Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges

We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coefficients and their uncertainties for the major gas-phase processes -- ion-neutral reactions, neutral-neutral reactions, radiative association, and dissociative recombination -- is reviewed. Emphasis is placed on those reactions that have been identified, by sensitivity analyses, as 'crucial' in determining the predicted abundances of the species observed in the interstellar medium. These sensitivity analyses have been carried out for gas-phase models of three representative, molecule-rich, astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the expanding circumstellar envelope IRC +10216. Our review has led to the proposal of new values and uncertainties for the rate coefficients of many of the key reactions. The impact of these new data on the predicted abundances in TMC-1 and L134N is reported. Interstellar dust particles also influence the observed abundances of molecules in the interstellar medium. Their role is included in gas-grain, as distinct from gas-phase only, models. We review the methods for incorporating both accretion onto, and reactions on, the surfaces of grains in such models, as well as describing some recent experimental efforts to simulate and examine relevant processes in the laboratory. These efforts include experiments on the surface-catalysed recombination of hydrogen atoms, on chemical processing on and in the ices that are known to exist on the surface of interstellar grains, and on desorption processes, which may enable species formed on grains to return to the gas-phase.Comment: Accepted for publication in Space Science Review

Quantification of segregation dynamics in ice mixtures

(Abridged) The observed presence of pure CO2 ice in protostellar envelopes is attributed to thermally induced ice segregation, but a lack of quantitative experimental data has prevented its use as a temperature probe. Quantitative segregation studies are also needed to characterize diffusion in ices, which underpins all ice dynamics and ice chemistry. This study aims to quantify the segregation mechanism and barriers in different H2O:CO2 and H2O:CO ice mixtures covering a range of astrophysically relevant ice thicknesses and mixture ratios. The ices are deposited at 16-50 K under (ultra-)high vacuum conditions. Segregation is then monitored at 23-70 K as a function of time, through infrared spectroscopy. Thin (8-37 ML) H2O:CO2/CO ice mixtures segregate sequentially through surface processes, followed by an order of magnitude slower bulk diffusion. Thicker ices (>100 ML) segregate through a fast bulk process. The thick ices must therefore be either more porous or segregate through a different mechanism, e.g. a phase transition. The segregation dynamics of thin ices are reproduced qualitatively in Monte Carlo simulations of surface hopping and pair swapping. The experimentally determined surface-segregation rates for all mixture ratios follow the Ahrrenius law with a barrier of 1080[190] K for H2O:CO2 and 300[100] K for H2O:CO mixtures. During low-mass star formation H2O:CO2 segregation will be important already at 30[5] K. Both surface and bulk segregation is proposed to be a general feature of ice mixtures when the average bond strengths of the mixture constituents in pure ice exceeds the average bond strength in the ice mixture.Comment: Accepted for publication in A&A. 25 pages, including 13 figure

Accurate rate coefficients for models of interstellar gas-grain chemistry

The methodology for modeling grain-surface chemistry has been greatly improved by taking into account the grain size and fluctuation effects. However, the reaction rate coefficients currently used in all practical models of gas-grain chemistry are inaccurate by a significant amount. We provide expressions for these crucial rate coefficients that are both accurate and easy to incorporate into gas-grain models. We use exact results obtained in earlier work, where the reaction rate coefficient was defined by a first-passage problem, which was solved using random walk theory. The approximate reaction rate coefficient presented here is easy to include in all models of interstellar gas-grain chemistry. In contrast to the commonly used expression, the results that it provides are in perfect agreement with detailed kinetic Monte Carlo simulations. We also show the rate coefficient for reactions involving multiple species.Comment: 4 pages, 2 figure

A Unified Monte Carlo Treatment of Gas-Grain Chemistry for Large Reaction Networks. I. Testing Validity of Rate Equations in Molecular Clouds

In this study we demonstrate for the first time that the unified Monte Carlo approach can be applied to model gas-grain chemistry in large reaction networks. Specifically, we build a time-dependent gas-grain chemical model of the interstellar medium, involving about 6000 gas-phase and 200 grain surface reactions. This model is used to test the validity of the standard and modified rate equation methods in models of dense and translucent molecular clouds and to specify under which conditions the use of the stochastic approach is desirable. We found that at temperatures 25--30 K gas-phase abundances of H$_2$O, NH$_3$, CO and many other gas-phase and surface species in the stochastic model differ from those in the deterministic models by more than an order of magnitude, at least, when tunneling is accounted for and/or diffusion energies are 3x lower than the binding energies. In this case, surface reactions, involving light species, proceed faster than accretion of the same species. In contrast, in the model without tunneling and with high binding energies, when the typical timescale of a surface recombination is greater than the timescale of accretion onto the grain, we obtain almost perfect agreement between results of Monte Carlo and deterministic calculations in the same temperature range. At lower temperatures ($\sim10$ K) gaseous and, in particular, surface abundances of most important molecules are not much affected by stochastic processes.Comment: 33 pages, 9 figures, 1 table. Accepted for publication in Ap

