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At least 145 records · Page 8

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NASA NTRS1976

Infrared observations of ices and silicates in molecular clouds

Spectrophotometric observations from 2 to 4 microns and from 8 to 13 microns of several infrared sources associated with molecular clouds are reported. Narrow absorption features at 3.08 microns, attributed to interstellar ices, appear in all sources with a molecular cloud in the intervening line of sight. All sources showing ice absorptions also show broad absorption features, attributed to cold silicates, from 8 to 13 microns. The observed ice absorption profiles are all quite similar; however, they do not fit in detail Mie theory predictions of extinction for pure H2O or NH3 ices. The ratio of ice-to-silicate optical depths is found to vary, with most sources showing a ratio in the range 0.1-0.4. The ratio of visual extinction to ice absorption is found to increase rapidly from inside to outside the molecular cloud in NGC 2024.

Merrill, K. M.↗

NASA NTRS2005

Real-Time Aerodynamic Flow and Data Visualization in an Interactive Virtual Environment

Significant advances have been made to non-intrusive flow field diagnostics in the past decade. Camera based techniques are now capable of determining physical qualities such as surface deformation, surface pressure and temperature, flow velocities, and molecular species concentration. In each case, extracting the pertinent information from the large volume of acquired data requires powerful and efficient data visualization tools. The additional requirement for real time visualization is fueled by an increased emphasis on minimizing test time in expensive facilities. This paper will address a capability titled LiveView3D, which is the first step in the development phase of an in depth, real time data visualization and analysis tool for use in aerospace testing facilities.

Schwartz, Richard J.↗

DOE OSTI2022

In crystallo observation of three metal ion promoted DNA polymerase misincorporation

Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Ultrafast nano-imaging and nano-spectroscopy

Ultrafast pump–probe nano-imaging combines scanning probe-based optical near-field microscopy with ultrafast spectroscopy to enable imaging with deep sub-wavelength spatial resolution, femtosecond temporal resolution and simultaneous spectral resolution. Ultrafast nano-imaging has gained increased attention for its ability to provide far-from-equilibrium excitation and excited-state contrast. With coherent and nonlinear probing, coupled electron, spin and lattice dynamics on elementary timescale and length scale can be resolved. Through nano-movies, ultrafast nano-imaging visualizes correlated quantum dynamics underlying the properties of solid-state materials, semiconductors, molecular electronic, photonic, photovoltaic and other functional materials. With nanometre spatial resolution, this method probes elementary dynamic processes across multiple length scales that are otherwise obscured in conventional ultrafast spectroscopy in which heterogeneities are spatially averaged. Furthermore, this Primer describes the theoretical background and experimental implementation of ultrafast nano-imaging; signal interpretation and modelling; representative examples and a perspective for the future development of the field.

Microscopy↗

NASA NTRS1981

The extinction toward the galactic center from observations of interstellar lines

H2CO absorption observations against Sgr A are used to select the molecular material lying in front of the galactic center, and an analysis similar to that of Blitz and Shu (1980) is carried out. The ratio of visual extinction to equivalent width of the 6 cm line of H2CO is found to be similar for several nearby interstellar clouds. By considering only the molecular components in front of the infrared cluster, the estimate for the extinction is decreased to 15-46 mag. These results are consistent with those from infrared observations toward the galactic center. Extinction estimates based on other interstellar species are also considered. Atomic gas is seen as contributing less than 10 mag of extinction.

Federman, S. R.↗

NASA NTRS1992

Is a pyrene-like molecular ion the cause of the 4,430-A diffuse interstellar absorption band?

The diffuse interstellar band (DIB) absorption features of astronomical spectra are suggested by recent results to be separable from the grains that cause visual extinction. Attention is presently given to laboratory measurements of the optical spectrum of the pyrene cation C16H10(+), which is one of the polycyclic aromatic hydrocarbon (PAH) molecular candidates proposed as carriers for DIBs. This ion exhibits an intense but strangely broad continuum similar to that of the naphthalene cation, so that this may be a common feature of all PAH cations and the basis of an explanation for PAHs' converting of an interstellar radiation fraction as large as that from the UV and visible range down to the IR.

