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NASA NTRS1995

FTP-Server for exchange, interpretation, and database-search of ion mobility spectra, literature, preprints and software

To assist current discussion in the field of ion mobility spectrometry, at the Institut fur Spectrochemie und angewandte Spektroskopie, Dortmund, start with 4th of December, 1994 work of an FTP-Server, available for all research groups at univerisities, institutes and research worker in industry. We support the exchange, interpretation, and database-search of ion mobility spectra through data format JCAMP-DS (Joint Committee on Atomic and Molecular Physical Data) as well as literature retrieval, pre-print, notice, and discussion board. We describe in general lines the entrance conditions, local addresses, and main code words. For further details, a monthly news report will be prepared for all common users. Internet email address for subscribing is included in document.

Baumbach, J. I.↗

NASA NTRS2000

The Evolution of Sulfide Tolerance in the Cyanobacteria

Understanding how the function of extant microorganisms has recorded both their evolutionary histories and their past interactions with the environment is a stated goal of astrobiology. We are taking a multidisciplinary approach to investigate the diversification of sulfide tolerance mechanisms in the cyanobacteria, which vary both in their degree of exposure to sulfide and in their capacity to tolerate this inhibitor of photosynthetic electron transport. Since conditions were very reducing during the first part of Earth's history and detrital sulfides have been found in Archean sediments, mechanisms conferring sulfide tolerance may have been important for the evolutionary success of the ancestors of extant cyanobacteria. Two tolerance mechanisms have been identified in this group: (1) resistance of photosystem II, the principal target of sulfide toxicity; and (2) maintenance of the ability to fix carbon despite photosystem II inhibition by utilizing sulfide as an electron donor in photosystem I - dependent, anoxygenic photosynthesis. We are presently collecting comparative data on aspects of sulfide physiology for laboratory clones isolated from a variety of habitats. These data will be analyzed within a phylogenetic framework inferred from molecular sequence data collected for these clones to test how frequently different mechanisms of tolerance have evolved and which tolerance mechanism evolved first. In addition, by analyzing these physiological data together with environmental sulfide data collected from our research sites using microelectrodes, we can also test whether the breadth of an organism's sulfide tolerance can be predicted from the magnitude of variation in environmental sulfide concentration it has experienced in its recent evolutionary past and whether greater average sulfide concentration and/or temporal variability in sulfide favors the evolution of a particular mechanism of sulfide tolerance.

Miller, Scott R.↗

NASA NTRS1988

Molecular and particulate contaminants - A contamination data base within ENVIRONET

The Space Transportation System contamination environment appears in the ENVIRONET data base in two parallel chapters, Molecular Contamination and Particulate Environment. The design objectives and a description of the content of this contamination data base are presented. A treatment of the use of the data base is intended to interest the reader in accessing and browsing these chapters. Future plans are discussed briefly, with the emphasis on the approach to providing a dynamic data base.

Barengoltz, Jack↗

NASA NTRS2006

Data Needs for Stellar Atmosphere and Spectrum Modeling

The main data need for stellar atmosphere and spectrum modeling remains atomic and molecular transition data, particularly energy levels and transition cross-sections. We emphasize that data is needed for bound-free (b - f) as well as bound-bound (b - b), and collisional as well as radiative transitions. Data is now needed for polyatomic molecules as well as atoms, ions, and diatomic molecules. In addition, data for the formation of, and extinction due to, liquid and solid phase dust grains is needed. A prioritization of species and data types is presented, and gives emphasis to Fe group elements, and elements important for the investigation of nucleosynthesis and Galactic chemical evolution, such as the -elements and n-capture elements. Special data needs for topical problems in the modeling of cool stars and brown dwarfs are described.

Short, C. I.↗

NASA NTRS1991

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts

A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

NASA Discipline Exobiology↗

NASA NTRS1982

Thermal Structure of Jupiter and Saturn

Temperatures in the sensible regions of the atmospheres of the outer planets are quite cold. The temperature structures for Jupiter, Saturn, Uranus and Neptune, derived from the equilibrium models are presented in preparation. The vertical temperature profiles for Jupiter and Saturn, the molecular spectroscopic data which form the basis for this type of analysis, and the problems involved with these models for molecular absorption and with the recovery technique in general, are discussed. Results for Jupiter and Saturn from the Pioneer and Voyager infrared experiments are also presented.

Orton, G.↗

NASA NTRS2004

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.

