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At least 397 records · Page 22

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancement of Rydberg Blockade via Microwave Dressing

Experimental control over the strength and angular dependence of interactions between atoms is a key capability for advancing quantum technologies. Here, in this work, we use microwave dressing to manipulate and enhance Rydberg-Rydberg interactions in an atomic ensemble. By varying the cloud length relative to the blockade radius and measuring the statistics of the light retrieved from the ensemble, we demonstrate a clear enhancement of the interaction strength due to microwave dressing. These results are successfully captured by a theoretical model that accounts for the excitation dynamics, atomic density distribution, and phase-matched retrieval efficiency. Our approach offers a versatile platform for further engineering interactions by exploiting additional features of the microwave fields, such as polarization and detuning, opening pathways for new quantum control strategies.

collective effects in quantum optics↗

Selected Uses of TSUNAMI in Critical Experiment Design and Analysis

Validation in criticality safety is performed by comparing the results of critical experiments with the calculated results from models of the experiments using the computational method to be validated. Laboratory critical experiments are controlled systems that achieve a k eff of approximately 1 and enable investigation of the parameters at which such a critical condition is achieved. For the critical experiments used in a validation to capture the biases of the materials and neutron energy spectra of interest, those materials must be included in the experiment such that they influence k eff or another observable parameter with statistical significance. This paper discusses the use of sensitivity uncertainty (S/U) methods to develop critical experiments for various purposes. S/U techniques are useful for understanding the underlying components of nuclear data which affect the k eff or another parameter of a given configuration. S/U calculations are most commonly used to compare existing experiments to applications of interest; however, S/U techniques can also be used to identify, optimize, or assess features of proposed experiments so that they can better test specific portions of nuclear data or match an application of interest. The S/U techniques discussed here are from the TSUNAMI code system. The two primary codes discussed in this work are TSUNAMI-3D, which implements the KENO criticality code to calculate the sensitivity of k eff to nuclear data, and TSAR, which calculates the sensitivity of a reactivity difference between two configurations based on their TSUNAMI-3D generated sensitivity profiles. The methods used in these tools are discussed in more detail in the SCALE manual. This paper is one of a series on the development and use of TSUNAMI tools. The other papers address development of TSUNAMI methods and a review of TSUNAMI applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optical properties of carbonaceous chondrites and their relationship to asteroids

Results of diffuse reflectance measurements of nine samples of carbonaceous chondrites (one C1, three C2, four C3, and one C4) and one iron meteorite, Odessa. Measurements were also made of mineral mixtures in an attempt to understand the cause of some features of the meteorite reflectances. The C1 and C2 carbonaceous chondrites have reflectances low enough to match the anomalously low albedos of some asteroids. Some asteroids have spectral reflectances similar to carbonaceous chondrites, whereas others with flat or F-type curves appear to match simulated mineral mixtures with slightly greater amounts of the carbonaceous component than those found in the meteorites. This observation suggests either that surface physical processes such as melting may be enhancing the optical effect of opaque carbonaceous material on some asteroid surfaces and/or that these asteroids contain even more carbonaceous material than the C1 meteorites.

Johnson, T. V.↗

A simulation survey of galaxy interactions

Many carefully selected samples of interacting galaxies have been observed extensively in attempts to clarify whether interaction produces activity in galaxies. Because the sample members represent a wide range of encounter parameters and times, one can then study whether there are correlations between observable encounter features and, for example, Seyfert activity. On the other hand, in theoretical studies, simulations typically deal with either time-consuming detailed modelling of single galaxy pairs or tracing a few model encounters over time. The authors extend the observational survey approach by combining it with a simulation survey. The authors are conducting a survey of model encounters, covering the most important encounter parameters over a wide range. Some parameters, such as companion structure and initial velocity, are demonstratably less important and can be ignored in a first pass. The parameter range must be richly enough sampled so that the authors can evaluate the uniqueness of the observable morphology and velocity structure of the resulting simulated pairs to diagnose unobservable companion orbit parameters. They are using a self-gravitating polar n-body code run on the Cray X-MP at the Alabama Supercomputer Network. For each simulation, the authors have stellar and gas distributions predicted over, typically, a billion years, along with information on gas motions within the disk and any material captured by the companion or lost to the system. Features of disturbed spiral galaxies are sensitive enough to time and encounter parameters so that a match of the simulation survey results to observations can be applied as starting points to infer unobservable orbital or system parameters in actual sample members. This should enable them to examine whether interesting observed properties (Seyfert activity, nuclear star-formation rate) are functions of unobservable dynamical properties which characterize each encounter. Any correlations (or lack of some expected ones) will provide strong clues as to how or whether these phenomena are related to interactions. Aside from its use with such observed samples, this survey should greatly speed determination of initial orbital parameters for more detailed subsequent simulations of individual systems.

