UCLCHEM has had a major update! The new version is v3.0 and has many changes. Here are some of the key updates:
Check out our docs pages for all the updates and tutorials on how to use the new version.
NGC 253 is a nearby starburst galaxy which hosts several large clouds of gas in its central molecular zone. These clouds are similar to GMCs but orders of magnitude more massive and much hotter, where the star formation rate is very high. The temperature of this gas is important because the star formation efficiency will be determined by how much internal energy that gas has.
Many mechanisms could be heating this gas including mechanical heating due to turbulent shocks, UV photons, X-ray photons, and cosmic-rays. Whilst all are reasonable suspects in the CMZ of NGC 253, previous studies have shown 1 2 that the cosmic-ray ionization rate (CRIR) is likely to be very high.
In a recent piece of work we have used UCLCHEM to show that the ratio of SO and H_3O^+ is a powerful probe of the CRIR. We model ALMA observations of emission from these molecules using UCLCHEM and SpectralRadex to infer the CRIR. We find that regardless of the temperature of the gas, the CRIR is around 10^4 times larger than in the Milky Way.
Interpreting molecular observations through chemical and radiative transfer models is a common but complex practice. Whilst many uncertainties affect chemical models, one in particular is addressed in this work: the issue of time dependence. When modelling a molecular cloud or protostellar disk, how do we initialize the abundances? When is an appropriate time to compare our model to the observed object? Our paper on History Independent Tracers (HITs) side steps this issue by producing a list of molecules which are insensitive to the chemical history of the gas, essentially reaching steady state very quickly across a very wide range of gas conditions.
However, having a list of molecules that are easy to model is only first step towards making useful inferences. We then use our HITs to determine which observables are the most informative about various physical parameters. We do this by producing a large dataset of synthetic observations using UCLCHEM and RADEX to produce line intensities for every transition of every HIT under a wide range of physical conditions. We then calculate the mutual information between each molecular transition and each physical parameter and use these to rank the transitions. The information scores are all available on the HITs website which can be used to plan observations.
By choosing transitions of a HIT that have a high mutual information with your physical parameter of interest, you can obtain the best possible constraint on that parameter. Moreover, as a HIT, the chemical modelling of this species will not be subject to much uncertainty from the gas history.
As part of the SOLIS observational programme, various isotopologues of HCN were observed towards L1157 in order to study the nitrogen fractionation in a protostellar outflow. The modelling work for this study was done using UCLCHEM. You can find the paper here and the abstract below.
The isotopic ratio of nitrogen presents a wide range of values in the Solar System and in star forming system whose origin is still unclear. Chemical reactions in the gas phase are one of the possible processes that could modify the 14 N/ 15 N ratio. We aim at investigating if and how the passage of a shock wave in the interstellar medium, can affect the relative fraction of nitrogen isotopes. The ideal place for such a study is the L1157 outflow, where several shocked clumps are present. We present the first measurement of the 14 N/ 15 N ratio in the two shocked clumps, B1 and B0, of the protostellar outflow L1157, derived from the interferomteric maps of the H 13 CN(1-0) and the HC 15 N(1-0) lines. In B1, we find that the H 13 CN(1-0) and HC 15 N(1-0) emission traces the front of the clump, with averaged column density of N (H 13 CN) ∼ 7 × 10 12 cm −2 and N (HC 15 N) ∼ 2 × 10 12 cm −2 . In this region the ratio H 13 CN(1-0)/HC 15 N(1-0) is quite uniform with an average value of ∼ 5 ± 1. The same average value is also measured in the smaller clump B0e. Assuming the standard 12 C/ 13 C = 68, we obtain 14 N/ 15 N = 340 ± 70, similar to those usually found in prestellar cores and protostars. We analysed the prediction of a chemical shock model for several shock conditions and we found that the nitrogen and carbon fractionations do not vary much for the first period after the shock. The observed H 13 CN/HC 15 N can be reproduced by a non-dissociative, C-type shock with parameters in agreement with previous modelling of L1157-B1. Both observations and chemical models indicate that the shock propagation does not affect the nitrogen isotopic ratio that remains similar to that measured in lower temperature gas in prestellar cores and in protostellar envelopes.
We're replacing our old website! The old site was essentially just a poster for UCLCHEM with some github links. The new website has a similar landing page but importantly, we've moved all the documentation for UCLCHEM online. We'll keep that up to date and are open to comments from users as we're keen to make UCLCHEM as easy to use as possible.
We'll also keep this blog updated with any major updates to UCLCHEM. As a rule, we'll push minor tweaks, bug fixes and background changes that won't affect how the user interacts with the code regularly. However, major changes, feature improvements and changes that will change how you interact with the code will be published as a new version on github and come with an explanatory blog post. Come back if your latest git pull leaves you wondering what happened to UCLCHEM!
The physical structure of a shock wave may take a form unique to its shock type, implying that the chemistry of each shock type is unique as well. In our recent paper, we investigate the different chemistries of J-type and C-type shocks using parameterised forms of their physical structures in order to identify unique molecular tracers of both shock types. We apply these diagnostics to the protostellar outflow L1157 to establish whether the B2 clump could host shocks exhibiting type-specific behaviour.
