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At least 631 records · Page 35

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↗

National Opacity Program: Analysis of Opacity-relevant X-ray Emission Spectra (Milestone Report ID 7121)

We have produced high energy density iron plasmas at temperatures above 1 keV and electron densities exceeding 1023 cm -3 (~ 1 g/cm 3 ) using the Orion laser at the Atomic Weapons Establishment. These plasmas were created by irradiating 50 µm diameter layered targets with frequency doubled (λ = 527 nm), 1 ps laser pulses focused to a 100 µm diameter producing an irradiance of ~ 2 x 10 18 W/cm 2 . The buried layer targets consist of 160 nm iron sulfide (FeS), 60 nm potassium chloride (KCl), and 15 nm carbon. The combined layers are tamped on both sides with 3 µm of parylene-N. The x-ray emission from the plasma was measured using two time-resolved, and four time-integrated Bragg crystal spectrometers, as well as one time-integrated imaging system. One time-resolved x-ray spectrometer measured emission from L-shell transitions in highly charged iron, the other from K-shell transitions in helium-like S 14+ and hydrogen-like S 15+ . The time-integrated spectrometers are intensity-calibrated and measured emission from K-shell transitions in sulfur, potassium, chlorine, and both K-shell and L-shell transitions in iron. The density and temperature of the plasma were determined by modeling the x-ray spectra using different spectral and hydrodynamic modeling packages. A brief overview of the uncertainties associated with the measurements and models are presented. We also give an overview of our 1-D HYDRA-DCA radiation-hydrodynamics model and improvements for future work. Our results aid in assessing experimental uncertainties associated with plasma uniformity and with x-ray emission employed as diagnostics in opacity experiments at temperatures and densities not achievable elsewhere and represent a significant step in creating and diagnosing plasmas near LTE. These results are summarized as part of the completion requirements for milestone 7121

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electron-Beam-Induced Molecular Plasmon Excitation and Energy Transfer in Silver Molecular Nanowires

In this work, we investigate (1) electron-beam-induced plasmon absorption spectra of Ag molecular nanowire dimers and (2) electron-beam-induced energy transfer between two nanowires. We employ linear-response time-dependent density functional theory (TDDFT) and real-time TDDFT methods to simulate the electron-beam-induced plasmonic excitations, dynamics, and corresponding electron energy loss spectrum for small models of a single molecular nanowire with four Ag atoms and for two Ag nanowires. An array of different relative orientations of nanowires and of different initial excitation conditions resulting from applying an electron beam at different positions with respect to the Ag nanowires is investigated. The results demonstrate (1) an electron beam can induce plasmonic excitations from the molecular Ag nanowire ground state to the excited states that are both optically allowed and forbidden, (2) a tunability for selective excitations that can be controlled by the position of a focused electron beam, and (3) kinetic and dynamic behaviors of time-dependent electron-beam-induced energy transfer between two Ag molecular nanowires depend on the position of the beam source and nanowire separation distance, providing insights into the spatial dependences of plasmonic couplings in nanowire arrays.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multimessengers from the Radioactive Decay of r -process Nuclei

The radioactive β-decay of nuclei synthesized in the rapid neutron capture process (r-process) releases a variety of particles, including electrons, γ-rays, neutrinos, and neutrons. These particles provide a rich set of multimessenger signals that carry information about the astrophysical environments where neutron-rich nucleosynthesis occurs. In this work, we calculate from first principles the emission spectra resulting from the β-decay of r-process nuclei. Our approach incorporates detailed nuclear structure and decay data to model the energy distributions of each particle species. We couple the spectra with a nuclear reaction network simulation to obtain the temporal evolution of these distributions. We find that the emission distributions vary significantly in time and are nonthermal, with substantial average energies. We investigate these nuclear signals as a direct probe of heavy element formation and show that they are complementary observables to kilonova.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Molybdenum and silver photoemission survey spectra from hard x-rays

