Fitting infrared ice spectra with genetic modelling algorithms

Rocha, W. R. M.; Perotti, G.; Kristensen, L. E.; Jørgensen, J. K.

doi:10.1051/0004-6361/202039360

Cited by 12 publications

(13 citation statements)

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“…Many different COMs have been identified in the gas phase through radio and submillimeter surveys (e.g., Blake et al 1987;Jørgensen et al 2012;McGuire et al 2016;Belloche et al 2020;van Gelder et al 2020;McGuire 2021;Jørgensen et al 2020;Nazari et al 2021;Rivilla et al 2021;Brunken et al 2022), but astronomical observations have not been able to unambiguously identify frozen COMs larger than CH 3 OH due to low spectral resolution or sensitivity. Nevertheless, tentative detections of CH 3 CHO (acetaldehyde) and CH 3 CH 2 OH (ethanol) ice have been reported in the literature (Schutte et al 1999;Öberg et al 2011;Terwisscha van Scheltinga et al 2018;Rocha & Pilling 2015;Rocha et al 2021). Consistently with these tentative detections, several laboratory experiments have shown that such molecules can be formed in ices.…”

Section: Introductionmentioning

confidence: 55%

“…It should be noted that such synthetic spectra allow the reproduction of observed data but do not necessarily provide a unique solution. Other public codes, such as the ENIIGMA fitting tool (Rocha et al 2021) have the goal of quantifying the degeneracy of those fits when a large dataset of inputs is taken into account.…”

Section: Synthetic Spectramentioning

confidence: 99%

“…IR spectroscopy is also the technique widely used to detect solid-phase molecules in the interstellar medium (ISM; e.g., Gillett & Forrest 1973;Schutte et al 1996;Pontoppidan et al 2003;Gibb et al 2004;Boogert et al 2008;Zasowski et al 2009;Bottinelli et al 2010;Boogert et al 2013;Penteado et al 2015;Perotti et al 2020;Rocha et al 2021;Onaka et al 2021). The light of a protostar, edge-on disk, or background star passes through the circumstellar material, and absorption features in the IR are seen in the protostellar spectral energy distribution (SED).…”

Section: Introductionmentioning

confidence: 99%

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LIDA: The Leiden Ice Database for Astrochemistry

Rocha

Rachid

Olsthoorn

et al. 2022

A&A

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Context. High-quality vibrational spectra of solid-phase molecules in ice mixtures and for temperatures of astrophysical relevance are needed to interpret infrared observations toward protostars and background stars. Such data are collected worldwide by several laboratory groups in support of existing and upcoming astronomical observations. Over the last 25 years, the Laboratory for Astrophysics at Leiden Observatory has provided more than 1100 (high-resolution) spectra of diverse ice samples. Aims. In time with the recent launch of the James Webb Space Telescope, we have fully upgraded the Leiden Ice Database for Astrochemistry (LIDA) adding recently measured spectra. The goal of this paper is to describe what options exist regarding accessing and working with a large collection of infrared (IR) spectra, and the ultraviolet-visible (UV/vis) to the mid-infrared refractive index of H 2 O ice. This also includes astronomy-oriented online tools to support the interpretation of IR ice observations. Methods. This ice database is based on open-source Python software, such as Flask and Bokeh, used to generate the web pages and graph visualization, respectively. Structured Query Language (SQL) is used for searching ice analogs within the database and Jmol allows for three-dimensional molecule visualization. The database provides the vibrational modes of molecules known and expected to exist as ice in space. These modes are characterized using density functional theory with the ORCA software. The IR data in the database are recorded via transmission spectroscopy of ice films condensed on cryogenic substrates. The real UV/vis refractive indices of H 2 O ice are derived from interference fringes created from the simultaneous use of a monochromatic HeNe laser beam and a broadband Xe-arc lamp, whereas the real and imaginary mid-IR values are theoretically calculated. LIDA not only provides information on fundamental ice properties, but it also offers online tools. The first tool, SPECFY, is directly linked to the data in the database to create a synthetic spectrum of ices towards protostars. The second tool allows the uploading of external files and the calculation of mid-infrared refractive index values.Results. LIDA provides an open-access and user-friendly platform to search, download, and visualize experimental data of astrophysically relevant molecules in the solid phase. It also provides the means to support astronomical observations; in particular, those that will be obtained with the James Webb Space Telescope. As an example, we analysed the Infrared Space Observatory spectrum of the protostar AFGL 989 using the resources available in LIDA and derived the column densities of H 2 O, CO and CO 2 ices.

