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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain–affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. Further, the integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Fragmentation of molecular clouds

Fragmentation is generally considered to be the initial process that a molecular cloud must undergo before stars can form. Yet its role in determining the final mass spectrum remains obscure. It appears that gravitational fragmentation, considered as a unique process, is unsatisfactory. Both fragmentation and complementary physical processes are, therefore, discussed. One of the principle aims of the discussion is to indicate how stars of solar mass (and more generally, how the initial mass spectrum of stars) can form. Attention is given to the evidence for fragmentation, opacity-limited fragmentation, magnetic flux-limited fragmentation, fragmentation induced by molecule formation and excitation, protostellar heat input, fragment coalescence, accretion, binary formation, and probabilistic theories.

Silk, J.↗
NASA NTRS1987

Diatomic molecules in the solar infrared spectrum from ATMOS-SL 3 high resolution observations

The ATMOS Fourier Transform Spectrometer has observed, for the first time, the solar infrared spectrum, from 2 to 16 microns, free of any telluric absorption. A very large number of molecular lines are present on these high quality spectra: vibration-rotation lines of CO (Delta-v = 1 and 2; including the isotopic species C-13, O-18 and O-17), CH, NH, OH and pure rotation lines of OH. The analysis of these lines will allow to derive accurate values for the solar abundances of C, N and O and the isotopic ratios C-13/C-12, O-18/O-16, and O-17/O-16, to test the photospheric model from high to deep layers, to test the electric dipole moment functions of the different molecules and to derive much better molecular constants for CH.

Grevesse, Nicolas↗
NASA NTRS1988

On the high-energy gamma-ray signature of cosmic-ray sources

Monte Carlo simulations of the gamma-ray emission from hypothetical cosmic-ray sources are performed. Sources which might correspond to acceleration by supernova shocks in 'average' interstellar conditions and deep within giant molecular clouds are considered. The consequences of dropping the common assumption that the cosmic-ray spectrum at the sources is the same as that observed at earth are examined. Spectral effects which can be related to the depth of the material shroud and the population of accelerated particles are explored using these simulations and are described. The results are compared with the COS B catalog of gamma-ray sources, and the implications for the underlying particle populations and source mechanisms are discussed.

Ormes, J. F.↗
NASA NTRS1993

The fundamental bands of HCl-35 and HCl-37 - Line positions from high-resolution laboratory data

Accurate measurements of the positions of lines of the (1-0) vibration-rotation bands of HCl-35 and HCl-37 are reported. The new measurements have been derived from a laboratory spectrum recorded with a Fourier transform spectrometer operated at an unapodized spectral resolution of 0.0060/cm. Molecular constants are reported from a simultaneous least-squares analysis of these measurements and selected infrared and far-infrared data taken from the literature. The motivation for the present investigation is the need for improved HCl line positions for use in IR atmospheric remote sensing investigations.

Rinslad, Curtis P.↗
NASA NTRS1994

Observations of ultraviolet-bright stars in globular clusters with the Hopkins Ultraviolet Telescope

Two UV-bright stars in globular clusters, UV5 in NGC 1851 and vZ 1128 in M3, were observed with the Hopkins Ultraviolet Telescope (HUT) during the Astro-1 space shuttle mission in 1990 December. The stars' spectra show weak absorption features and no significant emission features other than well known geocoronal lines. Detailed fitting of Kurucz (1991) stellar atmosphere models using a chi(sup 2) minimization technique indicates T(sub eff) = 16 000 K, log g = 2.5, and abundance (-1.0) (logarithm of abundance of elements heavier than helium relative to solar) for UV5, and T(sub eff) = 35 000 K, log g = 4.0, and abundance (-3.5) for vZ 1128. The Kurucz model which best fits vZ 1128 overpredicts the flux in the region below approximately 1000 A, an effect seen in previous models of O-type stars. Our results are robust (to within approximately 1000 K) with respect to uncertainties in interstellar reddening and atomic and molecular hydrogen column densities. We do not see significant molecular hydrogen absorption, which might have indicated material in a circumstellar shell, in either star's spectrum. We estimate the stellar luminosities to be log L/solar luminosity = 3.33 +/- 0.15 for UV5 and log L/solar luminosity = 3.21 +/- 0.12 for vZ 1128. These atmospheric parameters place both stars on the Schoenberner (post-AGB) tracks, though the stellar masses derived from the best-fitting Kurucz models are somewhat less than those predicted by the Schoenberner models. Examination of individual absorption line strengths reveals no significant abundance anomalies in either star.

