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DOE OSTI2022

Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures

Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.

mass spectrometry, FTICR, FTMS, ultrahigh mass res↗

DOE OSTI2023

Visualizing heterogeneous dipole fields by terahertz light coupling in individual nano-junctions

The challenge underlying superconducting quantum computing is to remove materials bottleneck for highly coherent quantum devices. The nonuniformity and complex structural components in the underlying quantum circuits often lead to local electric field concentration, charge scattering, dissipation and ultimately decoherence. Here we visualize interface dipole heterogeneous distribution of individual Al/AlO$_{x}$/Al junctions employed in transmon qubits by broadband terahertz scanning near-field microscopy that enables the non-destructive and contactless identification of defective boundaries in nano-junctions at an extremely precise nanoscale level. Our THz nano-imaging tool reveals an asymmetry across the junction in electromagnetic wave-junction coupling response that manifests as hot (high intensity) vs cold (low intensity) spots in the spatial electrical field structures and correlates with defected boundaries from the multi-angle deposition processes in Josephson junction fabrication inside qubit devices. The demonstrated local electromagnetic scattering method offers high sensitivity, allowing for reliable device defect detection in the pursuit of improved quantum circuit fabrication for ultimately optimizing coherence times.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2009

First Spectroscopic Identification of Massive Young Stellar Objects in the Galactic Center

We report the detection of several molecular gas-phase and ice absorption features in three photometrically-selected young stellar object (YSO) candidates in the central 280 pc of the Milky Way. Our spectra, obtained with the Infrared Spectrograph (IRS) onboard the Spitzer Space Telescope, reveal gas-phase absorption from CO2 (15.0 microns), C2H2 (13.7 microns) and HCN (14.0 microns). We attribute this absorption to warm, dense gas in massive YSOs. We also detect strong and broad 15 microns CO2 ice absorption features, with a remarkable double-peaked structure. The prominent long-wavelength peak is due to CH3OH-rich ice grains, and is similar to those found in other known massive YSOs. Our IRS observa.tions demonstra.te the youth of these objects, and provide the first spectroscopic identification of massive YSOs in the Galactic Center.

An, Deokkeun↗

NASA NTRS1995

Search for fine scale structures in high latitude solar wind

About 25 years ago, E. Parker suggested that, as a consequence of the inhomogeneous structure of the corona, the solar wind might consist of adjacent structures with different physical conditions. Since that suggestion was made, the solar wind plasma characteristics have been measured in situ through many experiments, but little has been done to check whether the solar wind shows any evidence for fine scale structures, and, in the affirmative, how far from the Sun these structures persist. A previous work on this subject, by Thieme, Marsch and Schwenn (1990), based on Helios data, lead these authors to claim that the solar wind, between 0.3 and 1 AU, is inhomogeneous on a scale consistent with the hypothesis that the plume-interplume plasmas, at those distances, still retain their identity. In this work we present preliminary results from an investigation of the solar wind fine structure from Ulysses high latitude observations. To this end, we have analyzed data over several months, during 1994, at times well after Ulysses's last encounter with the Heliospheric Current Sheet, when the spacecraft was at latitudes above 50 degrees. These data refer to high speed wind coming from southern polar coronal holes and are best suited for plume-interplume identification. We have performed a power spectra analysis of typical plasma parameters, to test whether the wind plasma consist of two distinct plasma populations. We also examined data to check whether there is any evidence for an horizontal pressure balance over the hypothesized distinct structures. Our results are discussed and compared with previous findings.

Livi, S.↗

DOE OSTI2024

e RPCA : Robust Principal Component Analysis for Exponential Family Distributions

Abstract Robust principal component analysis (RPCA) is a widely used method for recovering low‐rank structure from data matrices corrupted by significant and sparse outliers. These corruptions may arise from occlusions, malicious tampering, or other causes for anomalies, and the joint identification of such corruptions with low‐rank background is critical for process monitoring and diagnosis. However, existing RPCA methods and their extensions largely do not account for the underlying probabilistic distribution for the data matrices, which in many applications are known and can be highly non‐Gaussian. We thus propose a new method called RPCA for exponential family distributions (), which can perform the desired decomposition into low‐rank and sparse matrices when such a distribution falls within the exponential family. We present a novel alternating direction method of multiplier optimization algorithm for efficient decomposition, under either its natural or canonical parametrization. The effectiveness of is then demonstrated in two applications: the first for steel sheet defect detection and the second for crime activity monitoring in the Atlanta metropolitan area.