Byrd, Gene G.↗

C Language Integrated Production System, Ada Version

CLIPS/Ada provides capabilities of CLIPS v4.3 but uses Ada as source language for CLIPS executable code. Implements forward-chaining rule-based language. Program contains inference engine and language syntax providing framework for construction of expert-system program. Also includes features for debugging application program. Based on Rete algorithm which provides efficient method for performing repeated matching of patterns. Written in Ada.

Culbert, Chris↗

Traveling-Wave Maser for 32 GHz

The figure depicts a traveling-wave ruby maser that has been designed (though not yet implemented in hardware) to serve as a low-noise amplifier for reception of weak radio signals in the frequency band of 31.8 to 32.3 GHz. The design offers significant improvements over previous designs of 32-GHz traveling-wave masers. In addition, relative to prior designs of 32-GHz amplifiers based on high-electron-mobility transistors, this design affords higher immunity to radio-frequency interference and lower equivalent input noise temperature. In addition to the basic frequency-band and low-noise requirements, the initial design problem included a requirement for capability of operation in a closed-cycle helium refrigerator at a temperature .4 K and a requirement that the design be mechanically simplified, relative to prior designs, in order to minimize the cost of fabrication and assembly. Previous attempts to build 32- GHz traveling-wave masers involved the use of metallic slow-wave structures comprising coupled transverse electromagnetic (TEM)-mode resonators that were subject to very tight tolerances and, hence, were expensive to fabricate and assemble. Impedance matching for coupling signals into and out of these earlier masers was very difficult. A key feature of the design is a slow-wave structure, the metallic portions of which would be mechanically relatively simple in that, unlike in prior slow-wave structures, there would be no internal metal steps, irises, or posts. The metallic portions of the slow-wave structure would consist only of two rectangular metal waveguide arms. The arms would contain sections filled with the active material (ruby) alternating with evanescent-wave sections. This structure would be transparent in both the signal-frequency band (the aforementioned range of 31.8 to 32.3 GHz) and the pump-frequency band (65.75 to 66.75 GHz), and would impose large slowing factors in both frequency bands. Resonant ferrite isolators would be placed in the evanescent-wave sections to provide reverse loss needed to suppress reverse propagation of power at the signal frequency. This design is expected to afford a large gain-bandwidth product at the signal frequency and efficient coupling of the pump power into the paramagnetic spin resonances of the ruby sections. The more efficiently the pump power could be thus coupled, the more efficiently it could be utilized and the heat load on the refrigerator correspondingly reduced.

Shell, James↗

Measurement of $\nu_\mu$ CC Interactions With Two-Proton Final State in MINERvA

This dissertation presents a measurement of charged–current (CC) muon–neutrino interactions with exactly two protons and no pions in the final state (CC~$2p\,0\pi$), using data collected by the MINERvA detector in the NuMI medium–energy beam at Fermilab. Such two–proton topologies are a sensitive probe of nuclear dynamics in the few–GeV regime, including multi–nucleon correlations (npnh, notably $2p2h$) and intranuclear final–state interactions (FSI) such as pion absorption and nucleon rescattering. A precise experimental characterization of these processes is essential both for neutrino–interaction theory and for reducing systematic uncertainties in oscillation experiments that rely on accurate modeling of neutrino–nucleus interactions. Events are selected by requiring a $\nu_\mu$ CC interaction with a reconstructed $\mu^-$ and two proton tracks originating from a common vertex in MINERvA’s finely segmented scintillator tracker, with no reconstructed mesons. Muon charge and momentum are constrained by matching to the MINOS Near Detector, while proton identification exploits energy–loss profiles and stopping–proton features. Backgrounds from pion–producing channels that enter the signal region through FSI or reconstruction effects are constrained with data–driven sidebands (Michel–electron and isolated–cluster “blob” samples) and tuned via a simultaneous fit across signal and sideband regions. To correct detector resolution and acceptance effects, the analysis employs iterative Bayesian unfolding with extensive validation: statistical pseudo–experiments, and robustness checks against generator systematic “universes” and additional strong shape warps. Single–differential cross sections are reported for three observables tailored to the two–proton final state: the opening–angle cosine $\cos\!\left(\theta_{pp}\right)$, the leading–proton momentum, and the subleading–proton momentum. Systematic uncertainties include contributions from neutrino flux, interaction modeling (e.g., npnh and resonance parameters, pion FSI), and detector response (calibration, reconstruction efficiencies). The resulting distributions provide targeted constraints on the interplay of multi–nucleon dynamics and FSI that shape CC~$2p\,0\pi$ final states on hydrocarbon. Comparisons to modern GENIE–based simulations highlight kinematic regions where model components require refinement. These measurements thus inform generator tuning and improve the reliability of neutrino–energy reconstruction strategies for current and future long–baseline oscillation programs.