Влияние параметров одномассной системы с упругими ограничителями на характер ее колебаний

У статті розглянуто одномасну систему з пружними обмежувачами. Побудовано області існування різних режимів коливань системи, а також визначено вплив параметрів системи на межі цих областей.A one-mass system with elastic constraints is studied. Areas of existing of different oscillation modes are built. Also an influence of system parameters on limits of these areas is determined

Sensitivity Analysis of Grain Surface Chemistry to Binding Energies of Ice Species

Advanced telescopes, such as ALMA and the James Webb Space Telescope, are likely to show that the chemical universe may be even more complex than currently observed, requiring astrochemical modelers to improve their models to account for the impact of new data. However, essential input information for gas‑grain models, such as binding energies of molecules to the surface, have been derived experimentally only for a handful of species, leaving hundreds of species with highly uncertain estimates. We present in this paper a systematic study of the effect of uncertainties in the binding energies on an astrochemical two-phase model of a dark molecular cloud, using the rate equations approach. A list of recommended binding energy values based on a literature search of published data is presented. Thousands of simulations of dark cloud models were run, and in each simulation a value for the binding energy of hundreds of species was randomly chosen from a normal distribution. Our results show that the binding energy of H2 is critical for the surface chemistry. For high binding energies, H2 freezes out on the grain forming an H2 ice. This is not physically realistic, and we suggest a change in the rate equations. The abundance ranges found are in reasonable agreement with astronomical ice observations. Pearson correlation coefficients revealed that the binding energy of HCO, HNO, CH2, and C correlate most strongly with the abundance of dominant ice species. Finally, the formation route of complex organic molecules was found to be sensitive to the branching ratios of H2CO hydrogenation

Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring

Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3-13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease. © 2015 The American Society of Human Genetics

Laboratory evidence for efficient water formation in interstellar ices

Even though water is the main constituent in interstellar icy mantles, its chemical origin is not well understood. Three different formation routes have been proposed following hydrogenation of O, O2, or O3, but experimental evidence is largely lacking. We present a solid state astrochemical laboratory study in which one of these routes is tested. For this purpose O2 ice is bombarded by H- or D-atoms under ultra high vacuum conditions at astronomically relevant temperatures ranging from 12 to 28 K. The use of reflection absorption infrared spectroscopy (RAIRS) permits derivation of reaction rates and shows efficient formation of H2O (D2O) with a rate that is surprisingly independent of temperature. This formation route converts O2 into H2O via H2O2 and is found to be orders of magnitude more efficient than previously assumed. It should therefore be considered as an important channel for interstellar water ice formation as illustrated by astrochemical model calculations.Comment: 15 pages, 4 figures. ApJ, in pres

Laboratory H2O:CO2 ice desorption data: entrapment dependencies and its parameterization with an extended three-phase model

Ice desorption affects the evolution of the gas-phase chemistry during the protostellar stage, and also determines the chemical composition of comets forming in circumstellar disks. From observations, most volatile species are found in H2O-dominated ices. The aim of this study is first to experimentally determine how entrapment of volatiles in H2O ice depends on ice thickness, mixture ratio and heating rate, and second, to introduce an extended three-phase model (gas, ice surface and ice mantle) to describe ice mixture desorption with a minimum number of free parameters. Thermal H2O:CO2 ice desorption is investigated in temperature programmed desorption experiments of thin (10 - 40 ML) ice mixtures under ultra-high vacuum conditions. Desorption is simultaneously monitored by mass spectrometry and reflection-absorption infrared spectroscopy. The H2O:CO2 experiments are complemented with selected H2O:CO, and H2O:CO2:CO experiments. The results are modeled with rate equations that connect the gas, ice surface and ice mantle phases through surface desorption and mantle-surface diffusion. The fraction of trapped CO2 increases with ice thickness (10 - 32 ML) and H2O:CO2 mixing ratio (5:1 - 10:1), but not with one order of magnitude different heating rates. The fraction of trapped CO2 is 44 - 84 % with respect to the initial CO2 content for the investigated experimental conditions. This is reproduced quantitatively by the extended three-phase model that is introduced here. The H2O:CO and H2O:CO2:CO experiments are consistent with the H2O:CO2 desorption trends, suggesting that the model can be used for other ice species found in the interstellar medium to significantly improve the parameterization of ice desorption.Comment: 12 pages, 9 figures, published in A&

Targeted next generation sequencing as a reliable diagnostic assay for the detection of somatic mutations in tumours using minimal DNA amounts from formalin fixed paraffin embedded material

Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5%concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detectio