We find that a range of molecules including H2O and HCN have unique behaviour specific to a J-type shock, but that such differences in behaviour are only evident at low velocity and low density. We find that CH3OH is enhanced by shocks and is a reliable probe of the pre-shock gas density and is shock-type agnostic. Additionally, the fractional abundances within the B2 region are consistent with both C-type and J-type shock emission.
UCLCHEM has recently been used to study carbon fractionation in external galaxies. You can find the paper here and the abstract below.
In the interstellar medium carbon exists in the form of two stable isotopes 12C and 13C and their ratio is a good indicator of nucleosynthesis in galaxies. However, chemical fractionation can potentially significantly alter this ratio and in fact observations of carbon fractionation within the same galaxy has been found to vary from species to species. In this paper, we theoretically investigate the carbon fractionation for selected abundant carbon-bearing species in order to determine the conditions that may lead to a spread of the 12C/13C ratio in external galaxies. We find that carbon fractionation is sensitive to almost all the physical conditions we investigated, it strongly varies with time for all species but CO, and shows pronounced differences across species. Finally, we discuss our theoretical results in the context of the few observations of the 12C/13C in both local and higher redshift galaxies.
Felix Priestley has used UCLCHEM in an investigation of the chemical differences caused by the magnetic fields in prestellar cores. You can find the paper here and the abstract below.
We investigate differences in the molecular abundances between magnetically super- and subcritical pre-stellar cores, performing three-dimensional non-ideal magnetohydrodynamical (MHD) simulations with varying densities and magnetic field strengths, and post-processing the results with a time-dependent gas-grain chemical code. Most molecular species show significantly more central depletion in subcritical models, due to the longer duration of collapse. However, the directly observable quantities - the molecule to hydrogen column density ratios - are generally too similar for observational data to discriminate between models. The profiles of N2H+ and HCO+ show qualitative differences between supercritical and subcritical models on scales of 0.01 pc, which may allow the two cases to be distinguished. However, this requires knowledge of the hydrogen column density, which is not directly measureable, and predicted line intensity profiles from radiative transfer modelling are similar for these molecules. Other commonly observed species, such as HCN and CH3OH, have line intensity profiles that differ more strongly between models, and so are more promising as tracers of the mechanism of cloud collapse.
UCLCHEM has recently been used to study nitrogen fractionation in external galaxies. You can find the paper here and the abstract below.
In star-forming regions in our own Galaxy, the 14N/15N ratio is found to vary from ∼100 in meteorites, comets, and protoplanetary discs up to ∼1000 in pre-stellar and star-forming cores, while in external galaxies the very few single-dish large-scale measurements of this ratio lead to values of 100-450. The extent of the contribution of isotopic fractionation to these variations is, to date, unknown. In this paper, we present a theoretical chemical study of nitrogen fractionation in external galaxies in order to determine the physical conditions that may lead to a spread of the 14N/15N ratio from the solar value of ∼440 and hence evaluate the contribution of chemical reactions in the interstellar medium (ISM) to nitrogen fractionation. We find that the main cause of ISM enrichment of nitrogen fractionation is high gas densities, aided by high fluxes of cosmic rays.
Felix Priestley has used UCLCHEM to study the collapse of prestellar cores. In the process, he's created a new physics module collapse.f90 which follows a sphere of gas collapsing in different ways. The paper can be found here and the abstract is below.
Peptide bonds (N-C = O) play a key role in metabolic processes since they link amino acids into peptide chains or proteins. Recently, several molecules containing peptide-like bonds have been detected across multiple environments in the interstellar medium, growing the need to fully understand their chemistry and their role in forming larger pre-biotic molecules. We present a comprehensive study of the chemistry of three molecules containing peptide-like bonds: HNCO, NH2CHO, and CH3NCO. We also included other CHNO isomers (HCNO, HOCN) and C2H3NO isomers (CH3OCN, CH3CNO) to the study. We have used the UCLCHEM gas-grain chemical code and included in our chemical network all possible formation/destruction pathways of these peptide-like molecules recently investigated either by theoretical calculations or in laboratory experiments. Our predictions are compared to observations obtained towards the proto-star IRAS 16293-2422 and the L1544 pre-stellar core. Our results show that some key reactions involving the CHNO and C2H3NO isomers need to be modified to match the observations. Consistently with recent laboratory findings, hydrogenation is unlikely to produce NH2CHO on grain surfaces, while a combination of radical-radical surface reactions and gas-phase reactions is a better alternative. In addition, better results are obtained for NH2CHO when a slightly higher activation energy of 25 K is considered for the gas-phase reaction NH2 + H2CO → NH2CHO + H. Finally, our modelling shows that the observed correlation between NH2CHO and HNCO in star-forming regions may come from the fact that HNCO and NH2CHO react to temperature in the same manner rather than from a direct chemical link between the two species.
