Molecular Abundances Research Articles

The role of cloud particle properties in the WASP-39b transmission spectrum based on JWST/NIRSpec observations

Aerosols are capable of having a huge influence on reflected, emitted, and transmitted planetary spectra, especially at wavelengths similar to their average sizes, but also extending to much longer and shorter wavelengths. The Near InfraRed Spectrograph (NIRSpec) using the PRISM mode on board the James Webb Space Telescope (JWST) is providing valuable data of transit spectra over a wide spectral range that is able to cover the whole contribution of aerosols, potentially disentangling them from other constituents, and thus allowing us to constrain their properties. Our aim was to investigate whether NIRSpec/PRISM JWST transmission spectroscopy observations, in addition to being useful for detecting and determining the abundance of gases more accurately than any previous instruments, are also capable of studying the physical properties of the aerosols in exoplanetary atmospheres. We performed nested sampling Bayesian retrievals with the MultiNest library. We used the Planetary Spectrum Generator (PSG) and the Modelled Optical Properties of enSeMbles of Aerosol Particles (MOPSMAP) database as tools for the forward simulations and previously published NIRSpec/PRISM JWST observations of WASP-39b as input data. Retrievals indicate that models including an aerosol extinction weakly increasing or sharply decreasing with wavelength are decisively better than those with a flat transmission and that this increased degree of complexity is supported by the kind of data that JWST/NIRSpec can provide. Given other physical constraints from previous works, the scenario of weakly increasing particle extinction is favoured. We find that this also has an effect on the retrieved gas abundances. JWST observations give us the potential to study some physical characteristics of exoplanetary clouds, in particular their overall dependence of transmissivity on wavelength. It is important to implement more detailed aerosol models as their extinction may affect significantly retrieved molecular abundances.

A Population Analysis of 20 Exoplanets Observed from Optical to Near-infrared Wavelengths with the Hubble Space Telescope: Evidence for Widespread Stellar Contamination

Abstract We present a population study of 20 exoplanets, ranging from Neptune-like to inflated hot-Jupiter planets, observed during transit with the Space Telescope Imaging Spectrograph (STIS) and Wide Field Camera 3 (WFC3) instruments on board the Hubble Space Telescope (HST). To obtain spectral information from the near-ultraviolet to the near-infrared, we reanalyzed 16 WFC3 and over 50 STIS archival data sets with our dedicated HST pipeline. We also include 24 WFC3 data sets previously reduced with the same software. Across our target sample, we observe significant divergence among multiple observations conducted with the same STIS grating at various epochs, while we do not detect variations in the WFC3 data sets. These results are suggestive of stellar contamination, which we have investigated further using known Bayesian tools and other tailored metrics, facilitating a more objective assessment of stellar activity intensity within each system. Our findings reveal that stellar activity contaminates up to half of the studied exoplanet atmospheres, albeit at varying extents. Accounting for stellar activity can significantly alter planetary atmospheric parameters like molecular abundances (up to 6 orders of magnitude) and temperature (up to 145%), contrasting with the results of analyses that neglect activity. Our results emphasize the importance of considering the effects of stellar contamination in exoplanet transit studies; this issue is particularly true for data sets obtained with facilities that do not cover the optical and/or UV spectral range where the activity is expected to be more impactful but also more easily detectable. Our results also provide a catalog of potentially active stars for further investigation and monitoring.

Molecular Distributions and Abundances in the Binary-shaped Outflow of V Hya

Binaries are known to play a key role in the mass loss and dynamical environments of evolved stars. Stellar and substellar companion interactions produce complex wind morphologies including rotating/expanding disks, bipolar outflows, and spiral wind patterns; however, the connection between these many structures and the gas-phase chemistry they harbor is not well constrained. To expand the sample of chemical inventories in interacting systems, we present a detailed spectroscopic case study of the binary C-rich asymptotic giant branch (AGB) star V Hya. Using spatially resolved Atacama Large Millimeter/submillimeter Array observations at Bands 3, 6, and 7, we characterize the rotational emission lines and distributions of molecules in its surrounding disk undergoing dynamical expansion (DUDE). We detect emission from over 15 molecules and isotopologues toward this source, and present resolved maps for the brightest tracers of carbonaceous chemistry (e.g., CCH, C4H, HC5N, HNC, and CH3CN ). Employing LTE and non-LTE models of emission from the DUDE, we estimate the abundance distributions for optically thin species, and compare them with prototypical carbon-rich AGB envelopes. We find that the average abundances of detected species are within a factor of ∼5 from sources with similar mass-loss rates; however, the distribution of daughter species in V Hya is much more compact, with carbon chain species (CCH, C4H, and HC3N) appearing with abundances >10−7 even in the innermost sampled regions (200 au) of the disk.