Syrotenko, Vladyslav S. [Tufts U.]↗

Improved technique for localizing electropolishing features novel nozzles

Impingement electropolishing is accomplished by use of an electrolyte film, which is evenly distributed by an insulated nozzle designed to match the contour of the workpiece to be treated. The workpiece is connected to the positive terminal of a generator and the nozzle to the negative terminal.

Source record↗

Optical Properties of Multi-Layered Insulation

Multi-layer insulation, MLI, is a material used on rocket bodies and satellites mainly for thermal insulation. MLI can be comprised of a variety of materials, layer numbers, and dimensions based on its purpose. A common composition of MLI consists of outer facing copper-colored Kapton with an aluminized backing for the top and bottom layers and the middle consisting of alternating layers of DARCON or Nomex netting with aluminized Mylar. If this material became separated from the spacecraft or rocket body its orbit would vary greatly in eccentricity due to its high area to mass (A/m) and susceptibility to solar radiation pressure perturbations. Recently a debris population was found with high A/m, which could be MLI. Laboratory photometric measurements of one intact piece and three different layers of MLI is presented in an effort to predict the characteristics of a MLI light curve and aid in identifying the source of the new population. For this paper, the layers used will be consistent with the common MLI mentioned in the above paragraph. Using a robotic arm, the piece was rotated from 0-360 degrees in one degree increments along the object s longest axis. Laboratory photometric data was recorded with a CCD camera using various filters (Johnson B, Johnson V and Bessell R). The measurements were taken at an 18 degree (light-object-camera) phase angle. As expected, the MLI pieces showed characteristics similar to a bimodal magnitude plot of a flat plate, but with more photometric features, dependant upon the layer of MLI. Time exposures varied from piece to piece such that the amount of pixels saturated would be minimal. In addition to photometric laboratory measurements, laboratory spectral measurements are shown for the same MLI samples. Spectral data will be combined to match the wavelength region of photometric data so a measure of truth can be established for the photometric measurements. Spectral data shows a strong absorption feature near 4800 angstroms, which is due to the copper color of Kapton. If the debris is MLI and the outer layer of copper coloring of Kapton is present, evidence would be seen spectrally by the specific absorption feature as well as using R-B (red-blue) light curves. Using laboratory photometric measurements and the results from spectral laboratory measurements, an optical property database is provided for an object with a high A/m. The benefits of this database for remote optical measurements of orbital debris are shown by illustrating the optical properties expected for a high A/m object, specifically common satellite and rocket body MLI.

Rodriguez, Heather M.↗

Extraction of Dry Leaf Spectral Features from Reflectance Spectra of Green Vegetation

Reflectance spectra of green vegetation in the 1.4-2.5 micrometer region are dominated by liquid water absorptions. In this article, we describe the analysis of a set of reflectance spectra of green vegetation, dry vegetation, and liquid water measured in a laboratory using a nonlinear least squares spectral matching technique. We conclude that both the liquid water and the dry materials contribute to the reflectance spectra of green vegetation in the 1.0-2.5 micrometer region. Our matching of data acquired with the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over two vegetated areas in Oregon Transect with a pure water spectrum also shows a residual absorption feature near 1.72 micrometers.

