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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition

Motivation: Untargeted mass spectrometry experiments enable the profiling of metabolites in complex biological samples. The collected fragmentation spectra are the metabolite’s fingerprints that are used for molecule identification and discovery. Two main mass spectrometry strategies exist for the collection of fragmentation spectra: data-dependent acquisition (DDA) and data-independent acquisition (DIA). In the DIA strategy, all the metabolites ions in predefined mass-to-charge ratio ranges are co-isolated and co-fragmented, resulting in multiplexed fragmentation spectra that are challenging to annotate. In contrast, in the DDA strategy, fragmentation spectra are dynamically and specifically collected for the most abundant ions observed, causing redundancy and sub-optimal fragmentation spectra collection. Yet, DDA results in less multiplexed fragmentation spectra that can be readily annotated. Results: We introduce the MS2Planner workflow, an Iterative Optimized Data Acquisition strategy that optimizes the number of high-quality fragmentation spectra over multiple experimental acquisitions using topological sorting. Our results showed that MS2Planner increases the annotation rate by 38.6% and is 62.5% more sensitive and 9.4% more specific compared to DDA. Availability and implementation MS2Planner code is available at https://github.com/mohimanilab/MS2Planner. The generation of the inclusion list from MS2Planner was performed with python scripts available at https://github.com/lfnothias/IODA_MS.

47 OTHER INSTRUMENTATION↗
NASA NTRS2011

Application of Laser Mass Spectrometry to Art and Archaeology

REMPI laser mass spectrometry is a combination of resonance enhanced multiphoton ionization spectroscopy and time of flight mass spectrometry, This technique enables the collection of mass specific optical spectra as well as of optically selected mass spectra. Analytes are jet-cooled by entrainment in a molecular beam, and this low temperature gas phase analysis has the benefit of excellent vibronic resolution. Utilizing this method, mass spectrometric analysis of historically relevant samples can be simplified and improved; Optical selection of targets eliminates the need for chromatography while knowledge of a target's gas phase spectroscopy allows for facile differentiation of molecules that are in the aqueous phase considered spectroscopically indistinguishable. These two factors allow smaller sample sizes than commercial MS instruments, which in turn will require less damage to objects of antiquity. We have explored methods to optimize REMPI laser mass spectrometry as an analytical tool to archaeology using theobromine and caffeine as molecular markers in Mesoamerican pottery, and are expanding this approach to the field of art to examine laccaic acid in shellacs.

Gulian, Lase Lisa E.↗
NASA NTRS2019

Predicting the X-Ray Spectra of Stellar-mass Black Holes from Simulations

We describe results from a new technique for the prediction of complete, self-consistent X-ray spectra from three-dimensional general relativistic magnetohydrodynamic (GRMHD) simulations of black hole accretion flows. Density and cooling rate data from a harm3d GRMHD simulation are post-processed by an improved version of the Monte Carlo radiation transport code pandurata (in the corona) and the Feautrier solver PTRANSX (in the disk), with xstar subroutines. The codes are run in a sequential, iterative fashion to achieve globally energy-conserving and self-consistent radiation fields, temperature maps, and photoionization equilibria. The output is the X-ray spectrum as seen by a distant observer, including features, such as the Fe Kα emission line and corresponding K-edge absorption trough, due to disk reprocessing of coronal power. For the example cases we consider—a non-rotating 10 M(sub ⊙) black hole with solar abundances, accreting at 0.01, 0.03, 0.1, or 0.3 Eddington—we find spectra resembling actual observations of stellar-mass black holes in the soft or steep power-law state: broad thermal peaks (at 1–3 keV), steep power laws extending to high energy (Γ = 2.7–4.5), and prominent, asymmetric Fe Kα emission lines with equivalent widths in the range 40–400 eV (larger EW at lower accretion rates). By starting with simulation data, we obviate the need for parameterized descriptions of the accretion flow geometry—no a priori specification of the corona's shape or flux, or the disk temperature or density, etc., is needed. Instead, we apply the relevant physical principles to simulation output using appropriate numerical techniques; this procedure allows us to calculate inclination-dependent spectra after choosing only a small number of physically meaningful parameters: black hole mass and spin, accretion rate, and elemental abundances.