Rotational rate coefficients computation of MgS(X1Σ+) in collision with He(1S)

ABSTRACT Given its abundance in the interstellar medium recently justified by astronomical observations, the chemistry and reactivity of the metal-bearing molecule MgS require special attention. The availability of up-to-date collision data between this MgS molecule and the most abundant perturbing species H$_2$ and He in the interstellar medium is an essential resource to derive reliable values of its molecular abundance from astronomical observations. This work aims to provide improved scattering parameters for the MgS molecular system in collision with He. A new 2D potential energy surface (2D-PES) is derived by adopting the state-of-the-art level of theory of the explicitly correlated coupled cluster with single, double, and perturbative triple excitations (RCCSD(T)-F12) method in conjunction with the aug-cc-pVTZ basis sets. This PES was used to calculate inelastic cross-sections within the framework of the close-coupling (CC) theory for total energies $\le 500$ cm$^{-1}$ and J$\le 21$. Using the Maxwell–Boltzmann distribution of kinetic energies, these cross-sections were integrated to generate the collisional (de)-excitation rate coefficients for temperatures below 100 K. We expect that the new rate coefficients will help us to analyse present and future observations of this key molecule for the interstellar chemistry.

Discrimination of Healthy and Botrytis cinerea-Infected Grapes Using Untargeted Metabolomic Analysis with Direct Electrospray Ionization Mass Spectrometry.

Botrytis cinerea infections of grapes significantly reduce yield and quality and increase phenolic compound oxidation, resulting in color loss, off-flavors, and odors in wine. In this study, metabolites were extracted from grape homogenates comprising healthy or infected grapes from different vintages, cultivars, regions, and maturity stages. Samples were randomly analyzed by direct injection into an ion trap mass spectrometer, with data collected from 50 to 2000 m/z for 1 min. Molecular feature abundances from 0.1 to 0.4 min were normalized prior to Principal Components Analysis assessment of workflow. Samples were randomly assigned to a calibration and independent test sample set, with feature reduction, a two-class model Partial Least Squares-Discriminant Analysis, cross-validation, and permutation testing performed with the calibration data set. Prediction of sample class in the independent test samples demonstrated an overall predictive error of less than 5%. Feature importance was assessed using a combined variable importance in projection and selectivity ratio plot. Annotation of important molecular features using a high-resolution LC-QTOF mass spectrometry MS/MS of selected samples enabled key metabolites palmitic, oleic, linoleic and linolenic acids, succinate, and epicatechin to be identified and associated with infection. The proposed workflow establishes sensitive high-throughput rapid MS-based methods for phytosanitary testing of grape and fruit samples.

Recombinant Production of Bovine αS1-Casein in Genome-Reduced Bacillus subtilis Strain IIG-Bs-20-5-1.

Cow's milk represents an important protein source. Here, especially casein proteins are important components, which might be a promising source of alternative protein production by microbial expression systems. Nevertheless, caseins are difficult-to-produce proteins, making heterologous production challenging. However, the potential of genome-reduced Bacillus subtilis was applied for the recombinant production of bovine αS1-casein protein. A plasmid-based gene expression system was established in B. subtilis allowing the production of his-tagged codon-optimized bovine αS1-casein. Upscaling in a fed-batch bioreactor system for high cell-density fermentation processes allowed for efficient recombinant αS1-casein production. After increasing the molecular abundance of the recombinant αS1-casein protein using immobilized metal affinity chromatography, zeta potential and particle size distribution were determined in comparison to native bovine αS1-casein. Non-sporulating B. subtilis strain BMV9 and genome-reduced B. subtilis strain IIG-Bs-20-5-1 were applied for recombinant αS1-casein production. Casein was detectable only in the insoluble protein fraction of the genome-reduced B. subtilis strain. Subsequent high cell-density fed-batch bioreactor cultivations using strain IIG-Bs-20-5-1 resulted in a volumetric casein titer of 56.9 mg/L and a yield of 1.6 mgcasein/gCDW after reducing the B. subtilis protein content. Comparative analyses of zeta potential and particle size between pre-cleaned recombinant and native αS1-casein showed pH-mediated differences in aggregation behavior. The study demonstrates the potential of B. subtilis for the recombinant production of bovine αS1-casein and underlines the potential of genome reduction for the bioproduction of difficult-to-produce proteins.

