Abundances of Molecular Species in Barnard 68

This paper consolidates and extends the results of a large observational and chemical modeling study of translucent clouds. Thirty-eight molecular species have been observed in an ensemble of 38 translucent objects, for which detailed self-consistent physical models have been constructed. These are used with microturbulent radiative transfer analyses to obtain reliable fractional abundances. The abundances are essentially the same in translucent clouds and cold dense clouds (TMC-1). We have also scaled the column densities of the 12 species studied by Liszt & Lucas in diffuse clouds by adsorption against point-continuum sources to yield fractional abundances. These in turn are found to be remarkably similar to those in translucent and dense quiescent clouds. Thus a global abundance pattern emerges, which holds over a range of hundredfold in density, and transcends the completely photon-dominated chemistry regime to the collision-dominated regime. We have developed comprehensive quiescent gas-phase chemical models, based on the New Standard Model (NSM) reaction data set. We have found a single set of parameters (elemental abundances, depletion factors, and other physical conditions) that can explain the abundances of 34 of the 38 species observed in translucent clouds, spanning the transition region 1 ≤ Av0 ≤ 5 mag. The NSM is insensitive to density in the translucent region. The similarity of abundances in translucent and dense clouds (TMC-1) is explained by the same chemical model with a slightly higher depletion factor for C and O. To explain the diffuse cloud abundances, we need to augment the NSM reaction set of 4,300 reactions with just three turbulence-driven, weakly endothermic reactions as analyzed by Spaans. These latter reactions lose effect as the density increases from the diffuse to the translucent regime, in just such a way that the diffuse-cloud abundances seamlessly join with the translucent abundances, thus replicating the constancy of abundances from diffuse conditions (200 cm-3) to dense cloud conditions (20,000 cm-3). It seems clear that purely low-temperature gas-phase chemistry can explain many more observations than previously recognized.

Estimating spectral plane-of-array (POA) solar irradiance on inclined surfaces is an important step in the design and performance evaluation of both photovoltaic and concentrated solar plants. This work introduces a fast, line-by-line spectral, Monte Carlo (MC) radiative transfer model approach to simulate anisotropic distributions of shortwave radiation through the atmosphere as photon bundles impinge on inclined surfaces. This fast Monte Carlo approach reproduces the angular distribution of solar irradiance without the undesirable effects of spatial discretization and thus computes detailed POA irradiance values on surfaces at any orientation and also when surfaces are subjected to the anisotropic ground and atmospheric scattering. Polarization effects are also easily incorporated into this approach that can be considered as direct numerical simulation of the physics involved. Here, we compare our Monte Carlo radiative transfer model with the most widely used empirical transposition model, Perez4, under various conditions. The results show that the Perez4 model reproduces the more detailed Monte Carlo simulations with less than 10% deviation under clear skies for all relevant surface tilt and azimuth angles. When optically thin clouds are present, observed deviations are larger, especially when the receiving surface is strongly tilted. Deviations are also observed for large azimuth angle differences between the receiving surface and the solar position. When optically thick clouds are present, the two models agree within 15% deviation for nearly all surface orientation and tilt angles. The overall deviations are smaller when compared with cases for optically thin clouds. The Perez4 model performs very well (∼6.0% deviation) in comparison with the detailed MC simulations for all cases, thus validating its widespread use for practical solar applications. When detailed atmospheric profiles and cloud optical properties are available, the proposed fast Monte Carlo radiative model reproduces accurate spectral and angular POA irradiance levels for various atmospheric and cloud cover conditions, surface orientations, and different surface and ground properties.

Photodynamic therapy (PDT) has been theoretically investigated using a Monte Carlo radiation transfer (MCRT) model. By including complex three dimensional (3D) tumour models a more appropriate representation of the treatment was achieved. The 3D clustered tumour model was compared to a smooth model, resulting in a significantly deeper penetration associated with the clustered model. The results from the work presented here indicates that light might penetrate deeper than suggested by 2D or simple layered models.