Zheng, Xiaojun↗

DOE OSTI2023

Observation of a threshold cusp at the Λ η threshold in the pK - mass spectrum with Λ$^{+}_{c}$ → pK - π + decays

We observe a narrow peaking structure in the pK - invariant-mass spectrum near the Λη threshold. The peak is clearly seen in 1.5 million events of Λ$^{+}_{c}$ → pK - π + decay using the 980 fb -1 data sample collected by the Belle detector at the KEKB asymmetric-energy e + e - collider. We try two approaches to explain this structure: as a new resonance and as a cusp at the Λη threshold. The best fit is obtained with a coherent sum of a Flatte function and a constant background amplitude with the reduced X 2 of 257/243 (p = 0.25), while the fits to Breit-Wigner functions are unfavored by more than 7σ. The best fit explains the structure as a cusp at the Λη threshold, and the obtained parameters are consistent with the known properties of Λ(1670). The observation gives the first identification of a threshold cusp in hadrons from the spectrum shape.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Impact of nuclear data covariance libraries on uncertainty quantification of sodium cooled fast reactor simulation

Uncertainty quantification in core modelling to assess reactor performance is a regular practice to identify design safety limits. Best-estimate plus uncertainty (BEPU) methods are commonly used to propagate uncertainties to core responses from input parameters, characterized by variance-covariance libraries. This study evaluates the impact of different covariance libraries on the uncertainty associated with core safety parameters and their propagation through reactor transient modelling for a metallic core (ABR-1000). The COMAC-1.0, COMMARA-2.0, and COMMARA-2.1 covariance libraries are used to propagate nuclear data uncertainties to neutron feedback coefficients using the Generalized Perturbation Theory, then through transient safety analyses to establish the confidence interval for safety performance of the reactor using stochastic sampling. The considered transients include Unprotected Transient Over Power and Unprotected Loss Of Flow. Most influential nuclide and reaction pairs in different variance-covariance libraries are identified and their impact on the uncertainty of safety parameters are evaluated. Significant differences were observed between uncertainties from COMAC compared to COMMARA libraries. Uncertainties from COMMARA libraries were consistently larger than COMAC for all cases. For structure, coolant density feedback coefficients and control rod worth, total nuclear data uncertainties were approximately 50% larger for COMMARA than COMAC. Differences were also observed in identification of top contributors of uncertainty in terms of reaction-cross sections. For instance, largest contribution to total uncertainty of radial expansion coefficient from COMMARA-2.0 and 2.1 originates from Na{sup 23} P1 Elastic cross section (0.81%) but from Pu{sup 239} Fission (0.53%) with COM C-1.0. Such differences are evaluated in this research for all quantities of interest. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

MassIVE MSV000095714

Proteomic analysis reveals translation-related proteins are significantly altered in response to stabilized G4s. Identification of the importance of translation factors in overcoming G4s led to the question of how E. coli cells generally respond to chemicals that stabilize such structures. As a first step in addressing this question, a proteomic analysis was carried out to measure the quantitative effects of NMM on the levels of individual proteins in E. coli. Protein levels from early log-phase cultures of delta-tolC and delta-tolC tufA::kan strains grown in the presence or absence of NMM were measured to assess how reduced EF- Tu levels and NMM impacted expression.

Bottom-up proteomics↗

NASA NTRS1971

New techniques for the analysis of manual control systems

Studies are summarized on the application of advanced analytical and computational methods to the development of mathematical models of human controllers in multiaxis manual control systems. Specific accomplishments include the following: (1) The development of analytical and computer methods for the measurement of random parameters in linear models of human operators. (2) Discrete models of human operator behavior in a multiple display situation were developed. (3) Sensitivity techniques were developed which make possible the identification of unknown sampling intervals in linear systems. (4) The adaptive behavior of human operators following particular classes of vehicle failures was studied and a model structure proposed.