Gao, Bo-Cai↗

Optimization of WAAM Process to Produce AUSC Components with Increased Service Life

Additive manufacturing has the potential to revolutionize industrial hardware and unlock efficiency gains through the fabrication of geometries and architectures not possible by conventional processing. Wire Arc Additive manufacturing (WAAM) process is a class of directed energy deposition process enabling higher build rate and allowing custom wire feedstock allowing spatial variation of microstructure. The larger spot size and lower speed creates a larger melt pool, reducing residual stress and often time creating directional/columnar microstructure for Ni-superalloy. The use of flexible platform provides freedom in deposition strategy, which can accommodate complex substrates, including feature addition onto existing structures, non-flat layers, and repair methods. However, the certification of the final component needs to match the strength requirement. Hence, the quality of the component produced is stringently monitored to avoid buildup of residual stress, cracks, porosity and to reduce detrimental segregated phases commonly observed during alloy solidification. Simulation plays a huge role in predicting the melt pool dimension and can be used to optimize the process parameter. Similar development is also required to perform physics-based modeling of microstructural development in WAAM that can predict the microstructural features during solidification and can be used to optimize the process more effectively. To move toward this goal, Raytheon Technologies Research Center together with Siemens worked to create a set of computational tools to control the process parameters, enable on-line measurements and acquisition with feedback to the optimized process parameters, and eventually track material evolution through each step of the additive process. Computational fluid dynamics is used for accurate prediction and calibration of the thermal field during WAAM process. and phase field models for microstructure evolution as a function of processing parameters to establish a connection between additive parameters and the final microstructure. Here we report cellular automata (CA) model development to predict the dendritic microstructure evolution with surface and bulk nuclei for single track and multiple layers. The CA model was developed to account for secondary element addition and predict segregation, local melting, and latent heat release as well as prediction of Euler angles from orientation information and validated against experiments. This framework was utilized to tailor spatially-varying composition in a part by appropriately controlling the microstructure evolution during the additive process. Functionally graded Haynes 282 alloy with high Cr content at the surface was tested for oxidation and mechanical properties. An advanced physics-based reaction-diffusion model predicting the simultaneous creation of chromium oxide and alumina is developed and validated to extend life expectancy of the WAAM manufactured high temperature part. A machine-learning data-driven framework establishing the process-structure relationship from a dataset of real microstructure images and corresponding process history data has been developed and implemented in the NX Siemens design system. The digital twin configuration along with the tool path generation enabled prediction of WAAM component buildup time and the techno-economic analysis provided a favorable option for all 4 cases with 15-40% cost reduction.

33 ADVANCED PROPULSION SYSTEMS↗

Neptune Long-Lived Atmospheric Features in 2013 - 2015 from Small (28-cm) to Large (10-m) Telescopes

Since 2013, observations of Neptune with small telescopes (28-50 cm) have resulted in several detections of long-lived bright atmospheric features that have also been observed by large telescopes such as Keck II or Hubble. The combination of both types of images allows the study of the long-term evolution of major cloud systems in the planet. In 2013 and 2014 two bright features were present on the planet at southern mid-latitudes. These may have merged in late 2014, possibly leading to the formation of a single bright feature observed during 2015 at the same latitude. This cloud system was first observed in January 2015 and nearly continuously from July to December 2015 in observations with telescopes in the 2-10-m class and in images from amateur astronomers. These images show the bright spot as a compact feature at −40.1 +/- 1.6 deg planetographic latitude well resolved from a nearby bright zonal band that extended from −42 deg to −20 deg. The size of this system depends on wavelength and varies from a longitudinal extension of 8000 +/- 900 km and latitudinal extension of 6500 +/- 900 km in Keck II images in H and Ks bands to 5100 +/- 1400 km in longitude and 4500 +/- 1400 km in latitude in HST images in 657 nm. Over July to September 2015 the structure drifted westward in longitude at a rate of 24.48 +/- 0.03 deg/day or −94 +/- 3 m/s. This is about 30 m/s slower than the zonal winds measured at the time of the Voyager 2 flyby. Tracking its motion from July to November 2015 suggests a longitudinal oscillation of 16 deg in amplitude with a 90-day period, typical of dark spots on Neptune and similar to the Great Red Spot oscillation in Jupiter. The limited time covered by high-resolution observations only covers one full oscillation and other interpretations of the changing motions could be possible. HST images in September 2015 show the presence of a dark spot at short wavelengths located in the southern flank (planetographic latitude −47.0 deg) of the bright compact cloud observed throughout 2015. The drift rate of the bright cloud and dark spot translates to a zonal speed of −87.0 +/- 2.0 m/s, which matches the Voyager 2 zonal speeds at the latitude of the dark spot. Identification of a few other features in 2015 enabled the extraction of some limited wind information over this period. This work demonstrates the need of frequently monitoring Neptune to understand its atmospheric dynamics and shows excellent opportunities for professional and amateur collaborations.

