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All sourcesNASA NTRSDOE OSTI
NASA NTRS1988

The volatile composition of comets

Comets may be our best probes of the physical and chemical conditions in the outer regions of the solar nebula during that crucial period when the planets formed. The volatile composition of cometary nuclei can be used to decide whether comets are the product of a condensation sequence similar to that invoked to explain the compositions of the planets and asteroids, or if comets are simply agglomerations of interstellar grains which have been insignificantly modified by the events that shaped the other bodies in the solar system. Although cometary nuclei are not generally accessible to observation, observations of cometary comae can illuminate at least some of the mysteries of the nuclei provided one has a detailed knowledge of the excitation conditions in the coma and also has access to basic atomic and molecular data on the many species present in comets. Examined here is the status of our knowledge of the volatile composition of cometary nuclei and how these data are obtained.

Weaver, H. A.↗
NASA NTRS1991

Distances to diffuse interstellar clouds from IRAS measurements and observations of optical absorption lines

Distances to diffuse interstellar clouds were determined from the amount of ultraviolet radiation that penetrates into the cloud and that arises from a nearby B star. The environment around 67 Ophiuchi, 20 Aquilae, kappa Aquilae, and 9 Cephei were studied. The intensities at 60 and 100 micron, as measured by IRAS, were used to derive dust temperatures for the clouds. Enhanced dust temperatures would indicate an influence of the star's radiation field on a cloud. Observation of molecular absorption were compared to the results of simplified chemical models in order to search for enhanced photodissociation that is caused by the star. Enhanced dust temperatures were observed for clouds in the vicinities of 20 Aql, kappa Agl, and 9 Cep. The range of the star's influence was found to be typically 1-5 pc. On the other hand, chemical analyses of the molecular data, which pertain to foreground gas, did not reveal the presence of enhanced dissociative flux from the sample of stars. Thus, upper limits were derived for the distances from the sun to the foreground material.

Federman, S. R.↗
NASA NTRS1992

Densities and vibrational distribution of H(3+) in the Jovian auroral ionosphere

The assumption that H(3+) is in LTE in the region of the Jovian ionosphere from which the emissions originate is tested by calculating the vibrational distribution of H(3+) over the altitude range of 350 to 1500 km above the methane cloud tops. A model of the Jovian auroral ionosphere is constructed in which the neutral temperatures are enhanced over those of the midlatitude ionosphere, as suggested by observations and models of the auroral region. The energy and energy flux were found to be less than those involved in the production of the UV aurora. A computation of the densities and vibrational distribution shows that the distribution of the six lowest states of H(3+) can be determined fairly well in spite of uncertainties in the atomic and molecular data. The computed altitude profiles and vibrational distributions of H(3+) and H2 are consistent with the observations of IR emission in the 2- and 4-micron regions.

Kim, Y. H.↗
NASA NTRS2007

Methylhopane Biomarker and Carbon Isotopic Evidence for Late Archean Aerobic Ecosystems

Molecular fossils are particularly valuable in early Earth studies because they provide information about microbial sources and ecology. Here we report on the distribution of 2- methyl and 3-methylhopanes preserved in a 2.72-2.56 billion-year-old section of shallow and deepwater sediments of the Hamersley Province [Eigenbrode et aI., submitted]. These biomarkers are mostly from cyanobacteria and oxygen-respiring methanotrophs, respectively. The relative abundance of 2-methylhopanes increases with carbonate abundance in shallow-water facies indicating cyanobacteria were key microbes in shallow ecosystems and suggesting they supplied both molecular oxygen and fixed carbon. The relative abundance of 3-methylhopane strongly correlates with kerogen-carbon isotopic values, and is more abundant in the samples with 13C-enriched signatures. Thus, molecular data provides evidence for cycling of methane in shallow settings, even though the anoxic deeper environments bear stronger 13C-depletion, which together suggests a more complex methane cycle than previously envisioned. Detailed facies analysis of the Hamersley carbon-isotope record reveals temporal changes suggesting continued oxidation of shallow settings favoring the expansion of aerobic ecosystems and respiring organisms [Eigenbrode et aI., 2006, PNAS, 103: 15759]. Similar analysis of published carbon-isotopic records suggests similar, but diachronous, expansion of oxygenated habitats in shallow then deep waters as anaerobic microbial communities gave way to respiring communities fueled by oxygenic photosynthesis before the post 2.45-Ga atmospheric oxygenation event [Eigenbrode et aI., 2006]. The robust relationships observed provide geochemical support for methanogenesis, aerobic methanotrophy, and oxygenic photosynthesis in the late Archean, as well as major ecological shifts linked to biogeochemical reorganization.