Kinch, Brooks E.↗
DOE OSTI2015

Rest-frame optical spectra and black hole masses of 3 < z < 6 quasars

We present the rest-frame optical spectral properties of 155 luminous quasars at 3.3 < z < 6.4 taken with the AKARI space telescope, including the first detection of the Hα emission line as far out as z ∼ 6. We extend the scaling relation between the rest-frame optical continuum and the line luminosity of active galactic nuclei (AGNs) to the high-luminosity, high-redshift regime that has rarely been probed before. Remarkably, we find that a single log-linear relation can be applied to the 5100 Å and Hα AGN luminosities over a wide range of luminosity (10{sup 42} < L{sub 5100} < 10{sup 47} ergs s{sup −1}) or redshift (0 < z < 6), suggesting that the physical mechanism governing this relation is unchanged from z = 0 to 6, over five decades in luminosity. Similar scaling relations are found between the optical and the UV continuum luminosities or line widths. Applying the scaling relations to the Hβ black hole (BH) mass (M{sub BH}) estimator of local AGNs, we derive the M{sub BH} estimators based on the Hα, Mg ii, and C iv lines, finding that the UV-line-based masses are overall consistent with the Balmer-line-based, but with a large intrinsic scatter of 0.40 dex for the C iv estimates. Our 43 M{sub BH} estimates from Hα confirm the existence of BHs as massive as ∼ 10{sup 10} M{sub ⊙} out to z ∼ 5 and provide a secure footing for previous results from Mg ii-line-based studies that a rapid M{sub BH} growth has occurred in the early universe.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1986

Theoretical spectra of nonmagnetized low-mass X-ray binaries

Theoretical X-ray spectra of low-mass X-ray binaries with negligible magnetic fields are presented. The geometry of the X-ray emitting region, the energetic efficiency of the accretion in the disk and in the boundary layer which leads to a relation between the disk and the boundary layer luminosities, and the irradiation of the disk by the boundary layer are studied. The model of the radiation spectrum emerging from the neutron star and the innermost part of the disk is presented. The relativistic and Doppler effects and their influence on the spectrum as a function of inclination angle are discussed. A simple method for comparing the spectrum model with observations by studying the hardness ratio is given, and the results for three X-ray sources in globular clusters observed by the Einstein satellite are presented. The range of applicability of the spectrum models is also discussed.

Czerny, Bozena↗
DOE OSTI2011

Dimuon radiation at relativistic energies available at the CERN Super Proton Synchrotron within a (3 + 1)D hydrodynamic + cascade model

We analyze dilepton emission from hot and dense matter using a hybrid approach based on the ultrarelativistic quantum molecular dynamics (UrQMD) transport model with an intermediate hydrodynamic stage for the description of heavy-ion collisions at relativistic energies. During the hydrodynamic stage, the production of lepton pairs is described by radiation rates for a strongly interacting medium in thermal equilibrium. In the low-mass region, hadronic thermal emission is evaluated by assuming vector meson dominance including in-medium modifications of the {rho} meson spectral function through scattering from nucleons and pions in the heat bath. In the intermediate-mass region, the hadronic rate is essentially determined by multipion annihilation processes. Emission from quark-antiquark annihilation in the quark gluon plasma (QGP) is taken into account as well. When the system is sufficiently dilute, the hydrodynamic description breaks down and a transition to a final cascade stage is performed. In this stage dimuon emission is evaluated as commonly done in transport models. By focusing on the enhancement with respect to the contribution from long-lived hadron decays after freezeout observed at the SPS in the low-mass region of the dilepton spectra, the relative importance of the different thermal contributions and of the two dynamical stages is investigated. We find that three separated regions can be identified in the invariant mass spectra. Whereas the very low and the intermediate-mass regions mostly receive contribution from the thermal dilepton emission, the region around the vector meson peak is dominated by the cascade emission. Above the {rho}-peak region the spectrum is driven by QGP radiation. Analysis of the dimuon transverse mass spectra reveals that the thermal hadronic emission shows an evident mass ordering not present in the emission from the QGP. A comparison of our calculation to recent acceptance-corrected NA60 data on invariant as well as transverse mass spectra is performed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Constraining absolute neutrino masses via detection of galactic supernova neutrinos at JUNO

A high-statistics measurement of the neutrinos from a galactic core-collapse supernova is extremely important for understanding the explosion mechanism, and studying the intrinsic properties of neutrinos themselves. In this paper, we explore the possibility to constrain the absolute scale of neutrino masses m{sub ν} via the detection of galactic supernova neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO) with a 20 kiloton liquid-scintillator detector. In assumption of a nearly-degenerate neutrino mass spectrum and a normal mass ordering, the upper bound on the absolute neutrino mass is found to be m{sub ν}<(0.83±0.24) eV at the 95% confidence level for a typical galactic supernova at a distance of 10 kpc, where the mean value and standard deviation are shown to account for statistical fluctuations. For comparison, we find that the bound in the Super-Kamiokande experiment is m{sub ν}<(0.94±0.28) eV at the same confidence level. However, the upper bound will be relaxed when the model parameters characterizing the time structure of supernova neutrino fluxes are not exactly known, and when the neutrino mass ordering is inverted.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