We have made a survey of SiO in 29 of our standard sample of 11 cirrus cores and 27 Clemens-Barvainis translucent cores the structures and chemistry of which have been studied earlier in this series. SiO is detected in six objects, favoring those with large products of the local radiation field IUV and the column density. The fractional abundance of SiO is 1 × 10-10 in these six objects, and 1 × 10-11 over the remaining 23 searched objects for which an average of the observations yielded a detection. These SiO abundances are intermediate between those found in energetic star-forming regions (~1 × 10-8) and upper limits of ~2 × 10-12 found in cold dense clouds. We have analyzed the gas-phase chemistry of SiO and find that the temperature-dependent reactions Si + (OH, O2) → SiO cannot explain the strong dependence of SiO abundance upon cloud temperature, contrary to the conclusion of Langer & Glassgold. We have analyzed the SiO abundance characteristics in terms of accretion on and photodesorption from grains. Cosmic-ray desorption is found to be negligible. The same analysis applied to many other species studied in the translucent cloud series points to a uniquely strong binding of Si atoms onto grains, unlike the situation for other elements (C, N, O, S). We find this by determining a photodesorption yield factor for each molecular species which is consistent with the observations of the many species in both translucent and cold dense clouds, which agrees with experimental values for C, N, O, and S species, and which is much smaller for Si than for the other elements. Special binding mechanisms for Si onto grains are discussed.

We have developed comprehensive models, based on the New Standard Model reaction dataset, for the gas-phase chemistry of translucent clouds. These models predict satisfactorily the abundances of 34 of the 38 molecular species observed in both translucent and cold dense clouds. With 3 additional reactions, the models also appear able to explain diffuse cloud abundances.

This study aims to assess the influence of growth and culture conditions of the Euglena gracilis protist on the cellular chemical composition. Fourier transform infrared spectroscopy (FT-IR) and direct infusion Orbitrap electrospray ionization mass spectrometry (ESI-MS) were used in tandem for confirmation of functional groups, and to decipher the normalized percentage abundances of compound classes, molecular species, and aromaticity and oxygenation within each growth condition. Abundances of molecular species and compound classes varied with growth and culture conditions. No major differences in the qualitative FT-IR-based screening of functional groups were found between growth conditions. This contrasts with ESI-MS-based results where polyphenols, carbohydrate, and condensed aromatic compounds were the most abundant in dark-grown conditions with glucose supplementation, revealing the differences in physiological states of the cell in different growth conditions. Dark-grown conditions promoted CHO molecular species while light-grown conditions favored CHON, CHOS, and CHONS molecular species. The dark-grown exponential E. gracilis cells grown in glucose-supplemented media showed the greatest normalized abundances of aromatics, carbohydrate, polyphenols, and protein, which are compound classes typically involved in metal binding.

Glycerophosphoethanolamine (GPEtn) and glycerophosphoserine (GPSer) lipids were reacted with a multiplexed set of differentially isotopically enriched N-methylpiperazine acetic acid N-hydroxysuccinimide ester reagents, which place isobaric mass labels at a primary amino group. The resulting derivatized aminophospholipids were isobaric and chromatographically indistinguishable but yielded positive reporter ions (m/z 114 or 117) after collisional activation that could be used to identify and quantify individual members of the multiplex set. The chromatographic and mass spectrometric response of N-methylpiperazine amide-tagged aminophospholipids was probed using glycerophosphoethanolamine and glycerophosphoserine lipid standards. The [M+H]+ of each tagged aminophospholipid shifted 144 Da, and during collision-induced dissociation the major fragmentation ion was either m/z 114 or 117. This mode of detecting aminophospholipids was useful for an unbiased analysis of plasmalogen GPEtn lipids. Molecular species information on the esterified fatty acyl substituents was obtained by collisional activation of the [M-H]- ions. The isotope-tagged reagents were used to assess changes in the distribution of GPEtn lipids after exposure of liposomes made from phospholipids extracted from RAW 264.7 cells to Cu2+/H2O2 to illustrate the ability of these reagents to aid in the mass spectrometric identification of aminophospholipid changes that occur during biological stimuli.

