FIR 4

We use mid-infrared to submillimeter data from the Spitzer, Herschel, and APEX telescopes to study the bright sub-mm source OMC-2 FIR 4. We find a point source at 8, 24, and 70 $\mu$m, and a compact, but extended source at 160, 350, and 870 $\mu$m. The peak of the emission from 8 to 70 $\mu$m, attributed to the protostar associated with FIR 4, is displaced relative to the peak of the extended emission; the latter represents the large molecular core the protostar is embedded within. We determine that the protostar has a bolometric luminosity of 37 Lsun, although including more extended emission surrounding the point source raises this value to 86 Lsun. Radiative transfer models of the protostellar system fit the observed SED well and yield a total luminosity of most likely less than 100 Lsun. Our models suggest that the bolometric luminosity of the protostar could be just 12-14 Lsun, while the luminosity of the colder (~ 20 K) extended core could be around 100 Lsun, with a mass of about 27 Msun. Our derived luminosities for the protostar OMC-2 FIR 4 are in direct contradiction with previous claims of a total luminosity of 1000 Lsun (Crimier et al 2009). Furthermore, we find evidence from far-infrared molecular spectra (Kama et al. 2013, Manoj et al. 2013) and 3.6 cm emission (Reipurth et al 1999) that FIR 4 drives an outflow. The final stellar mass the protostar will ultimately achieve is uncertain due to its association with the large reservoir of mass found in the cold core.Comment: Accpeted by ApJ, 17 pages, 11 figure