Salama, F.↗

NASA NTRS1993

Localization of the chaperone binding site

The hypothesis derived from models of the multi-oligomeric chaperone complex suggests that partially denatured proteins bind in a central cavity in the aggregate. To test this hypothesis, the molecular chaperone, alpha crystallin, was bound to partially denatured forms of gamma crystallin, and the binding site was visualized by immunogold localization. In an alternative approach, gold particles were directly complexed with gamma crystallin, followed by binding to the alpha crystallin aggregate. In both cases, binding was localized to the central region of the aggregate, confirming for the first time that partially denatured proteins do indeed bind to a central region of the molecular chaperone aggregate.

Non-NASA Center↗

NASA NTRS1976

Highlights in planetary spectroscopy 1962-75

Recent advances in spectroscopic studies of the planets with ground-based telescopes in the photomultiplier and IR spectral ranges are reviewed. Results of spectroscopic observations of Venus and Mars are briefly summarized, noting that the crucial problem confronting the interpretation of the Venusian spectrum is the nature of the clouds and that the outstanding problem in understanding the Martian atmosphere is the N2 or Ar concentration that may be present. Spectroscopic results for Jupiter, Saturn, Uranus, and Neptune are discussed, emphasizing observations of molecular hydrogen, HD, water, (C-13)H4, other hydrocarbons, and deuterated hydrocarbons. IR and visual spectroscopic observations of Titan and Io are reviewed which show that the CH4 bands in Titan's spectrum are pressure broadened and that a flattened ring of sodium is situated around Jupiter in the orbital plane of Io.

Muench, G.↗

NASA NTRS1987

Ultraluminous infrared galaxies

The IRAS survey of the local universe has revealed the existence of a class of ultraluminous infrared galaxies with L(8 to 1000 micrometer) greater than 10 to the 12th L sub 0 that are slightly more numerous, and as luminous as optically selected quasars at similar redshift. Optical CCD images of these infrared galaxies show that nearly all are advanced mergers. Millimeter wave CO observations indicate that these interacting systems are extremely rich in molecular gas with total H2 masses 1 to 3 x 10 to the 10th power M sub 0. Nearly all of the ultraluminous infrared galaxies show some evidence in their optical spectra for nonthermal nuclear activity. It is proposed that their infrared luminosity is powered by an embedded active nucleus and a nuclear starburst both of which are fueled by the tremendous reservoir of molecular gas. Once these merger nuclei shed their obscuring dust, allowing the AGN to visually dominate the decaying starburst, they become the optically selected quasars.

Sanders, D. B.↗

NASA NTRS1988

Ultraviolet Spectra of Two Magnetic White Dwarfs and Ultraviolet Spectra of Subluminous Objects Found in the Kiso Schmidt Survey and Ultraviolet Absorptions in the Spectra of DA White Dwarfds

Research under NASA Grant NAG5-287 has carried out a number of projects in conjunction with the International Ultraviolet Explorer (IUE) satellite. These include: (1) studies of the UV spectra of DA white dwarfs which show quasi-molecular bands of H2 and H2(+); (2) the peculiar star HR6560; (3) the UV spectra of two magnetic white dwarfs that also show the quasi-molecular features; (4) investigations of the UV spectra of subluminous stars, primarily identified from visual wavelength spectroscopy in the Kiso survey of UV excess stars, some of which show interesting metal lines in their UV spectra; and (5) completion of studies of UV spectra of DB stars. The main result of this research has been to further knowledge of the structure and compositions of subluminous stars which helps cast light on their formation and evolution.