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Section: Introductionmentioning

confidence: 55%

Section: Synthetic Spectramentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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LIDA: The Leiden Ice Database for Astrochemistry

Rocha

Rachid

Olsthoorn

et al. 2022

A&A

Self Cite

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“…ENIIGMA global fitting and local fits: We used the ENIIGMA fitting tool 49,50 to simultaneously fit multiple features across the NIRSpec and MIRI/LRS range by scaling laboratory ice spectra to match the optical depths in Figure 1. A full list with data used in this paper is shown in Table 3.…”

Section: Data Qualitymentioning

confidence: 99%

“…The ENIIGMA global fitting tool 49 is publicly available on GitHub at the following URL: https://github.com/willastro/EN fitting-tool…”

Section: Data Availabilitymentioning

confidence: 99%

An Ice Age JWST inventory of dense molecular cloud ices

McClure,

Rocha,

Pontoppidan

et al. 2023

Preprint

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Icy grain mantles are the main reservoir of the volatile elements that link chemical processes in dark, interstellar clouds with the formation of planets and composition of their atmospheres. The initial ice composition is set in the cold, dense parts of molecular clouds, prior to the onset of star formation. With the exquisite sensitivity of JWST, this critical stage of ice evolution is now accessible for detailed study. Here we show the first results of the Early Release Science program "Ice Age" that reveal the rich composition of these dense cloud ices. Weak ices, including, 13 CO 2 , OCN − , 13 CO, OCS, and COMs functional groups are now detected along two pre-stellar lines of sight. The 12 CO 2 ice profile indicates modest growth of the icy grains. Column densities of the major and minor ice species indicate that ices contribute between 2 and 19% of the bulk budgets of the key C, O, N, and S elements. Our results suggest that the formation of simple and complex molecules could begin early in a water-ice rich environment. CH 3 COCH 3 :CO (1:5) CH 3 CH 2 OH CH 3 CHO A V = 60 mag A V = 95 mag CCC s-str. CH 3 s-def. CH 3 s-def. CH 3 s-def. CH 3 a-def. CH 3 a-def.

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Atomic and Molecular Databases Open Science for a sustainable world

Dubernet,

Berriman,

Barklem

et al. 2022

Proc. IAU

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The building of online atomic and molecular databases for astrophysics and for other research fields started with the beginning of the internet. These databases have encompassed different forms: databases of individual research groups exposing their own data, databases providing collected data from the refereed literature, databases providing evaluated compilations, databases providing repositories for individuals to deposit their data, and so on. They were, and are, the replacement for literature compilations with the goal of providing more complete and in particular easily accessible data services to the users communities. Such initiatives involve not only scientific work on the data, but also the characterization of data, which comes with the “standardization” of metadata and of the relations between metadata, as recently developed in different communities. This contribution aims at providing a representative overview of the atomic and molecular databases ecosystem, which is available to the astrophysical community and addresses different issues linked to the use and management of data and databases. The information provided in this paper is related to the keynote lecture “Atomic and Molecular Databases: Open Science for better science and a sustainable world” whose slides can be found at DOI : doi.org/10.5281/zenodo.6979352 on the Zenodo repository connected to the “cb5-labastro” Zenodo Community (https://zenodo.org/communities/cb5-labastro).

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Fitting infrared ice spectra with genetic modelling algorithms

Cited by 12 publications

References 96 publications

LIDA: The Leiden Ice Database for Astrochemistry

LIDA: The Leiden Ice Database for Astrochemistry

An Ice Age JWST inventory of dense molecular cloud ices

Atomic and Molecular Databases Open Science for a sustainable world

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