HIGH-RESOLUTION IR ABSORPTION SPECTROSCOPY OF POLYCYCLIC AROMATIC HYDROCARBONS: THE REALM OF ANHARMONICITY

We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3-μm CH stretching region of polycyclic aromatic hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold (∼4 K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main bands that fall within 0.5% of the experimental frequencies. The implications for the aromatic infrared bands, specifically the 3-μm band, are discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Effect of in-medium parameters of ρ meson in its photoproduction reactions on nuclei

There exist model calculations showing the modification of the hadronic parameters of ρ meson in the nuclear environment. From these parameters, we extract the ρ-meson-nucleus optical potential and show the medium effect due to this potential on the ρ-meson mass distribution spectra in the photonuclear reactions. The calculated results reproduced reasonably the measured e{sup +}e{sup −} invariant mass, i.e., ρ-meson mass, distribution spectra in γ, ρ{sup 0} → e{sup +}e{sup −} reactions on nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2012

Simulation of BF{sub 3} plasma immersion ion implantation into silicon

Plasma immersion ion implantation from a BF{sub 3} plasma into crystalline (100) silicon was performed using the PULSION plasma doping tool. Implanted boron profiles were measured with the SIMS method and simulated using models with different levels of sophistication. The physical implantation model is based on an analytical energy distribution for ions from the plasma and uses a Monte-Carlo simulation code. An analytical model of plasma immersion ion implantation that assumes a uniform and isotropic implantation was implemented in a software module called IMP3D. The functionality of this module which was initially envisaged for the three-dimensional simulation of conventional ion implantation was extended to plasma immersion ion implantation and examples of 2D and 3D simulations from this are presented.

36 MATERIALS SCIENCE↗
DOE OSTI2014

A NEW COSMOLOGICAL DISTANCE MEASURE USING ACTIVE GALACTIC NUCLEUS X-RAY VARIABILITY

We report the discovery of a luminosity distance estimator using active galactic nuclei (AGNs). We combine the correlation between the X-ray variability amplitude and the black hole (BH) mass with the single-epoch spectra BH mass estimates which depend on the AGN luminosity and the line width emitted by the broad-line region. We demonstrate that significant correlations do exist that allow one to predict the AGN (optical or X-ray) luminosity as a function of the AGN X-ray variability and either the Hβ or the Paβ line widths. In the best case, when the Paβ is used, the relationship has an intrinsic dispersion of ∼0.6 dex. Although intrinsically more disperse than supernovae Ia, this relation constitutes an alternative distance indicator potentially able to probe, in an independent way, the expansion history of the universe. With respect to this, we show that the new mission concept Athena should be able to measure the X-ray variability of hundreds of AGNs and then constrain the distance modulus with uncertainties of 0.1 mag up to z ∼ 0.6. We also discuss how our estimator has the prospect of becoming a cosmological probe even more sensitive than the current supernovae Ia samples by using a new dedicated wide-field X-ray telescope able to measure the variability of thousands of AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Comparison of PID Shunting in Polycrystalline and Single-Crystal Silicon Modules via Multi-Scale, Multi-Technique Characterization

We used the methods we reported last year to investigate potential-induced degradation (PID). We have now applied these methods to single-crystalline silicon modules that have degraded during field deployment, as well as in minimodules stressed in the laboratory. We will compare these results to the polycrystalline results presented last year. Small cores have been removed from the modules and subjected to analysis. We use a combination of photoluminescence and dark lock-in thermography imaging, laser marking, electron-beam induced current measurements, and subsequent focused ion-beam marking to allow analysis of individual defects via time-of-flight secondary-ion mass spectrometry (TOF-SIMS) to investigate the root-cause mechanism for PID shunting. We see a direct correlation between recombination active shunts and sodium content. The sodium content in shunted areas peaks at the SiN/Si interface and is consistently observed at a concentration of 0.1%-1% in shunted areas. TOF-SIMS data taken on degraded and non-degraded single-crystalline sample areas show a similar trend as in the polycrystalline samples: more sodium is seen in the degraded areas.