Evolution, Molecular↗

NASA NTRS2001

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

For several decades the NASA Glenn Research Center has been providing a file of thermodynamic data for use in several computer programs. These data are in the form of least-squares coefficients that have been calculated from tabular thermodynamic data by means of the NASA Properties and Coefficients (PAC) program. The source thermodynamic data are obtained from the literature or from standard compilations. Most gas-phase thermodynamic functions are calculated by the authors from molecular constant data using ideal gas partition functions. The Coefficients and Properties (CAP) program described in this report permits the generation of tabulated thermodynamic functions from the NASA least-squares coefficients. CAP provides considerable flexibility in the output format, the number of temperatures to be tabulated, and the energy units of the calculated properties. This report provides a detailed description of input preparation, examples of input and output for several species, and a listing of all species in the current NASA Glenn thermodynamic data file.

Zehe, Michael J.↗

NASA NTRS2002

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

Zehe, Michael J.↗

NASA NTRS1990

An IRAS survey of the Taurus-Auriga molecular cloud

IRAS data are used to search for young premain-sequence stars not previously associated with molecular cloud cores in the Taurus-Auriga region. NIR photometry and optical spectroscopy suggest that many of the objects are young stars. The sample includes six new embedded sources with luminosities comparable to that of the average T Tauri star, suggesting that surveys for premain-sequence stars in the cloud are essentially complete for luminosities greater than 0.5 solar luminosities. A disagreement is found between accretion rates derived from the duration of the embedded phase and those derived from the bolometric luminosity. It is found that this disagreement may be reconciled if a star accretes most of its mass in a time that is short compared to the duration of the embedded phase or if the ages of T Tauri stars have been underestimated.

Kenyon, Scott J.↗

NASA NTRS1966

On the formation of graphite grains in cool stars

Graphite grain formation in cool stars examined on basis of molecular equilibrium data for stellar atmospheres

CRYSTAL GROWTH↗

NASA NTRSDate not supplied

Fracture Prediction of Epoxy Resin using Morse Bond Potential Embedded in GAFF using Molecular Dynamics Simulations

A generic method is developed to investigate the fracture behavior of an epoxy resin using atomistic molecular (MD) dynamics simulations. The epoxy system consisted of the stoichiometric mixture of tetra-/tri-functional epoxies and di-functional hardener molecules and was cured with a step-growth crosslinking algorithm. A hybrid force field (hFF) in which Morse bond function were added in second generation-general Amber Force Field (GAFF2) was used to capture bond breaking of the crosslinked epoxy system under uniaxial deformation. The Morse bond parameters for covalent bonds in the crosslinked backbone were fit to dissociation curves computed by CASPT2/6-311+G**. After the systems in various crosslink densities were obtained and equilibrated, the full length of stress-strain (𝜎-𝜀) curve was produced including initial elastic regime, yielding, plastic flow, strain hardening, and progressive failure. We found that the hFF was effective in studying the dissociation of crosslinked polymers and understanding the failure mechanism. In the results, the hFF delivered the same elastic property obtained from the unmodified force field GAFF. The stress-strain curve, however, began to be distinct in the plastic regime due to broken covalent bonds capable of altering the tensile behavior. Once the stress reached maximum, it progressively decreased until the ultimate failure (𝜎=0). Since hFF employed the existing GAFF functions with including a minimal change of its bond potential, this approach is easier to perform and computationally more efficient for unveiling the fracture behavior of polymer materials at the molecular level than other approaches with reactive force fields. We expect this approach will be utilized to accelerate the material-by-design process for thermosets by incorporate data from molecular models.

Changwoon Jang↗

NASA NTRS1995

Exchange, interpretation, and database-search of ion mobility spectra supported by data format JCAMP-DX

To assist peak assignment in ion mobility spectrometry it is important to have quality reference data. The reference collection should be stored in a database system which is capable of being searched using spectral or substance information. We propose to build such a database customized for ion mobility spectra. To start off with it is important to quickly reach a critical mass of data in the collection. We wish to obtain as many spectra combined with their IMS parameters as possible. Spectra suppliers will be rewarded for their participation with access to the database. To make the data exchange between users and system administration possible, it is important to define a file format specially made for the requirements of ion mobility spectra. The format should be computer readable and flexible enough for extensive comments to be included. In this document we propose a data exchange format, and we would like you to give comments on it. For the international data exchange it is important, to have a standard data exchange format. We propose to base the definition of this format on the JCAMP-DX protocol, which was developed for the exchange of infrared spectra. This standard made by the Joint Committee on Atomic and Molecular Physical Data is of a flexible design. The aim of this paper is to adopt JCAMP-DX to the special requirements of ion mobility spectra.