Electron emission from thick polished samples of polycrystalline molybdenum (Mo) and single crystalline $\langle$111$\rangle$ silver (Ag) was measured with hard x-ray photoemission spectroscopy. Six different excitation x-ray energies were used, nominally 8.0, 11.0, 13.0, 15.0, 18.0, and 21.5 keV. Survey spectra were recorded with each excitation to a kinetic energy of at most 15 keV, often capturing the entire emission range. The Mo 1s core peak was measured. Detailed LMM Auger spectra of Mo show marked increases in intensity and altered shape when x-ray energy exceeds the Mo 1s binding energy. The Mo and Ag L-shell photoelectron peaks are measured at four x-ray energies up to 18 keV showing the transition from 2p3/2 to 2s photoionization dominance.

47 OTHER INSTRUMENTATION↗

FRAM Isotopic Analysis of High-Resolution CZT Data

H3D Inc. has introduced a new type of CZT detectors that has resolution several times better than that of a typical, single crystal CZT detector. The better resolution has made it easier for software codes to analyze its spectra for isotopic composition of nuclear materials. The Fixed-energy Response-function Analysis with multiple efficiency (FRAM) is one of such software codes. The good peak resolution of the H3D CZT detectors allows the current FRAM v.6.1 and earlier to successfully analyze uranium spectra with minimal modification of the parameter sets and get reasonable results. (A parameter set governs how an analysis is performed.) The exceptionally large high-energy tail of the peaks makes it difficult to achieve good uranium results and impossible to successfully analyze plutonium spectra. The FRAM code needed to be modified to better fit the high-energy tail of the peaks in order to analyze plutonium data and to get better uranium analysis results. Results of this modification, encoded in beta version FRAM v.7.0i, are reported herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effects of dissipative baryon current in heavy-ion collisions at RHIC-BES energies

The CLVisc (3+1)D viscous hydrodynamic model is extended to include the equation of net baryon conservation and the Israel-Stewart-like equations for dissipative baryon current. Using the NEOSB equation of state, we simulate the dynamical evolution and collectivity of the quark-gluon plasma with finite chemical potential, assuming smooth energy density and net baryon density distributions at the initial proper time. Numerical results are shown for the impact of net-baryon dissipation on particle yields and p T spectra in heavy-ion collisions at beam energy scan energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Evidence for anti-synergism between ion-assisted etching and in-plasma photoassisted etching of silicon in a high-density chlorine plasma

Etching of p-Si in 60 mTorr 10%Cl2/90%Ar Faraday-shielded inductively coupled high density plasmas was investigated under both ionassisted etching (IAE) and photoassisted etching (PAE) conditions. Real-time etching rates and after-etching Si surface chemical compositions were obtained by laser interferometry and vacuum-transfer x-ray photoelectron spectroscopy (XPS), respectively. Precisely controlled ion energy distributions (IEDs) were generated by applying pulsed negative DC bias on the conductive sample stage. Above a 36 eV threshold at a total flow rate of 250 SCCM, the IAE rate increased with the square root of the ion energy. In contrast to the DC bias, etching under RF bias did not exhibit a threshold ion energy because of the wide IED. XPS spectra revealed that the surface layer under PAE conditions had a significantly lower chlorine content, composed of only SiCl. Under IAE conditions, however, silicon dangling bonds (Si•), SiCl 2 , and SiCl 3 were found on the surface, in addition to SiCl, with a relative abundance of SiCl > SiCl 2 , and SiCl 3 . The absence of higher chlorides and Si• under PAE conditions suggested that vacuum ultraviolet photons and above threshold-energy ions interact with the surface very differently. By varying the duty cycle of the pulsed DC bias, it was found that the IAE rate scaled with the energetic ion dose, but only for low duty cycles. For higher duty cycles, the apparent IAE yield fell off with an increasing Cl coverage on the surface, as the duty cycle went up, which pointed to a negative synergy (antisynergism) between PAE and IAE as the explanation. This antisynergism was further supported by the observed decrease of the total etching rate with an increasing period of the pulsed DC bias. A plausible mechanism is that increasing the pulsing period causes more near-surface damage, creating more recombination centers that lead to a higher loss rate of electron-hole pairs through recombination, thereby reducing the PAE rate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Understanding 2p core-level excitons of late transition metals by analysis of mixed-valence copper in a metal–organic framework