Eigenbrode, Jennifer L.↗
NASA NTRS2018

Interstellar Ices and Radiation-Induced Oxidations of Alcohols

Infrared spectra of ices containing alcohols that are known or potential interstellar molecules are examined before and after irradiation with 1 MeV protons at ~20 K. The low-temperature oxidation (hydrogen loss) of six alcohols is followed, and conclusions are drawn based on the results. The formation of reaction products is discussed in terms of the literature on the radiation chemistry of alcohols and a systematic variation in their structures. The results from these new laboratory measurements are then applied to a recent study of propargyl alcohol. Connections are drawn between known interstellar molecules, and several new reaction products in interstellar ices are predicted.

astrochemistry – infrared: ISM – ISM: molecules – ↗
NASA NTRSDate not supplied

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning (ML) methods hold the promise to improve our ability to identify important signals within highly dimensional molecular data. However, the inherent limitation of study subject numbers within a spaceflight mission minimizes the utility of ML approaches. To overcome the sample power limitations, data from multiple spaceflight missions must be aggregated while appropriately addressing intra- and inter-study variabilities. Here we describe an approach to log transform, scale and normalize data from six heterogeneous, mouse liver derived transcriptomics datasets (ntotal=137) which enabled ML-methods to perform well (AUC ≥ 0.87) in classifying spaceflown vs ground control animals rather than mission-of-origin. Concordance was found between liver-specific biological processes identified from harmonized ML-based analysis and study-by-study classical omics analysis. This work demonstrates the feasibility of applying ML methods on integrated, heterogeneous datasets of small sample size.

Machine Learning↗
DOE OSTI2021

Data Science in Chemical Engineering: Applications to Molecular Science

Chemical engineering is being rapidly transformed by the tools of data science. On the horizon, artificial intelligence (AI) applications will impact a huge swath of our work, ranging from the discovery and design of new molecules to operations and manufacturing and many areas in between. Early adoption of data science, machine learning, and early examples of AI in chemical engineering has been rich with examples of molecular data science—the application tools for molecular discovery and property optimization at the atomic scale. Here, we summarize key advances in this nascent subfield while introducing molecular data science for a broad chemical engineering readership. We introduce the field through the concept of a molecular data science life cycle and discuss relevant aspects of five distinct phases of this process: creation of curated data sets, molecular representations, data-driven property prediction, generation of new molecules, and feasibility and synthesizability considerations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1977

Distribution of molecular weight in glyceride polymerizates or aggregates of them after contact with lunar grains

An attempt is made to report on experiments in which a molecular-weight increase was determined in thin layers of triglyceride-containing glycerides after thin-layer contact for two years with lunar topsoil grains at 25 C without any thermal activation. It is noted that solidification was observed on both dielectric grains and metal-rich areas and that changes in viscosity and molecular weights were first detected by solidification of surface layers. Gel permeation chromatography is described which detected a general shift of the Gaussian distribution of the molecular-weight data toward generally higher molecular weights as well as an increase in mean molecular weight. Reaction mechanisms are considered, and results of spectrographic analysis are cited which support the interpretations of the molecular-weight data.

Asunmaa, S. K.↗
DOE OSTI2021

Towards high data-rate diffusive molecular communications: A review on performance enhancement strategies

Diffusive molecular communications (DiMC) have recently gained attention as a candidate for nano- to micro- and macro-scale communications due to its simplicity and energy efficiency. As signal propagation is solely enabled by Brownian motion mechanics, DiMC faces severe inter-symbol interference (ISI), which limits reliable and high data-rate communications. Herein, recent literature on DiMC performance enhancement strategies is surveyed; key research directions are identified. Signaling design and associated design constraints are presented. Here, studies on fundamental information theoretic limits of DiMC channel are reviewed. Classical and novel transceiver designs are discussed with an emphasis on methods for ISI mitigation and performance-complexity tradeoffs. Key parameter estimation strategies such as synchronization and channel estimation are considered in conjunction with asynchronous and timing error robust receiver methods. Finally, source and channel coding in the context of DiMC is presented.