Baumback, J. I.↗

NASA NTRS2024

Multiscale Modeling of Thermoplastics Using Atomistic-informed Micromechanics

A multiscale repeating unit cell model of a single spherulite containing four disparate length scales was developed to predict the thermoelastic behavior of semicrystalline thermoplastic materials for composite aerospace applications. The continuum level scales were fully coupled and modeled using the generalized method of cells and the high fidelity generalized method of cells micromechanics theories. Data from molecular dynamics simulations were used as inputs for the amorphous and crystalline constituents in the multiscale continuum models. Effective Young’s modulus, shear modulus, Poisson’s ratio, coefficient of thermal expansion, and thermal conductivity were predicted for polyether ether ketone and polyether ketone ketone, showing good agreement with the available experimental data from the open literature. Moreover, it is shown that predicted properties are fairly insensitive to the fidelity of the micromechanics model used at the highest continuum scale or the assumed shape of the spherulite.

thermoplastics↗

NASA NTRS1994

Far Outer Galaxy H II Regions

We have made a multifrequency (6, 3.6, and 2 cm), high-resolution (3"-6"), radio continuum survey of IRAS selected sources from the catalogue of Wouterloot & Brand (1989) to search for and study H II regions in the far outer Galaxy. We identified 31 sources in this catalog with well determined galactocentric distances, and with R approx.. greater than 15 kpc and L(sub FIR) approx.greater than 10(exp 4) solar luminosity, indicating the presence of high-mass star-formation. We have observed 11 of these sources with the Very Large Array (VLA). We observed the sources at 6 and 2 cm using "scaled arrays", making possible a direct and reliable comparison of the data at these two wavelengths for the determination of spectral indices. We detected a total of 12 radio sources, of which 10 have spectral indices consistent with optically-thin free-free emission from H II regions. Combined with previous VLA observations by other investigators, we have data on a total of 15 H II regions at galactocentric distances of 15 to 18.2kpc, among the most remote H II regions found in our Galaxy. The sizes of the H II regions range from approx. less than 0.10 to 2.3 pc. Using the measured fluxes and sizes, we determine the electron densities, emission measures, and excitation parameters of the H II regions, as well as the fluxes of Lyman continuum photons needed to keep the nebulae ionized. The sizes and electron densities are consistent with most of the sources detected in this survey being compact or ultracompact H II regions. Seven of the fifteen H II regions have sizes approx. less than 0.20 pc. Assuming simple pressure-driven expansion of the H II regions, these sizes indicate ages approx. less than 5 x 10(exp 4) yr, or only 1% of the lifetime of an O star, which implies an unlikely overabundance of O stars in the outer Galaxy. Thus, the large number of compact H II regions suggests that the time these regions spend in a compact phase must be much longer than their dynamical expansion times. Five of the fifteen H II regions have cometary shapes; the remainder are spherical or unresolved. Comparison of the radio continuum data with molecular line maps suggests that the cometary shape of the two H II regions in S 127 may be due to pressure confinement of the expanding ionized gas, as in the "blister" or "champagne flow" models of H II regions. Comparison of the radio continuum data with the IRAS far-infrared data indicates that the five most luminous H II regions are consistent with a single 0 or B star exciting a dust-free H II region. Subject headings: stars: formation - ISM: H II regions - ISM: individual objects: S 127 radio continuum: interstellar

Rudolph, A. L.↗

NASA NTRS2001

The molecular responses of skeletal muscle satellite cells to continuous expression of IGF-1: implications for the rescue of induced muscular atrophy in aged rats

Approximately 50% of humans older than 85 years have physical frailty due to weak skeletal muscles. This indicates a need for determining mechanisms to combat this problem. A critical cellular factor for postnatal muscle growth is a population of myogenic precursor cells called satellite cells. Given the complex process of sarcopenia, it has been postulated that, at some point in this process, a limited satellite cell proliferation potential could become rate-limiting to the regrowth of old muscles. It is conceivable that if satellite cell proliferative capacity can be maintained or enhanced with advanced age, sarcopenia could potentially be delayed or prevented. Therefore, the purposes of this paper are to describe whether IGF-I can prevent muscular atrophy induced by repeated cycles of hindlimb immobilization, increase the in vitro proliferation in satellite cells from these muscles and, if so, the molecular mechanisms by which IGF-I mediates this increased proliferation. Our results provide evidence that IGF-I can enhance aged muscle regrowth possibly through increased satellite cell proliferation. The results also suggest that IGF-I enhances satellite cell proliferation by decreasing the cell cycle inhibitor, p27Kip1, through the PI3'-K/Akt pathway. These data provide molecular evidence for IGF-I's rescue effect upon aging-associated skeletal muscle atrophy.