14 SOLAR ENERGY↗
DOE OSTI2010

On the structure of X(3872) particle

The property of X(3872) particle is discussed by carefully studying the experimental data available. We find that two poles near the D*{sup 0}D{sup 0}-bar threshold are required in order to describe the data better. The stability of the pole locations is further tested by varying fit methods and it is found that our qualitative result is unchanged. We conclude that the X(3872) particle is a c-barc state heavily distorted by the D*{sup 0}D{sup 0}-bar threshold.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Mass measurement using energy spectra in three-body decays

In previous works we have demonstrated how the energy distribution of massless decay products in two body decays can be used to measure the mass of decaying particles. In this study, we show how such results can be generalized to the case of multi-body decays. The key ideas that allow us to deal with multi-body final states are an extension of our previous results to the case of massive decay products and the factorization of the multi-body phase space. The mass measurement strategy that we propose is distinct from alternative methods because it does not require an accurate reconstruction of the entire event, as it does not involve, for instance, the missing transverse momentum, but rather requires measuring only the visible decay products of the decay of interest. To demonstrate the general strategy, we study a supersymmetric model wherein pair-produced gluinos each decay to a stable neutralino and a bottom quark-antiquark pair via an off -shell bottom squark. The combinatorial background stemming from the indistinguishable visible final states on both decay sides can be treated by an “event mixing” technique, the performance of which is discussed in detail. In conclusion, taking into account dominant backgrounds, we are able to show that the mass of the gluino and, in favorable cases, that of the neutralino can be determined by this mass measurement strategy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2011

Dynamical fermion mass generation and exciton spectra in graphene

The Coulomb interaction between massless Dirac fermions may induce dynamical chiral symmetry breaking by forming excitonic pairs in clean graphene, leading to semimetal-insulator transition. If the Dirac fermions have zero bare mass, an exact continuous chiral symmetry is dynamically broken and thus there are massless Goldstone excitons. If the Dirac fermions have a small bare mass, an approximate continuous chiral symmetry is dynamically broken and the resultant Goldstone-type excitons become massive, which is analogous to what happens in QCD. In this paper, after solving the Dyson-Schwinger gap equation in the presence of a small bare fermion mass, we found a remarkable reduction of the critical Coulomb interaction strength for excitonic pair formation and a strong enhancement of dynamical fermion mass. We then calculate the masses of Goldstone-type excitons using the Shifman-Vainshtein-Zakharov sum-rule method and operator product expansion technique developed in QCD and find that the exciton masses are much larger than bare fermion mass but smaller than the width of dynamical fermion mass gap. We also study the spin susceptibilities and estimate the masses of non-Goldstone-type excitons using the same tools.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

Structural properties and spatial ordering in multilayered ZnMgTe/ZnSe type-II quantum dot structures

We report the structural properties and spatial ordering of multilayer ZnMgTe quantum dots (QDs) embedded in ZnSe, where sub-monolayer quantities of Mg were introduced periodically during growth in order to reduce the valence band offset of ZnTe QDs. The periodicity, period dispersion, individual layer thickness, and the composition of the multilayer structures were determined by comparing the experimental high resolution x-ray diffraction (HRXRD) spectra to simulated ones for the allowed (004) and quasi-forbidden (002) reflections in combination with transmission electron microscopy (TEM) results. Secondary ion mass spectroscopy (SIMS) profiles confirmed the incorporation of Mg inside the QD layers, and the HRXRD analysis revealed that there is approximately 32% Mg in the ZnMgTe QDs. The presence of Mg contributes to higher scattering intensity of the HRXRD, leading to the observation of higher order superlattice peaks in both the (004) and (002) reflections. The distribution of scattered intensity in the reciprocal space map (RSM) shows that the diffuse scattered intensity is elongated along the q{sub x} axis, indicating a vertical correlation of the dots, which is found to be less defined for the sample with larger periodicity. The diffuse scattered intensity is also found to be weakly correlated along the q{sub z} direction indicating a weak lateral correlation of the dots.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1

Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to “mine” information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O -formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S -cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N -termini recovered by concanavalin A binding or from a previous study, only M. mazei S -layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more. This study supplements limited, existing experimental datasets of mature archaeal N -termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Spectra of low-mass helium star models and the type Ic supernova SN 1987M

The question of whether the low-mass helium star models reproduce the helium-poor Type Ic spectrum of SN 1987M is investigated by comparing the theoretical spectrum from the 3.3-solar-mass model of Shigeyama et al. (1990) to observations of SN 1987M reported by Filippenko et al. (1990). The results indicate a number of positive correlations between the observed and the computed spectra. In both types of spectra, Ca II, O I, and Mg I emission lines dominate at late times, and, if extensive composition mixing is imposed, good fits can be made to the shapes of the emission features and good agreement can be found with the observed ratio of the forbidden and IR triplet blends of Ca II. The former indicates that the 3.3-solar-mass model predicts the proper density/velocity structure, and the latter indicates that the computed temperature structure is consistent with the observation though the lines are too strong relative to the continuum. This result is roughly independent of the He abundance. The computed and observed spectra are consistent with a small Ni-56 production in contrast to Type Ia thermonuclear events whose spectra are dominated by Fe-group lines at late times.

Swartz, Douglas A.↗