42 ENGINEERING↗
NASA NTRS1975

Interdisciplinary study of atmospheric processes and constituents of the mid-Atlantic coastal region. Attachment 4: Data set for background investigation of atmospheric constituents for Nansemond River site

Background data was provided for the assessment of the environmental impact of a proposed oil refinery location. Climatic background, particulate data, digitized portrayal of site molecular and meteorological data, graphical portrayal of molecular data, hourly meteorological data, and streamflow charts and radiosonde data are given

Kindle, E. C.↗
DOE OSTI2021

New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna , while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya , was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya , still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

Ma, Mingzhen↗
NASA NTRS1975

Interdisciplinary study of atmospheric processes and constituents of the mid-Atlantic coastal region. Attachment 5: Data set for background investigation of atmospheric constituents for Richmond, Virginia area

Background data is provided for the photochemical oxident problem in the Richmond area. Particulate data, digitized portrayal of site molecular and meteorological data, and graphical portrayal of molecular data, hourly meteorological data, and streamflow charts and radiosonde data are also given.

Kindle, E. C.↗
NASA NTRS2008

Utilizing Ion-Mobility Data to Estimate Molecular Masses

A method is being developed for utilizing readings of an ion-mobility spectrometer (IMS) to estimate molecular masses of ions that have passed through the spectrometer. The method involves the use of (1) some feature-based descriptors of structures of molecules of interest and (2) reduced ion mobilities calculated from IMS readings as inputs to (3) a neural network. This development is part of a larger effort to enable the use of IMSs as relatively inexpensive, robust, lightweight instruments to identify, via molecular masses, individual compounds or groups of compounds (especially organic compounds) that may be present in specific environments or samples. Potential applications include detection of organic molecules as signs of life on remote planets, modeling and detection of biochemicals of interest in the pharmaceutical and agricultural industries, and detection of chemical and biological hazards in industrial, homeland-security, and industrial settings.

Duong, Tuan↗
NASA NTRS1977

A survey of interstellar molecular hydrogen. I

Data from the Copernicus satellite's ultraviolet telescope were used to survey column densities of atomic and molecular hydrogen from a large sample of early-type stars; these data have bearing on an eventual understanding of diffuse and dense interstellar clouds. Column densities are derived by fitting damping profiles to the observed spectra, most of which exhibit strong damping lines in the lower rotational levels surveyed. Plots of dust column density, fractional abundance of molecular hydrogen, and the logarithm of fractional abundance versus total gas column density are given for many of the stars; stars with abnormally large or small hydrogen column densities, as well as some distant stars at high galactic latitudes, are considered. Equilibrium and nonequilibrium theories accounting for the abundance of interstellar hydrogen are compared, and support is found in the data for an account which balances hydrogen formation on interstellar grains with destruction through photodissociation. Overall averages for atomic and molecular hydrogen levels in the galactic plane are also calculated.

Savage, B. D.↗
DOE OSTI2025

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Midlik, Adam [European Bioinformatics Institute (U↗
DOE OSTI2025

Data from "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions"

Data and input files related to the paper "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions" (https://doi.org/10.1116/6.0004027). This includes the final DP model used in all simulations, training data set, example input files to run DeepMD (with LAMMPS), and data tables summarizing the results obtained from the simulations.

machine learning models↗
NASA NTRS1991

An engineering assessment of gas/surface interactions in free-molecular aerodynamics

Data available on the gas/surface interaction (GSI) phenomenon, particularly in the rarefied to near-free-molecular flow regime are collected, categorized, and analyzed with a purpose of developing a GSI model that could be used as a guide to spacecraft designers. The study shows that there are not enough useful data for building a high-confidence GSI model. However, sufficient results are obtained to suggest that continued reliance on the diffuse GSI model is inappropriate, particularly in the near-free-molecular regime.

Knox, E. C.↗