Bekey, G. A.↗

NASA NTRS1975

FORTRAN Automated Code Evaluation System (faces) system documentation, version 2, mod 0

A system is presented which processes FORTRAN based software systems to surface potential problems before they become execution malfunctions. The system complements the diagnostic capabilities of compilers, loaders, and execution monitors rather than duplicating these functions. Also, it emphasizes frequent sources of FORTRAN problems which require inordinate manual effort to identify. The principle value of the system is extracting small sections of unusual code from the bulk of normal sequences. Code structures likely to cause immediate or future problems are brought to the user's attention. These messages stimulate timely corrective action of solid errors and promote identification of 'tricky' code. Corrective action may require recoding or simply extending software documentation to explain the unusual technique.

Source record↗

NASA NTRS1980

Preparation and evaluation of advanced electrocatalysts for phosphoric acid fuel cells

Results are presented for hydrogen oxidation and hydrogen oxidation poisoned by carbon monoxide at levels between 0 and 30%. Due to the high activities that are now being observed for our platinum based electrocatalysts, the hydrogen concentrations were reduced to 10% levels in the gas supplies. Perturbation techniques were used to determine that a mechanism for the efficient operation of our porous gas diffusion electrodes is diffusion of the carbon monoxide out of the electrode structure through the electrolyte film on the electro-catalyst. A survey of the literature on platinum group materials (PGM) was carried out so that an identification of successful electrocatalysts could be made. Two PGM electrocatalysts were prepared and performance data for hydrogen oxidation in hot phosphoric acid in the presence of high carbon monoxide concentrations showed that they matched the best platinum on carbon electrocatalysts but with an electrocatalyst cost that was half of the platinum catalyst cost.

Stonehart, P.↗

NASA NTRS1981

Application of a flight test and data analysis technique to flutter of a drone aircraft

Modal identification results presented were obtained from recent flight flutter tests of a drone vehicle with a research wing (DAST ARW-1 for Drones for Aerodynamic and Structural Testing, Aeroelastic Research Wing-1). This vehicle is equipped with an active flutter suppression system (FSS). Frequency and damping of several modes are determined by a time domain modal analysis of the impulse response function obtained by Fourier transformations of data from fast swept sine wave excitation by the FSS control surface on the wing. Flutter points are determined for two different altitudes with the FSS off. Data are given for near the flutter boundary with the FSS on.

Bennett, R. M.↗

NASA NTRS1987

Behavior sensitivities for control augmented structures

During the past few years it has been recognized that combining passive structural design methods with active control techniques offers the prospect of being able to find substantially improved designs. These developments have stimulated interest in augmenting structural synthesis by adding active control system design variables to those usually considered in structural optimization. An essential step in extending the approximation concepts approach to control augmented structural synthesis is the development of a behavior sensitivity analysis capability for determining rates of change of dynamic response quantities with respect to changes in structural and control system design variables. Behavior sensitivity information is also useful for man-machine interactive design as well as in the context of system identification studies. Behavior sensitivity formulations for both steady state and transient response are presented and the quality of the resulting derivative information is evaluated.

Manning, R. A.↗

NASA NTRS2001

Exploration of the Eltanin Impact Area (Bellingshausen Sea): Expedition ANT XVIII5a

The impact of the Eltanin asteroid into the Bellingshausen Sea (2.15 Ma) is the only known impact in a deep-ocean (approx. 5 km) basin. On 26 March 2001, the FS Polarstern returned to the impact area during expedition ANT XVIII/5a. Over a period of 14 days, this region was explored by detailed bathymetric mapping, acoustic profiling of sediment deposits, and direct sampling with 18 piston cores and four gravity cores. Preliminary shipboard examination of microfossils showed that sixteen of the piston cores and three gravity cores contained sediments at least as old as the impact event and have a high probability of containing a record of the disturbances caused by the impact. During the expedition, portions of eleven piston cores were opened for preliminary examination of the impact deposits. Visual examination of cores and microscopic identification of suspect impact melt particles were were used to identify ejecta and X-ray radiographs of the opened core segments permitted analysis of sediment structures. Impact deposits were found in nine of the eleven opened cores, and a similar success rate is anticipated in the seven cores remaining to be opened. These preliminary observations indicate that the highest concentrations of meteoritic ejecta and the largest particle sizes appear to occur in the region north of the San Martin seamounts. Recovered debris includes cm-sized melt rocks and a 2.5 cm meteorite. This expedition has confirmed the presence of high concentrations of meteoritic ejecta across a region at least as large as 10(exp 5) sq km. Quantitative analyses of ejecta distribution within this region will require further study, but previous estimates of 1 km for the minimum diameter of the Eltanin asteroid, appear safe.