Lipidomics is a rapidly expanding research field in which multiple techniques are utilized to quantitate the hundreds of chemically distinct lipids in cells and determine the molecular mechanisms through which they facilitate cellular function. Recent developments in electrospray ionization mass spectrometry (ESI/MS) have made possible, for the first time, the precise identification and quantification of alterations in a cell's lipidome after cellular perturbations. This review provides an overview of the essential role of ESI/MS in lipidomics, presents a broad strategy applicable for the generation of lipidomes directly from cellular extracts of biological samples by ESI/MS, and summarizes salient examples of strategies utilized to conquer the lipidome in physiologic signaling as well as pathophysiologically relevant disease states. Because of its unparalleled sensitivity, specificity, and efficiency, ESI/MS has provided a critical bridge to generate highly accurate data that fingerprint cellular lipidomes to facilitate insight into the functional role of subcellular membrane compartments and microdomains in mammalian cells. We believe that ESI/MS-facilitated lipidomics has now opened a critical door that will greatly increase our understanding of human disease.

In recent years we have seen an important increase in the number of protonated molecules detected in cold dense clouds. Here we report the detection in TMC-1 of HCCNCH+, the protonated form of HCCNC, which is a metastable isomer of HC3N. This is the first protonated form of a metastable isomer detected in a cold dense cloud. The detection was based on observations carried out with the Yebes 40 m telescope and the 30 m telescope of the Institut de Radioastronomie Millimétrique (IRAM), which revealed four harmonically related lines. We derived a rotational constant B = 4664.431891 ± 0.000692 MHz and a centrifugal distortion constant D = 519.14 ± 4.14 Hz. From a high level ab initio screening of potential carriers, we confidently assigned the series of lines to the ion HCCNCH+. We derived a column density of (3.0 ± 0.5) × 1010 cm−2 for HCCNCH+, which results in a HCCNCH+/HCCNC abundance ratio of 0.010 ± 0.002. This value is well reproduced by a state-of-the-art chemical model which, however, is subject to important uncertainties regarding the chemistry of HCCNCH+. The observational and theoretical status of protonated molecules in cold dense clouds indicate that there exists a global trend in which protonated-to-neutral abundance ratios MH+/M increase with increasing proton affinity of the neutral M, although if one is restricted to species M with high proton affinities (> 700 kJ mol−1), MH+/M ratios fall in the range 10−3–10−1, with no apparent correlation with the proton affinity. We suggest various protonated molecules that are good candidates for detection in cold dense clouds in the near future.

The identity of the major phospholipid component of human lens membrane extracts, previously referred to as the 'unknown phospholipid', was recently proposed to be 4,5-dihydrosphingomyelin (DHS). Using high-performance liquid-chromatographic separation with atmospheric pressure chemical ionization and electrospray ionization mass-spectrometric detection, we report here the first identification of the molecular species of DHSs and sphingomyelins (SPMs) of the human eye lens. The most abundant molecular species were palmitic and tetracosenoic (24:1) DHSs, representing 57.8 and 23.3% of human lens DHSs, respectively. Lesser amounts of hexacosanoic, hexacosenoic, tetracosanoic, docosanoic, docosenoic, stearic, palmitoleic, myristic and other DHSs were found. The most abundant normal SPM molecular species in the human lens were similar to those of DHS. Palmitic SPM represented 53.9% of the uncorrected SPM peak areas, while tetracosenoic SPM represented 17.6% of the SPM in the human lens. The sphingolipids of the human lens were determined to be composed of 76.9% DHS species and 23.1% SPM species. Commercially available SPM was also found to contain significant amounts of DHS species.

We report the detection of large hydrocarbon cycles toward several cold dense clouds. We observed four sources (L1495B, Lupus-1A, L483, and L1527) in the Q band (31−50 GHz) using the Yebes 40 m radiotelescope. Using the line stack technique, we find statistically significant evidence of benzonitrile (C6H5CN) in L1495B, Lupus-1A, and L483 at levels of 31.8σ, 15.0σ, and 17.2σ, respectively, while there is no hint of C6H5CN in the fourth source, L1527. The column densities derived are in the range (1.7−3.8) × 1011 cm−2, which is somewhat below the value derived toward the cold dense cloud TMC-1. When we simultaneously analyze all the benzonitrile abundances derived toward cold clouds in this study and in the literature, a clear trend emerges in that the higher the abundance of HC7N, the more abundant C6H5CN is. This indicates that aromatic cycles are especially favored in those interstellar clouds where long carbon chains are abundant, which suggests that the chemical processes that are responsible for the formation of linear carbon chains are also behind the synthesis of aromatic rings. We also searched for cycles other than benzonitrile, and found evidence of indene (C9H8), cyclopentadiene (C5H6), and 1-cyano cyclopentadiene (1-C5H5CN) at levels of 9.3σ, 7.5σ, and 8.4σ, respectively, toward L1495B, which shows the strongest signal from C6H5CN. The relative abundances between the various cycles detected in L1495B are consistent – within a factor of three – with those previously found in TMC-1. It is therefore likely that not only C6H5CN but also other large aromatic cycles are abundant in clouds rich in carbon chains.