Van Dyke Dixon, W.↗
NASA NTRS2002

Rayleigh Scattering Diagnostic for Measurement of Velocity and Density Fluctuation Spectra

A new molecular Rayleigh scattering based flow diagnostic is used for the first time to measure the power spectrum of gas density and radial velocity component in the plumes of high speed jets. The technique is based on analyzing the Rayleigh scattered light with a Fabry-Perot interferometer used in the static, imaging mode. The PC based data acquisition system is capable of simultaneous sampling of velocity and density at rates to 100 kHz and data record lengths to 10 million. Velocity and density power spectra and velocity-density cross spectra are presented for a subsonic jet, an underexpanded screeching jet, and for Mach 1.4 and Mach 1.8 supersonic jets. Software and hardware interfaces were developed to allow computer control of all aspects of the experiment and data acquisition.

Seasholtz, Richard G.↗
DOE OSTI2024

Machine learning the electric field response of condensed phase systems using perturbed neural network potentials

Abstract The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å −1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields.

Science & Technology - Other Topics↗
NASA NTRS1996

Assessment of the polycyclic aromatic hydrocarbon-diffuse interstellar band proposal

The potential link between neutral and/or ionized polycyclic aromatic hydrocarbons (PAHs) and the diffuse interstellar band (DIB) carriers is examined. Based on the study of the general physical and chemical properties of PAHs, an assessment is made of their possible contribution to the DIB carriers. It is found that, under the conditions reigning in the diffuse interstellar medium, PAHs can be present in the form of neutral molecules as well as positive and/or negative ions. The charge distribution of small PAHs is dominated, however, by two charge states at one time with compact PAHs present only in the neutral and cationic forms. Each PAH has a distinct spectral signature depending on its charge state. Moreover, the spectra of ionized PAHs are always clearly dominated by a single band in the DIB spectral range. In the case of compact PAH ions, the strongest absorption band is of type A (i.e., the band is broad, falls in the high-energy range of the spectrum, and possesses a large oscillator strength), and seems to correlate with strong and broad DIBs. For noncompact PAH ions, the strongest absorption band is of type I (i.e., the band is narrow, falls in the low-energy range of the spectrum, and possesses a small oscillator strength), and seems to correlate with weak and narrow DIBs. Potential molecular size and structure constraints for interstellar PAHs are derived by comparing known DIB characteristics to the spectroscopic properties of PAHs. It is found that (i) only neutral PAHs larger than about 30 carbon atoms could, if present, contribute to the DIBs. (ii) For compact PAHs, only ions with less than about 250 carbon atoms could, if present, contribute to the DIBs. (iii) The observed distribution of the DIBs between strong/moderate and broad bands on the one hand and weak and narow bands on the other can easily be interpreted in the context of the PAH proposal by a distribution of compact and noncompact PAH ions, respectively. A plausible correlation between PAH charge states and DIB "families" is thus provided by the PAH-DIB proposal. Following this proposal, DIB families would reflect conditions within a cloud which locally determine the relative importance of cations, anions, and neutral species, rather than tracers of a specific species. Observational predictions are given to establish the viability of the PAH hypothesis. It is concluded that small PAH ions are very promising candidates as DIB carriers provided their population is dominated by a finite number (100-200) of species. A key test for the PAH proposal, consisting of laboratory and astronomical investigations in the ultraviolet range, is called for.

NASA Discipline Number 52-10↗
DOE OSTI2020

Kβ X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase

Cu(I) active sites in metalloproteins are involved in O 2 activation, but their O 2 reactivity is difficult to study due to the Cu(I) d 10 closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kβ XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kβ XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kβ 2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kβ 2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d–p mixing. A Kβ XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GO pre ) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. Finally, the high-energy Kβ 2,5 emission feature in the Cu(I)-GO pre data has information about the MO containing mostly Cu 3d x 2 –y 2 character that is the frontier molecular orbital (FMO) for O 2 activation, which shows the potential of Kβ XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Benchmark of few-level quantum theory vs ab initio numerical solutions for the strong-field Autler–Townes effect in photoionization of hydrogen

Abstract The temporal and spectral consequences of an intermediate resonance en route to photoionization are investigated theoretically in two ways: by solving few-level model equations and by ab initio numerical solution of the time-dependent Schrödinger equation, in both cases for hydrogen in three dimensions. The model consists of atomic states resonantly field-dressed in a three-level reduction of the hydrogen atom that consists of the 2 p –3 d (Balmer) transition and one energetically-distant continuum state. The model’s level occupation probabilities are derived from three Schrödinger amplitude equations and are benchmarked against an ab initio numerical solution for the hydrogen electron’s wavefunction under the same field. We examine contrasts between the results of the two approaches with a particular focus on Autler–Townes doublets that appear in the photoelectron spectrum.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2008