The physical and chemical structure of Sagittarius B2

Context. The giant molecular cloud complex Sagittarius B2 (Sgr B2) in the central molecular zone of our Galaxy hosts several high-mass star formation sites, with Sgr B2(M) and Sgr B2(N) being the main centers of activity. This analysis aims to comprehensively model each core spectrum, considering molecular lines, dust attenuation, and free-free emission interactions. We describe the molecular content analysis of each hot core and identify the chemical composition of detected sources. Aims. Using ALMA’s high sensitivity, we aim to characterize the hot core population in Sgr B2(M) and N, gaining a better understanding of the different evolutionary phases of star formation processes in this complex. Methods. We conducted an unbiased ALMA spectral line survey of 47 sources in band 6 (211-275 GHz). Chemical composition and column densities were derived using XCLASS, assuming local thermodynamic equilibrium. Quantitative descriptions for each molecule were determined, considering all emission and absorption features across the spectral range. Temperature and velocity distributions were analyzed, and derived abundances were compared with other spectral line surveys. Results. We identified 65 isotopologs from 41 different molecules, ranging from light molecules to complex organic compounds, originating from various environments. Most sources in the Sgr B2 complex were assigned different evolutionary phases of high-mass star formation. Conclusions. Sgr B2(N) hot cores show more complex molecules such as CH3OH, CH3OCHO, and CH3OCH3, while M cores contain lighter molecules such as SO2, SO, and NO. Some sulfur-bearing molecules are more abundant in N than in M. The derived molecular abundances can be used for comparison and to constrain astrochemical models. Inner sources in both regions were generally more developed than outer sources, with some exceptions.

Validation of millimetre and sub-millimetre atmospheric collision-induced absorption at Chajnantor

Due to the importance of a reference atmospheric radiative transfer model for both planning and calibrating ground-based observations at millimetre and sub-millimetre wavelengths, we have undertaken a validation campaign consisting of acquiring atmospheric spectra under different weather conditions, in different diurnal moments and seasons, with the Atacama Pathfinder EXperiment (APEX), due to the excellent stability of its receivers and the very high frequency resolution of its back-ends. As a result, a dataset consisting of 56 spectra within the 157.3-742.1 GHz frequency range, at kilohertz resolution (smoothed to sim 2-10 MHz for analysis), and spanning one order of magnitude (sim 0.35-3.5 mm) in precipitable water vapour columns, has been gathered from October 2020 to September 2022. These data are unique for their quality and completeness and, due to the proximity of APEX to the Atacama Large Millimeter/Submillimeter Array (ALMA), they provide an excellent opportunity to validate the atmospheric radiative transfer model currently installed in the ALMA software. The main issues addressed in the study are possible missing lines in the model, line shapes, vertical profiles of atmospheric physical parameters and molecular abundances, seasonal and diurnal variations, and collision-induced absorption (CIA), to which this paper is devoted, in its N$_2$-N$_2$ + N$_2$-O$_2$ + O$_2$-O$_2$ (dry) and N$_2$-H$_2$O + O$_2$-H$_2$O (`foreign' wet) mechanisms. All these CIA terms should remain unchanged in the above-mentioned ALMA atmospheric model as a result of this work.

