1,800 research outputs found
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
(NH, HCO) 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, -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 m, and a compact, but extended source at 160, 350,
and 870 m. The peak of the emission from 8 to 70 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
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