Wegner, Gary A.↗

DOE OSTI2020

Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets

Thousands of chemical properties can be calculated for small molecules, which can be used to place the molecules within the context of a broader “chemical space.” These definitions vary based on compounds of interest and the goals for the given chemical space definition. Here, we introduce a customizable (i.e., modular) Python module, chespa, built to easily assess different chemical space definitions through cluster-ing of compounds in these spaces and visualize trends of these clusters. To demonstrate this, chespa currently streamlines prediction of vari-ous molecule descriptors (predicted chemical properties, molecular substructures, AI-based chemical space, and chemical class ontology) in order to test 6 different chemical space definitions. Furthermore, we investigated how these varying definitions trend with mass spectrometry (MS)-based observability, i.e., the ability of a molecule to be observed with MS (e.g., as a function of the molecule ionizability), using an example data set from the U.S. EPA's Non-Targeted Analysis Collaborative Trial (ENTACT), where blinded samples had been analyzed previously, providing 1,398 data points. Improved understanding of observability would offer many advantages in small molecule identifica-tion, such as (i) a priori selection of experimental conditions based on suspected sample composition, (ii) the ability to reduce the number of candidate structures during compound identification by removing those less likely to ionize, and, in turn, (iii) a reduced false discovery rate and increased confidence in identifications. Factors controlling observability are not fully understood, making prediction of this property non-trivial and a prime candidate for chemical space analysis. Chespa is available at github.com/pnnl/chespa.

Nunez, Jamie↗

NASA NTRS1977

Infrared studies of H II regions and dust clouds near K3-50

Ground-based infrared observations of the K3-50 region are reported at wavelengths between 2 and 34 microns as well as at 1 mm. The main results are that (1) the visible nebular K3-50 is displaced from its infrared and radio counterparts; (2) component Cl (the OH source ON-3) appears very faint at wavelengths not exceeding 20 microns and is therefore probably obscured by several hundred magnitudes of visual extinction; (3) both K3-50 and component C are associated with separate condensations of molecular hydrogen, each of about 3000 solar masses; and (4) there are no strong sources in this region at 20 microns other than those associated with H II condensations.

Wynn-Williams, C. G.↗

NASA NTRS1978

The ratio of carbon monoxide to molecular hydrogen in interstellar dark clouds

LTE (C-13)O column densities are compared with the corresponding values of beam-convolved visual extinction at more than 100 locations within 38 different interstellar dark clouds. A roughly linear correlation is found to exist between these two quantities for visual extinctions in the range from about 1.5 to 5 mag. It is argued that this correlation can be extended up to about 10 mag and that the standard gas-to-extinction ratio can be expected to remain valid in the sources studied. The correlation of LTE (C-13)O column density with visual extinction is used to obtain an equation for the H2 column density associated with a given (C-13)O column density. It is shown that if the clouds studied are assumed to be chemically homogeneous, the equation obtained implies that at least 12% of all gas-phase carbon is in the form of CO. Comparison of the observational data with various theories proposed for molecule formation in dark clouds indicates that Langer's (1977) ion-molecule scheme accounts well for the observations when the fractionation channel of Watson et al. (1976) is included.

Dickman, R. L.↗

DOE OSTI2021

Students authoring molecular case studies as a partial course-based undergraduate research experience (CURE) for lab instruction

Understanding the relationship between protein structure and function is a core-learning goal in biochemistry. Students often struggle to visualize proteins as three-dimensional objects that interact with other molecules to affect its biochemical consequences. We describe here a partial course-based undergraduate research experiences that has students exploring protein structure and function hands-on while authoring a molecular case study intended for others to use.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1996