Considerations for Photochemical Modeling of Possible Hycean Worlds

JWST is revolutionising the study of temperate sub-Neptunes, starting with the first detection of carbon-bearing molecules in the habitable-zone sub-Neptune K2-18 b. The retrieved abundances of CH4 and CO2 and nondetection of NH3 and CO in K2-18 b are consistent with prior predictions of photochemical models for a Hycean world with a habitable ocean. However, recent photochemical modeling raised the prospect that the observed abundances may be explained by a mini-Neptune scenario instead. In this study, we explore these scenarios using independent photochemical modeling with K2-18 b as a case study. We find the previous results to be sensitive to a range of model assumptions, such as the photochemical cross sections, incident stellar spectrum, surface pressure, UV albedo, and metallicity, significantly affecting the resulting abundances. We explore a wide model space to investigate scenarios that are compatible with the retrieved molecular abundances for K2-18 b. Our analysis shows that the previously favored mini-Neptune scenario is not compatible with most of the retrieved abundances, while the Hycean scenarios, both inhabited and uninhabited, provide better agreement. An uninhabited Hycean scenario explains most of the abundance constraints, except CH4, which is generally underabundant but dependent on the model assumptions. The inhabited Hycean scenario is compatible with all the abundances if the observed CH4 is assumed to be predominantly biogenic. Our results underscore the importance of systematic photochemical modeling and accurate interpretation of chemical abundance constraints for candidate Hycean worlds.

Neural Network Constraints on the Cosmic-Ray Ionization Rate and Other Physical Conditions in NGC 253 with ALCHEMI Measurements of HCN and HNC

We use a neural network model and Atacama Large Millimeter/submillimeter Array (ALMA) observations of HCN and HNC to constrain the physical conditions, most notably the cosmic-ray ionization rate (CRIR, ζ), in the Central Molecular Zone (CMZ) of the starburst galaxy NGC 253. Using output from the chemical code UCLCHEM, we train a neural network model to emulate UCLCHEM and derive HCN and HNC molecular abundances from a given set of physical conditions. We combine the neural network with radiative transfer modeling to generate modeled integrated intensities, which we compare to measurements of HCN and HNC from the ALMA Large Program ALCHEMI. Using a Bayesian nested sampling framework, we constrain the CRIR, molecular gas volume and column densities, kinetic temperature, and beam-filling factor across NGC 253's CMZ. The neural network model successfully recovers UCLCHEM molecular abundances with ∼3% error and, when used with our Bayesian inference algorithm, increases the parameter-inference speed tenfold. We create images of these physical parameters across NGC 253's CMZ at 50 pc resolution and find that the CRIR, in addition to the other gas parameters, is spatially variable with ζ ∼ a few ×10−14 s−1 at r ≳ 100 pc from the nucleus, increasing to ζ > 10−13 s−1 at its center. These inferred CRIRs are consistent within 1 dex with theoretical predictions based on nonthermal emission. Additionally, the high CRIRs estimated in NGC 253's CMZ can be explained by the large number of cosmic-ray-producing sources as well as a potential suppression of cosmic-ray diffusion near their injection sites.

A Survey of Sulfur-bearing Molecular Lines toward the Dense Cores in 11 Massive Protoclusters

Sulfur-bearing molecules are commonly detected in dense cores within star-forming regions, but the total sulfur budget is significantly lower when compared to the interstellar medium value. The properties of sulfur-bearing molecules are not well understood due to the absence of large sample studies with uniform observational configurations. To deepen our understanding of this subject, we conducted a study using Atacama Large Millimeter/submillimeter Array 870 μm observations of 11 massive protoclusters. By checking the spectra of 248 dense cores in 11 massive protoclusters, a total of 10 sulfur-bearing species (CS, SO, H2CS, NS, SO2, 33SO, 34SO2, 33SO2, SO18O, and OC34S) were identified. The parameters including systemic velocities, line widths, gas temperatures, column densities, and abundances were derived. Our results indicate that SO appears to be more easily detected in a wider range of physical environments than H2CS, despite these two species showing similarities in gas distributions and abundances. Molecules 34SO2 and H2CS are good tracers of the temperature of sulfur-bearing species, in which H2CS traces the outer warm envelope and 34SO2 is associated with high-temperature central regions. High-mass star-forming feedback (outflow and other nonthermal motions) significantly elevates the sulfur-bearing molecular abundances and detection rates specifically for SO2 and SO. A positive correlation between the SO2 abundance increasing factor (F) and temperatures suggests that SO2 could serve as a sulfur reservoir on the grain mantles of dense cores and then can be desorbed from dust to gas phase as the temperature rises. This work shows the importance of a large and unbiased survey to understand the sulfur depletion in dense cores.