The effects of ageing and skin type on Photodynamic Therapy (PDT) for different treatment methods have been theoretically investigated. A multilayered Monte Carlo Radiation Transfer model is presented where both daylight activated PDT and conventional PDT are compared. It was found that light penetrates deeper through older skin with a lighter complexion, which translates into a deeper effective treatment depth. The effect of ageing was found to be larger for darker skin types. The investigation further strengthens the usage of daylight as a potential light source for PDT where effective treatment depths of about 2 mm can be achieved.

Remote sensing of the OI 130.4‐nm emission is potentially a useful means for routine monitoring of the atomic oxygen abundance in the upper atmosphere, especially for altitudes above 300 km where the OI 135.6‐nm emission becomes too dim to be useful. However, to date, the interpretation of the OI 130.4‐nm emission as a proxy for the O density remains ambiguous in that the relative contribution of the external and internal sources to the production of this emission has not been fully understood. In this study, we perform a comparative analysis of the OI 130.4‐nm dayglow observed by NASA's Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) mission using a Monte Carlo radiative transfer model to investigate the consistency between models and the TIMED/Global UltraViolet Imager (GUVI) data. The solar 130.4‐nm flux is measured by TIMED/Solar EUV Experiment (SEE). The Global Airglow (GLOW) and the Atmospheric Ultraviolet Radiance Integrated Code (AURIC) models are used to calculate the initial volume emission rates due to photoelectron impact excitation, and the NRLMSISE‐00 model is used to provide the atmospheric density and temperature profiles. Our data‐model comparisons suggest that the model predicted contributions from photoelectron impact excitation need to be scaled by a factor of 0.1–0.5 to achieve good fits with the data. Moreover, the modeled solar contributions need to be scaled up/down to fit the observations at small ( 20 )/large ( 60 ) solar zenith angles, with a factor of 0.5–1.7. These scale factors are larger than the uncertainties in the GUVI and SEE instrument calibrations, which might suggest inaccurate model predictions of the dayside O density and temperature variations with solar zenith angles.

Theoretical extension of universal forward and backward Monte Carlo radiative transfer modeling for passive and active polarization observation simulations

Abstract. A new multiple-scattering Monte Carlo 3-D radiative transfer model named McSCIA (Monte Carlo for SCIAmachy) is presented. The backward technique is used to efficiently simulate narrow field of view instruments. The McSCIA algorithm has been formulated as a function of the Earth's radius, and can thus perform simulations for both plane-parallel and spherical atmospheres. The latter geometry is essential for the interpretation of limb satellite measurements, as performed by SCIAMACHY on board of ESA's Envisat. The model can simulate UV-vis-NIR radiation. First the ray-tracing algorithm is presented in detail, and then successfully validated against literature references, both in plane-parallel and in spherical geometry. A simple 1-D model is used to explain two different ways of treating absorption. One method uses the single scattering albedo while the other uses the equivalence theorem. The equivalence theorem is based on a separation of absorption and scattering. It is shown that both methods give, in a statistical way, identical results for a wide variety of scenarios. Both absorption methods are included in McSCIA, and it is shown that also for a 3-D case both formulations give identical results. McSCIA limb profiles for atmospheres with and without absorption compare well with the one of the state of the art Monte Carlo radiative transfer model MCC++. A simplification of the photon statistics may lead to very fast calculations of absorption features in the atmosphere. However, these simplifications potentially introduce biases in the results. McSCIA does not use simplifications and is therefore a relatively slow implementation of the equivalence theorem.