Gersonde, Rainer↗

NASA NTRS2004

Far-Infrared and Submillimeter Spectroscopy of Low to Moderate Redshift Normal and Active Galaxies

Broadband surveys with planned observatories such as SIRTF, ASTRO-F, NGST, Herschel, SMA, and ALMA will provide large samples of dust-enshrouded galaxies undergoing varying proportions of star formation and accretion onto supermassive black holes. Recent evidence suggests that the mass of supermassive central black holes are proportional to central velocity dispersions of their host galaxy bulges, but it is not yet known how these properties are evolutionarily connected. To trace the evolution of these components during the important luminous, dusty merger episodes as a function of redshift, sensitive mid- to far-infrared spectroscopic diagnostic observations from space will be necessary. The high sensitivity and spatial resolution of a large aperture, natural background limited far-infrared/submillimeter telescope such as SAFAIR will allow detection and identification of the far-infrared/submillimeter components of galaxies and of a multitude of rest-frame mid- to far-infrared recombination, fine-structure, and molecular lines toward dusty galactic nuclei. The line diagnostics beginning to be developed from ISO work will help determine important parameters such as the intrinsic spectral energy distribution, ionization parameters, metallicities, densities, extinction to the embedded energy sources, and ultimately the star-formation and accretion rates in these galaxies. Ultimately, the higher spatial resolution provided by a cold, far-infrared submillimeter interferometer is needed to view the distribution of structure in galaxies in order to unravel the as yet untold story of the evolution of galaxies over the lifetime of the Universe.

Fischer, Jacqueline↗

NASA NTRS2011

Polymer Electrolyte-Based Ambient Temperature Oxygen Microsensors for Environmental Monitoring

An ambient temperature oxygen microsensor, based on a Nafion polymer electrolyte, has been developed and was microfabricated using thin-film technologies. A challenge in the operation of Nafion-based sensor systems is that the conductivity of Nafion film depends on the humidity in the film. Nafion film loses conductivity when the moisture content in the film is too low, which can affect sensor operation. The advancement here is the identification of a method to retain the operation of the Nafion films in lower humidity environments. Certain salts can hold water molecules in the Nafion film structure at room temperature. By mixing salts with the Nafion solution, water molecules can be homogeneously distributed in the Nafion film increasing the film s hydration to prevent Nafion film from being dried out in low-humidity environment. The presence of organics provides extra sites in the Nafion film to promote proton (H+) mobility and thus improving Nafion film conductivity and sensor performance. The fabrication of ambient temperature oxygen microsensors includes depositing basic electrodes using noble metals, and metal oxides layer on one of the electrode as a reference electrode. The use of noble metals for electrodes is due to their strong catalytic properties for oxygen reduction. A conducting polymer Nafion, doped with water-retaining components and extra sites facilitating proton movement, was used as the electrolyte material, making the design adequate for low humidity environment applications. The Nafion solution was coated on the electrodes and air-dried. The sensor operates at room temperature in potentiometric mode, which measures voltage differences between working and reference electrodes in different gases. Repeat able responses to 21-percent oxygen in nitrogen were achieved using nitrogen as a baseline gas. Detection of oxygen from 7 to 21 percent has also been demonstrated. The room-temperature oxygen micro sensor developed has extremely low power consumption (no heating for operation, no voltage applied to the sensor, only a voltmeter is needed to measure the output), is small in size, is simple to batch-fabricate, and is high in sensor yield. It is applicable in a wide humidity range, with improved operation in low humidity after the additives were added to the Nafion film. Through further improvement and development, the sensor can be used for aerospace applications such as fuel leak detection, fire detection, and environmental monitoring.

Hunter, Gary W.↗

DOE OSTI2021

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry

Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