Understory Environmental Conditions Drive Leaf Level-Lipid Biosynthesis in a Deciduous and Evergreen Tree Species.

Plants in the understory experience climatic conditions affected by the overstory canopy that influence physiological and biochemical processes. Here, we investigate the relationships of leaf lipid molecular abundances to leaf water content, transmitted irradiance, and free-air temperature (Tair) from deciduous angiosperm (Quercus buckleyi) and evergreen gymnosperm (Juniperus ashei) understory trees across an elevation gradient in a central Texas (USA) woodland. Monthly sampling from 04/2019 to 01/2020 revealed that long-chain leaf waxes (≥ C27) accumulated with leaf water deficit over the growing season for both tree species. Higher transmitted light during the hottest, driest months was due to a decreased leaf area index (LAI) in the canopy as leaf shedding is a common drought response. Isoprenoids (sesqui-, di-terpenoids, phytosterols) in leaves changed by month with changing LAI and transmittance associated with monthly Tair changes. The chain length of n-alkanols in Q. buckleyi shifted with seasonal LAI at different topographic positions. The unsaturation of fatty acids in both tree species decreased with increased seasonal Tair but showed topography sensitivity. Leaf-level metabolites responded to understory microclimatic variables that were influenced by seasonality and topography.

CHEMOUT: CHEMical complexity in star-forming regions of the OUTer Galaxy

Context. Single-dish observations suggest that the abundances of organic species in star-forming regions of the outer Galaxy, which are characterised by sub-solar metallicities, are comparable to those found in the local Galaxy. Aims. To understand this counter-intuitive result and avoid a misleading interpretation due to beam dilution effects at these large distances, spatially resolved molecular emission maps are needed to correctly link the measured abundances and local physical properties. Methods. We observed several organic molecules with the Atacama Large Millimeter Array towards WB89-671, the source with the largest galactocentric distance (23.4 kpc) of the project CHEMical complexity in star-forming regions of the OUTer Galaxy (CHEMOUT) at a resolution of ~15 000 au. We compared the observed molecular abundances with chemical model predictions. Results. We detected emission of c-C3H2, C4H, CH3OH, H2CO, HCO, H13CO+, HCS+, CS, HN13C, and SO. The emission morphology is complex, extended, and different in each tracer. In particular, the most intense emission in H13CO+, H2CO and c-C3H2 arises from two millimeter-continuum infrared-bright cores. The most intense CH3OH and SO emission predominantly arises from the part of the filament that lacks continuum sources. The narrow line widths across the filament indicate quiescent gas in spite of the two embedded protostars. The derived molecular column densities are comparable with those in local star-forming regions, and they suggest an anti-correlation between hydrocarbons, ions, HCO, and H2CO on the one hand, and CH3OH and SO on the other. Conclusions. The static chemical models that match the observed column densities best favour low-energy conditions that are expected at large galactocentric radii, but they also favour carbon elemental abundances that exceed those derived by extrapolating the [C/H] galactocentric gradient at 23 kpc by three times. This would indicate a flatter [C/H] trend at large galactocentric radii, which is in line with a flat abundance of organics. However, to properly reproduce the chemical composition of each region, models should include dynamical evolution.

Simba-EoR: early galaxy formation in the simba simulation including a new sub-grid interstellar medium model

ABSTRACT We update the dust model present within the simba galaxy simulations with a self-consistent framework for the co-evolution of dust and molecular hydrogen populations in the interstellar medium, and use this to explore $z \ge 6$ galaxy evolution. In addition to tracking the evolution of dust and molecular hydrogen abundances, our model fully integrates these species into the simba simulation, explicitly modelling their impact on physical processes such as star formation and cooling through the inclusion of a novel two-phase sub-grid model for interstellar gas. Running two cosmological simulations down to $z \sim 6$ we find that our simba-EoR model displays a generally tighter concordance with observational data than fiducial simba. Additionally we observe that our simba-EoR models increase star formation activity at early epochs, producing larger dust-to-gas ratios consequently. Finally, we discover a significant population of hot dust at $\sim 100$ K, aligning with contemporaneous observations of high-redshift dusty galaxies, alongside the large $\sim 20$ K population typically identified.