The L 2,3 -edge X-ray absorption spectra of late transition metals such as Cu, Ag, and Au exhibit absorption onsets lower in energy for higher oxidation states, which is at odds with the measured spectra of earlier transition metals. Time-dependent density functional theory calculations for Cu 2+ /Cu + reveal a larger 2p core-exciton binding energy for Cu 2+ , overshadowing shifts in single-particle excitation energies with respect to Cu + . Finally, we explore this phenomenon in a Cu + metal–organic framework with ~12% Cu 2+ defects and find that corrections with self-consistent excited-state total energy differences provide accurate XAS peak alignment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An improved methodology for modeling short pulse buried layer x-ray emission spectra

Radiation-hydrodynamic and spectroscopic modeling are important aspects of high energy density experimental design. In this paper, we improve the performance and capabilities over those obtainable with a previous methodology used for simulating x-ray emission spectra from buried layer targets heated by short pulse lasers. The improvement incorporates post-processing HYDRA radiation-hydrodynamic output with a non-local thermodynamic equilibrium atomic-kinetics radiation transport code, Cretin. Each code uses an independent radiation field which allows decoupling HYDRA's radiation group structure from Cretin's spectral output to improve the speed and flexibility of the design methodology. The execution time decreases from 2–3 days to a few hours while the flexibility of the improved methodology allows for performing sensitivity studies including a comparison of steady-state and time-dependent atomic kinetics and differences in the radiation group structure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

X-Ray Spectra and Multiwavelength Machine Learning Classification for Likely Counterparts to Fermi 3FGL Unassociated Sources

We conduct X-ray spectral fits on 184 likely counterparts to Fermi-LAT 3FGL unassociated sources. Characterization and classification of these sources allows for more complete population studies of the high-energy sky. Most of these X-ray spectra are well fit by an absorbed power-law model, as expected for a population dominated by blazars and pulsars. A small subset of seven X-ray sources have spectra unlike the power law expected from a blazar or pulsar and may be linked to coincident stars or background emission. We develop a multiwavelength machine learning classifier to categorize unassociated sources into pulsars and blazars using gamma-ray and X-ray observations. Training a random forest (RF) procedure with known pulsars and blazars, we achieve a cross-validated classification accuracy of 98.6%. Applying the RF routine to the unassociated sources returned 126 likely blazar candidates (defined as P {sub bzr} ≥ 90%) and five likely pulsar candidates (P {sub bzr} ≤ 10%). Our new X-ray spectral analysis does not drastically alter the RF classifications of these sources compared to previous works, but it builds a more robust classification scheme and highlights the importance of X-ray spectral fitting. Our procedure can be further expanded with UV, visual, or radio spectral parameters or by measuring flux variability.

79 ASTRONOMY AND ASTROPHYSICS↗

Learning Spectral Templates for Photometric Redshift Estimation from Broadband Photometry

Estimating redshifts from broadband photometry is often limited by how accurately we can map the colors of galaxies to an underlying spectral template. Current techniques utilize spectrophotometric samples of galaxies or spectra derived from spectral synthesis models. Both of these approaches have their limitations: either the sample sizes are small and often not representative of the diversity of galaxy colors, or the model colors can be biased (often as a function of wavelength), which introduces systematics in the derived redshifts. In this paper, we learn the underlying spectral energy distributions from an ensemble of ∼100 K galaxies with measured redshifts and colors. We show that we are able to reconstruct emission and absorption lines at a significantly higher resolution than the broadband filters used to measure the photometry for a sample of 20 spectral templates. We find that our training algorithm reduces the fraction of outliers in the derived photometric redshifts by up to 28%, bias up to 91%, and scatter up to 25%, when compared to estimates using a standard set of spectral templates. We discuss the current limitations of this approach and its applicability for recovering the underlying properties of galaxies. Our derived templates and the code used to produce these results are publicly available in a dedicated Github repository: https://github.com/dirac-institute/photoz-template-learning.