A Search for Star Formation in the Translucent Cloud MBM 40

The star formation status of the translucent high-latitude molecular cloud, MBM 40, is explored through analysis of radio, infrared, optical, and X-ray data. With a peak visual extinction of 1 to 2 mag, MBM 40 is an example of a high-latitude cloud near the diffuse/translucent demarcation. However, unlike most translucent clouds, MBM 40 exhibits a compact morphology and a kinetic energy-to gravitational potential energy ratio near unity. Our radio data, encompassing the CO (J = 1-0), CS (J = 2-1), and H2CO 1(sub 11-1(sub 10), spectral line transitions, reveal that the cloud contains a ridge of molecular gas with n greater than or equal to 10(exp 3)/ cc. In addition, the molecular data, together with IRAS data, indicate that the mass of MBM 40 is approx. 40 solar mass. In light of the ever-increasing number of recently formed stars far from any dense molecular clouds or cores, we searched the environs of MBM 40 for any trace of recent star formation. We used the ROSAT All-Sky Survey X-ray data and a ROSAT PSPC pointed observation toward MBM 40 to identify 33 stellar candidates with properties consistent with pre-main-sequence (PMS) stars. Follow-up optical spectroscopy of the candidates with V less than 15.5 was conducted with the 1.5 m Fred Lawrence Whipple Observatory telescope in order to identify signatures of T Tauri or pre-main- sequence stars (such as the Li 6708 A resonance line). Since none of our optically observed candidates display standard PMS signatures, we conclude that MBM 40 displays no evidence of recent or ongoing star formation. The absence of high-density molecular cores in the cloud and the relatively low column density compared to star-forming interstellar clouds may be the principal reasons that MBM 40 is devoid of star formation. More detailed comparison between this cloud and other, higher extinction translucent and dark clouds may elucidate the necessary initial conditions for the onset of low-mass star formation.

Magnani, Loris↗

DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

NASA NTRS1990

Visualization of yeast chromosomal DNA

The DNA molecule is the most significant life molecule since it codes the blue print for other structural and functional molecules of all living organisms. Agarose gel electrophoresis is now being widely used to separate DNA of virus, bacteria, and lower eukaryotes. The task was undertaken of reviewing the existing methods of DNA fractionation and microscopic visualization of individual chromosonal DNA molecules by gel electrophoresis as a basis for a proposed study to investigate the feasibility of separating DNA molecules in free fluids as an alternative to gel electrophoresis. Various techniques were studied. On the molecular level, agarose gel electrophoresis is being widely used to separate chromosomal DNA according to molecular weight. Carl and Olson separate and characterized the entire karyotype of a lab strain of Saccharomyces cerevisiae. Smith et al. and Schwartz and Koval independently reported the visualization of individual DNA molecules migrating through agarose gel matrix during electrophoresis. The techniques used by these researchers are being reviewed in the lab as a basis for the proposed studies.

Lubega, Seth↗

NASA NTRS1995

Hot shocked gas along the jets of NGC 4258 (M106)

The ROSAT High Resolution Interferometer (HRI) and Position Sensitive Proportional Counter (PSPC) detectors have been used to study the soft X-ray emission of the nearby SABbc galaxy NGC 4258 (M106). The helically twisted, nuclear jets, previously detected in radio continuum and visual emission-line studies, are found to dominate the X-ray images. After correcting pointing errors of up to +/- 7 sec in our HRI observation, we find that the southeast jet is spatially unresolved transversely along much of its 2.5 min (5 kpc) length. The northwest jet is more diffuse, and the extensive radio 'plateaus' also emit X-rays. The energy spectrum of the jets from the PSPC exposure is noisy but is best fitted as a Raymond-Smith plasma with kT = 0.3 keV, log N(sub H) approximately = 20.0/sq cm, and luminosity 1.6 x 10(exp 40) ergs/s between 0.1 and 2.4 keV. Gas at this temperature can arise from planar shocks of 500 km/s and may have been entrained as the jets scrape along the molecular clous that are known to be adjacent to the jets. The range of radial velocities from our published visual emission-line spectra of the jet are consistent with such a shock speed. We estimate that the mass of hot gas in the jets is 6 x 10(exp 4) (1/cc/n(sub e)) solar mass, with n(sub e) the average electron density. The inferred pressure of hot gas in the southeast jet may be similar to the radio equipartition pressure and to the ambient pressure of the interstellar medium (ISM). The X-ray spectral fit is poor above 0.7 keV and requires an additional hard component that peaks near the nucleus.

Cecil, G.↗