From the Shadows: The Impact of Nightside Thermal Emission on Ultrahot Jupiter Transmission Spectrum Retrievals

Transmission spectroscopy is the most widely used technique for studying exoplanet atmospheres. Since the planetary nightside faces the observer during a transit, highly irradiated giant exoplanets with warm nightsides emit thermal radiation that can contaminate transmission spectra. Observations of ultrahot Jupiters in the near- and mid-infrared with JWST are especially susceptible to nightside contamination. However, nightside thermal emission is generally not considered in atmospheric retrievals of exoplanet transmission spectra. Here, we quantify the potential biases from neglecting nightside thermal emission in multidimensional atmospheric retrievals of an ultrahot Jupiter. Using simulated JWST transmission spectra of the ultrahot Jupiter WASP-33b (0.8–12 μm), we find that transmission spectrum retrievals without nightside emission can overestimate molecular abundances by almost an order of magnitude and underestimate the dayside temperature by ≳400 K. We show that a modified retrieval prescription, including both transmitted light and nightside thermal emission, correctly recovers the atmospheric properties and is favored by Bayesian model comparisons. Nightside thermal contamination can be readily implemented in retrieval models via a first-order approximation, and we provide formulae to estimate whether this effect is likely to be significant for a given planet. We recommend that nightside emission should be included as standard practice when interpreting ultrahot Jupiter transmission spectra with JWST.

Molecular-chemical characterization of soil organic matter in wetlands by pyrolysis-gas chromatography/mass spectrometry

The carbon cycle in ecosystems is fundamentally controlled by the composition and transformation of organic molecules. Alpine wetland soils have enormous carbon storage, but they are sensitive to climate change, and can easily shift from carbon sink to carbon source. However, we currently lack understanding in molecular-chemical composition of soil organic matter (SOM) in alpine wetlands. In this study, we tried to decipher molecular-chemical features of SOM in typical alpine wetlands using the pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). Results indicated that nitrogen-containing compounds were the most abundant moieties among pyrolytic products of SOM. More than 83 % of pyrolytic moieties had a molecular weight of no more than 200 Daltons and a H/C ratio of no more than 2.0. O/C ratio of most pyrolytic products were less than 0.5. A van Krevelen diagram potentially indicated that SOM in wetlands might consist of massive heterogeneous molecules where aromatic compounds and their derivatives served as the core, with aliphatic hydrocarbon molecules of varying carbon chain lengths attached externally. About 72.25 % of variances in SOM were explained by 50 pyrolytic products, of which toluene was the most important. A significantly negative relation was observed between molecular weight (MW) and abundance of pyrolytic products, while positive relations were found between H/C, O/C, and abundance of pyrolytic products. Our work implied that SOM in wetlands was mainly composed of molecules with low MW and aromatic function groups.

JWST-TST High Contrast: Spectroscopic Characterization of the Benchmark Brown Dwarf HD 19467 B with the NIRSpec Integral Field Spectrograph

We present the atmospheric characterization of the substellar companion HD 19467 B as part of the pioneering James Webb Space Telescope Guaranteed Time Observer program to obtain moderate resolution spectra (R ∼ 2700, 3–5 μm) of a high-contrast companion with the NIRSpec integral field unit (IFU). HD 19467 B is an old, ∼9 Gyr, companion to a solar-type star with multiple measured dynamical masses. The spectra show detections of CO, CO2, CH4, and H2O. We forward model the spectra using Markov Chain Monte Carlo methods and atmospheric model grids to constrain the effective temperature and surface gravity. We then use NEWERA-PHOENIX grids to constrain nonequilibrium chemistry parameterized by K zz and explore molecular abundance ratios of the detected molecules. We find an effective temperature of 1103 K, with a probable range from 1000 to 1200 K, a surface gravity of 4.50 dex, with a range of 4.14–5.00, and deep vertical mixing, log10(K zz ), of 5.03, with a range of 5.00–5.44. All molecular mixing ratios are approximately solar, leading to a C/O ∼ 0.55, which is expected from a T5.5 brown dwarf. Finally, we calculate an updated dynamical mass of HD 19467 B using newly derived NIRCam astrometry, which we find to be 71.6−4.6+5.3MJup , in agreement with the mass range we derive from evolutionary models, which we find to be 63–75 M Jup. These observations demonstrate the excellent capabilities of the NIRSpec IFU to achieve detailed spectral characterization of substellar companions at high contrast close to bright host stars, in this case at a separation of ∼1.″6 with a contrast of 10−4 in the 3–5 μm range.