79 ASTRONOMY AND ASTROPHYSICS↗

Validation of the SCEPTRE Boltzmann-CSD Solver

A new Boltzmann-CSD solver has been developed within the SCEPTRE radiation-transport code, based on the 1st-order form of the transport equation, using discontinuous finite elements in space and energy and discrete ordinates in angle. The Boltzmann-CSD solver has been validated against experimental data for electron energy deposition distributions and for electron emission spectra. Comparison of the calculated results with experimental data shows excellent agreement for many of the test configurations and reasonable agreement for other test configurations. The tests have also been modeled with the ITS Monte Carlo code, which also shows excellent to reasonable agreement with the SCEPTRE results and experimental data. The SCEPTRE Boltzmann-CSD solver relies on electron cross sections generated by the legacy CEPXS code, which currently is limited to electron-only Boltzmann-CSD cross sections. Performing full electron-photon radiation transport with the Boltzmann-CSD solver will require further development in the cross section generating code. For the energy- deposition calculations, neglecting photon transport results in at most about 5% overprediction of the energy deposition for high-energy electrons on high-Z targets, and relatively insignificant difference for the other test configurations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Robustness of electronic screening effects in electron spectroscopies: Example of V 2 O 5

In bulk and low-dimensional extended systems, the screening of excitations by the electron cloud is a key feature governing spectroscopic properties. Widely used computational approaches, especially in the framework of many-body perturbation theory, such as the GW approximation and the resulting approximate Bethe-Salpeter equation, are explicitly formulated in terms of the screened Coulomb interaction. In the present work, we explore the effect of screening in absorption and electron energy loss spectroscopy, concentrating on the effect of local distortions on the screening and elucidating the resulting changes in the various spectra. Using the layered bulk oxide V 2 O 5 as prototype material, we show in which way local distortions affect the screening, and in which way changes in the screening impact electron energy loss and absorption spectra including excitons. We highlight cancellations that make many-body effects in the spectra very robust with respect to structural modifications, while the band structure undergoes significant changes and the nature of the excitations may also be affected. Here, this yields insight concerning the structure-properties relations that are crucial for the use of V 2 O 5 as energy storage material, and more generally, that may be used to optimize the analysis and the calculation of electronic spectra in complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Variable magnetic field electron spectrometer to measure hot electrons in the range of 50–460 keV

Resonance absorption (RA) occurs when a p-polarized electromagnetic wave, obliquely incident on an inhomogeneous plasma, tunnels past its turning point and resonantly excites an electron plasma wave (EPW) at the critical density. This phenomenon is important, for instance, in the direct drive approach to inertial fusion energy and is a particular example of a wider phenomenon in plasma physics known as mode conversion, which is crucial for heating magnetic fusion devices, such as tokamaks, via RF heating. Direct measurement of these RA-generated EPW accelerated hot electrons, with energy in the range of a few tens to a few hundreds of keV, is a challenging task due to the relatively low deflecting magnetic fields needed. The solution described here is a magnetic electron spectrometer (MES) with a continually changing magnetic field, lower at the entrance of the MES and gradually increasing toward the end, that enables the measurement of a wide spectral range of electrons with energies between 50 and 460 keV. Electron spectra taken in a LaserNetUS RA experiment were acquired from plasmas generated by irradiating polymer targets with the combination of an ~300 ps pulse followed by a series of ten high intensity 50–200 fs duration laser pulses from the ALEPH laser at Colorado State University. In conclusion, the high intensity beam is designed as spike trains of uneven duration and delay pulses in order to modify the RA phenomenon.