dynamics↗

Longitudinal-mode control in integrated semiconductor laser phased arrays by phase velocity matching

The spectrum of semiconductor-laser arrays with separate contacts is investigated. It is demonstrated that the individual laser currents can be selected such that the array operates in a single longitudinal mode, in contrast to the multimode nature of its individual constituents. Moreover, it is possible to tune the lasing frequency by varying the laser currents. Wavelength tuning range of about 50 A, with tuning rate of about 5 A per milliampere, is demonstrated. It is suggested that these spectral features, characteristic of lasers which are coupled in parallel, result from the strong frequency dependence of their spatial mode pattern near the phase-matching frequency of their coupled waveguides.

Kapon, E.↗

Applying Configurational Complexity to the 2D Ruddlesden–Popper Crystal Structure

The layered Ruddlesden–Popper crystal structure can host a broad range of functionally important behaviors. In this work, we establish extraordinary configurational disorder in a layered Ruddlesden–Popper (RP) structure using entropy stabilization assisted synthesis. A protype A 2 CuO 4 RP cuprate oxide with five cations on the A-site sublattice is designed and fabricated into epitaxial single crystal films using pulsed laser deposition. When grown on a near lattice matched substrate, the (La 0.2 Pr 0.2 Nd 0.2 Sm 0.2 Eu 0.2 ) 2 CuO 4 film features a T'-type RP structure with uniform A-site cation mixing and square-planar CuO4 units. These observations are made with a range of combined characterizations using X-ray diffraction, atomic-resolution scanning transmission electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray absorption spectroscopy measurements. It is further found that heteroepitaxial strain plays an important role in crystal phase formation during synthesis. Compressive strain over ~1.5% results in the formation of a non-RP cubic phase consistent with a Cu X 2O 4 spinel structure. The ability to manipulate configurational complexity and move between 2D layered RP and 3D cubic crystal structures in cuprate and related materials promises to enable flexible design strategies for a range of functionalities, such as magnetoresistance, unconventional superconductivity, ferroelectricity, catalysis, and ion transport.

36 MATERIALS SCIENCE↗

Unconventional surface state pairs in a high-symmetry lattice with anti-ferromagnetic band-folding

Many complex magnetic structures in a high-symmetry lattice can arise from a superposition of well-defined magnetic wave vectors. These “multi-q” structures have garnered much attention because of interesting real-space spin textures such as skyrmions. However, the role multi-q structures play in the topology of electronic bands in momentum space has remained rather elusive. Here we show that the type-I anti-ferromagnetic 1q, 2q and 3q structures in an face-centered cubic sublattice with band inversion, such as NdBi, can induce unconventional surface state pairs inside the band-folding hybridization bulk gap. Our density functional theory calculations match well with the recent experimental observation of unconventional surface states with hole Fermi arc-like features and electron pockets below the Neel temperature. We further show that these multi-q structures have Dirac and Weyl nodes. Our work reveals the special role that band-folding from anti-ferromagnetism and multi-q structures can play in developing new types of surface states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Heterogeneous data-processing optimization with CLARA’s adaptive workflow orchestrator

The hardware landscape used in HEP and NP is changing from homogeneous multi-core systems towards heterogeneous systems with many different computing units, each with their own characteristics. To achieve maximum performance with data processing, the main challenge is to place the right computing on the right hardware. In this paper, we discuss CLAS12 charge particle tracking workflow orchestration that allows us to utilize both CPU and GPU to improve the performance. The tracking application algorithm was decomposed into micro-services that are deployed on CPU and GPU processing units, where the best features of both are intelligently combined to achieve maximum performance. In this heterogeneous environment, CLARA aims to match the requirements of each micro-service to the strength of a CPU or a GPU architecture. A predefined execution of a micro-service on a CPU or a GPU may not be the most optimal solution due to the streaming data-quantum size and the data-quantum transfer latency between CPU and GPU. So, the CLARA workflow orchestrator is designed to dynamically assign micro-service execution to a CPU or a GPU, based on the online benchmark results analyzed for a period of real-time data-processing.

Gyurjyan, Vardan↗