Middle UV to Near-IR Spectrum of Electron-Excited SO2

We investigated the electron impact-induced fluorescence spectrum of SO2 to provide excitation cross sections for modeling Io's mission spectrum and analyzing Cassini Imaging Science Subsystem observations. The electron-excited middle-ultraviolet visible optical near-infrared (VOIR) emission spectrum of SO2 gas was generated in the laboratory and studied from 2000 to 11,000 A at a resolution of (Delta)(lamda) approximately 2.5 A full width at half maximum (FWHM). The VOIR laboratory spectrum longward of 6000 A consists entirely of S I, II and O I, II multiplets for electron impact energies above approximately 15 eV. Between 2000 and 6000 A, we find previously identified molecular bands from both SO and SO2. This work represents a significant improvement in spectral resolution over our earlier work done at 18 A FWHM. From a measurement of the medium-resolution spectrum, we provide detailed 25- and 100-eV emission cross sections for spectral features from 2000 to 11,000 A . On the basis of these data, we suggest future ground-based and satellite telescopic observations in the VOIR that are of promise for understanding Io's atmosphere.

sulpher dioxide↗
DOE OSTI2022

Air resonance enhanced multiphoton ionization tagging velocimetry

Air resonance enhanced multiphoton ionization (REMPI) tagging velocimetry (ART) was demonstrated in quiescent and supersonic flows. The ART velocimetry method utilizes a wavelength tunable laser beam to resonantly ionize molecular oxygen in air and generate additional avalanche-type ionization of molecular nitrogen. The fluorescence emissions from the first negative and first positive bands of molecular nitrogen are, thus, produced and used for flow tagging. Detailed characterization of ART was conducted, including the effects of oxygen resonance to fluoresce nitrogen, nitrogen fluorescence spectrum, laser energy deposition into quiescent flow showing minimal perturbations in flow, fluorescence lifetime study at various pressures, and line tagging without breakdown. Pointwise velocity measurements within a supersonic flow from a nominal Mach 1.5 nozzle have been conducted and characterized.

Clark, Aleksander↗
DOE OSTI2022

PCP consensus protein/peptide alphavirus antigens stimulate broad spectrum neutralizing antibodies

Vaccines based on proteins and peptides may be safer and if calculated based on many sequences, more broad-spectrum than those designed based on single strains. Physicochemical Property Consensus (PCP con ) alphavirus (AV) antigens from the B-domain of the E2 envelope protein were designed, synthesized recombinantly and shown to be immunogenic (i.e. sera after inoculation detected the antigen in dotspots and ELISA). Antibodies in sera after inoculation with B-region antigens based on individual AV species (eastern or Venezuelan equine encephalitis (EEEV con , VEEV con ), or chikungunya (CHIKV con ) bound only their cognate protein, while those designed against multiple species (Mosaik con and EVC con ) recognized all three serotype specific antigens. The VEEV con and EEEV con sera only showed antiviral activity against their related strains (in plaque reduction neutralization assays (PRNT 50/80 ). Peptides designed to surface exposed areas of the E2-A-domain of CHIKV con were added to CHIKV con inocula to provide anti-CHIKV antibodies. EVC con , based on three different alphavirus species, combined with E2-A-domain peptides from AllAV con , a PCPcon of 24 diverse AV, generated broad spectrum, antiviral antibodies against VEEV, EEEV and CHIKV, AV with less than 35% amino acid identity to each other (>65% diversity). This is a promising start to a molecularly defined vaccine against all AV. A further study with these antigens can illuminate what areas are most important for a robust immune response, resistant to mutations in rapidly evolving viruses. The validated computational methods can also be used to design broad spectrum antigens against many other pathogen families.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments

Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two-dimensional correlation analysis for x-ray photoelectron spectroscopy

Abstract X-ray photoelectron spectroscopy (XPS) measures the binding energy of core-level electrons, which are well-localised to specific atomic sites in a molecular system, providing valuable information on the local chemical environment. The technique relies on measuring the photoelectron spectrum upon x-ray photoionisation, and the resolution is often limited by the bandwidth of the ionising x-ray pulse. This is particularly problematic for time-resolved XPS, where the desired time resolution enforces a fundamental lower limit on the bandwidth of the x-ray source. In this work, we report a novel correlation analysis which exploits the correlation between the x-ray and photoelectron spectra to improve the resolution of XPS measurements. We show that with this correlation-based spectral-domain ghost imaging method we can achieve sub-bandwidth resolution in XPS measurements. This analysis method enables XPS for sources with large bandwidth or spectral jitter, previously considered unfeasible for XPS measurements.

47 OTHER INSTRUMENTATION↗