47 OTHER INSTRUMENTATION↗

Controlled Experiments and Optimized Theory of Absorption Spectra of Li Metal and Salts

Investigation of Li metal and ionic compounds through experimental and theoretical spectroscopy has been of tremendous interest due to their prospective applications in Li-metal and Li-ion batteries. Li K-edge soft X-ray absorption spectroscopy (sXAS) provides the most direct spectroscopic characterization; unfortunately, due to the low core-level energy and the highly reactive surface, Li-K sXAS of Li metal has been extremely challenging, as evidenced by many controversial reports. Here, through controlled and ultra-high energy resolution experiments of two kinds of in situ prepared samples, we report the intrinsic Li-K sXAS of Li-metal that displays a prominent leading peak that has not been revealed before. Furthermore, theoretical simulations show that, due to the low number of valence electrons in Li, the Li-K sXAS is strongly affected by the response of the valence electrons to the core hole. We successfully reproduce the Li-K sXAS by state-of-the-art calculations with considerations of a number of relevant parameters such as temperature, energy resolution, and, especially, contributions from transitions which are forbidden in the single-particle treatment. Such a comparative experimental and theoretical investigation is further extended to a series of Li ionic compounds, which highlight the importance of considering the total and single-particle energies for obtaining an accurate alignment of the spectra. Furthermore, our work provides the first reliable Li-K sXAS of the Li metal surface with advanced theoretical calculations. The experimental and theoretical results provide a critical benchmark for studying Li chemistry in both metallic and ionic states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Preliminary Design of a New Pulsed-Neutron Die--Away Experiments with Absorbers (IER-552 CED-1)

This report presents the preliminary design (CED-1) of IER-552, pulsed-neutron die-away (PNDA) experiments with absorbers, to be conducted by Lawrence Livermore National Laboratory (LLNL). The goal of the PNDA experiments with absorbing materials is to produce high-quality, low-cost integral benchmarks that can be used to validate cross sections that are high priority nuclear data for the Department of Energy’s Nuclear Criticality Safety Program (NCSP). PNDA experiments can be used to generate nuclear data validation benchmarks quickly and cheaply, as they do not require fissile material or a nuclear facility to conduct them. The original PNDA experiments were set up at LLNL under IER-501. Extending the PNDA experiments to include absorbing materials leverages existing facilities and resources at LLNL to validate cross sections, with a basic experiment design that uses a neutron generator to impinge a short, mono-energetic neutron pulse on a poisoned, moderating target sample. The neutron pulse lasts 100 µs, after which the neutron population in the sample reaches thermal equilibrium and later spatial equilibrium. In this fully equilibrized state, the neutron population has a characteristic decay-time eigenvalue. The eigenvalue can be used as an integral parameter to validate nuclear data involved with neutron scattering and absorption. Two observables can be measured: the neutron population and the population of secondary γ-rays produced by inelastic and capture reactions. This report explores the feasibility of both approaches. For γ-ray measurements, this allows for direct measurement of reactions of interest for validation. During the neutron burst time, inelastic (prompt) γ-rays dominate, and these data can be isolated for validation of neutron inelastic scattering data. After the pulse ends, neutron capture (delayed) γ-rays dominate and are produced by many reaction channels as neutrons slow down to thermal energies. Two sets of γ-ray spectra (inelastic, capture) can be produced for validation. Additionally, the time-dependent decay of the capture γ-ray population when the neutron population is thermalized and in its fundamental mode can be used for validation. Two experiments can be imagined where pulsed neutrons are used to validate the nuclear data of absorbing materials. The first integrates well into the existing PNDA testbed at LLNL. The absorber material would be introduced into a moderating target and the same neutron generator, neutron detectors, electronics, and shielding box used for IER-501 would be employed. From the same experimental setup, many absorbing materials can be validated by simply changing the neutron poison in the moderator. The only significant modification would be the introduction of a γ-ray detector. Such an experiment would primarily serve to validate nuclear data in the thermal energy range. The second kind of experiment would validate the fast and epithermal energy range. It would involve pulsing neutron into a bare assembly of the absorber material and measuring the die-away of neutrons. The fast leakage of such an assembly requires nanosecond neutron-generator pulse widths and fast detectors/electronics that could measure ~200 ns die-away curves. This kind of experiment would ideally be performed at a cyclotron, like that available at Lawrence Berkeley National Laboratory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