Characterizing the nonmonotonic behavior of mutual information along biochemical reaction cascades.

Cells sense environmental signals and transmit information intracellularly through changes in the abundance of molecular components. Such molecular abundances can be measured in single cells and exhibit significant heterogeneity in clonal populations even in identical environments. Experimentally observed joint probability distributions can then be used to quantify the covariability and mutual information between molecular abundances along signaling cascades. However, because stationary state abundances along stochastic biochemical reaction cascades are not conditionally independent, their mutual information is not constrained by the data-processing inequality. Here, we report the conditions under which the mutual information between stationary state abundances increases along a cascade of biochemical reactions. This nonmonotonic behavior can be intuitively understood in terms of noise propagation and time-averaging stochastic fluctuations that are short-lived compared to an extrinsic signal. Our results reemphasize that mutual information measurements of stationary state distributions of cellular components may be of limited utility for characterizing cellular signaling processes because they do not measure information transfer.

Molecular Oxygen Abundance in Galactic Massive Star Formation Regions Based on SWAS Observations

Molecular oxygen abundance is a key parameter in understanding the chemical network of the interstellar medium. We estimate the molecular oxygen column density and abundance for a sample of Galactic massive star formation regions based on observations from the Submillimiter Wave Astronomy Satellite (SWAS) survey. We obtained an averaged O2 spectrum based on this sample using the (SWAS) survey data (O2, 487.249 GHz, N = 3–1, J = 3–2). No emission or absorption feature is seen around the supposed central velocity with a total integration time of t total = 8.67 × 103 hr and an rms noise per channel of 1.45 mK. Assuming a kinetic temperature T kin = 30 K, we derive the 3σ upper limit of the O2 column density to be 3.3 × 1015 cm−2, close to the lowest values reported in Galactic massive star formation regions in previous studies. The corresponding O2 abundance upper limit is 6.7 × 10−8, lower than all previous results based on SWAS observations and is close to the lowest reported value in massive star formation regions. On a galactic scale, our statistical results confirm a generally low O2 abundance for Galactic massive star formation regions. This abundance is also lower than results reported in extragalactic sources.

The 2024 KIDA network for interstellar chemistry

Context. The study of the chemical composition of the interstellar medium (ISM) requires a strong synergy between laboratory astrophysics, modeling, and observations. In particular, astrochemical models have been developed for decades now and include an increasing number of processes studied in the laboratory or theoretically. These models follow the chemistry both in the gas phase and at the surface of interstellar grains. Since 2012, we have provided complete gas-phase chemical networks for astrochemical codes that can be used to model various environments of the ISM. Aims. Our aim is to introduce the new up-to-date astrochemical network kida.uva.2024 together with the ice chemical network and the fortran code to compute time dependent compositions of the gas, the ice surface, and the ice mantles under physical conditions relevant for the ISM. Methods. The gas-phase chemical reactions, as well as associated rate coefficients, included in kida.uva.2024 were carefully selected from the KIDA online database and represent the most recent values. The model predictions for cold core conditions and for when considering only gas-phase processes were computed as a function of time and compared to the predictions obtained with the previous version, kida.uva.2014. In addition, key chemical reactions were identified. The model predictions, including both gas and surface processes, were compared to the molecular abundances as observed in the cold core TMC1-CP. Results. Many gas-phase reactions were revised or added to produce kida.uva.2024. The new model predictions are different by several orders of magnitude for some species. The agreement of this new model with observations in TMC-1 (CP) is, however, similar to the one obtained with the previous network.