NASA Discipline Musculoskeletal↗

NASA NTRS2022

Physical and Chemical Conditions in the N113 Star-Forming Region in the Low-Metallicity Large Magellanic Cloud

The Large Magellanic Cloud (LMC) is the nearest (~50 kpc) star-forming galaxy characterized by a low metallicity (Z~0.3-0.5 Z⨀) similar to galaxies during the early phases of their assembly. As a result, star formation studies in the LMC provide a stepping stone to understanding star formation at earlier epochs of the universe where these processes cannot be directly observed. N113 is one of the most prominent star-forming regions in the LMC hosting one of the most massive giant molecular clouds.N113 is small enough to be imaged in its entirety, but large enough to showcase many important phenomena such as multiple generations of stars, stellar feedback, and different environments. We present our findings from an investigation of the early stages of star formation in the N113 region using the Atacama Large Millimeter/submillimeter Array (ALMA)molecular line data probing a wide density range: 12CO, 13CO, and C18O (2-1), 13COand C18O (1-0), HCN (1-0), HCO+ (1-0), H13CN (1-0) and (3-2), H13CO+ (1-0) and (3-2), CS (2-1) and (5-4), as well as 1.3 mm and 3 mm continuum. We used the Python package quick clump to identify molecular clumps. We utilized the multiline non-LTE fitting tool based on models from RADEX developed by Finn et al. (2021, ApJ, 917, 106)to construct the CO, HCN, HCO+, and CS temperature and column density, and the H2density maps of N113. We constructed a catalog of molecular clumps including their physical properties, chemical abundances, sizes, velocities, and velocity dispersions. To establish the evolutionary status of the clumps, their positions were compared with previously identified young stellar objects (YSOs) from the Spitzer/SAGE and Herschel/HERITAGE surveys, as well as water and OH masers. We compared the properties of the clumps in N113 to those in the Galaxy and other regions in the LMC to assess the impact of the environment (e.g., metallicity, stellar feedback) on the star formation process.

Jonathon Noswitz↗

NASA NTRS2023

The First Extragalactic Detection of Higher-Order Hydrogen Recombination Lines

The Large Magellanic Cloud (LMC) is the nearest (~50 kpc) star-forming galaxy characterized by a low metallicity (Z~0.3-0.5 Z⨀) similar to galaxies during the early phases of their assembly. As a result, star formation studies in the LMC provide a stepping stone to understanding star formation at earlier epochs of the universe where these processes cannot be directly observed. N113 is one of the most prominent star-forming regions in the LMC hosting one of the most massive giant molecular clouds. N113 is small enough to be imaged in its entirety, but large enough to showcase many important phenomena such as multiple generations of stars, stellar feedback, and different environments. We present our findings from an investigation of the early stages of star formation in the N113 region using the Atacama Large Millimeter/submillimeter Array (ALMA) molecular line data probing a wide density range: 12CO, 13CO, and C18O (2-1), 13CO and C18O (1-0), HCN (1-0), HCO+ (1-0), H13CN (1-0) and (3-2), H13CO+ (1-0) and (3-2), CS (2-1) and (5-4), as well as 1.3 mm and 3 mm continuum. We used the Python package quickclump to identify molecular clumps. We utilized the multiline non-LTE fitting tool based on models from RADEX developed by Finn et al. (2021, ApJ, 917, 106) to construct the CO, HCN, HCO+, and CS temperature and column density, and the H2 density maps of N113. We constructed a catalog of molecular clumps including their physical properties, chemical abundances, sizes, velocities, and velocity dispersions. To establish the evolutionary status of the clumps, their positions were compared with previously identified young stellar objects (YSOs) from the Spitzer/SAGE and Herschel/HERITAGE surveys, as well as water and OH masers. We compared the properties of the clumps in N113 to those in the Galaxy and other regions in the LMC to assess the impact of the environment (e.g., metallicity, stellar feedback) on the star formation process.

Marta M Sewilo↗