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DOE OSTI2020

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Comparison of sleep parameters from wrist-worn ActiGraph and Actiwatch devices

Abstract Sleep and physical activity, two important health behaviors, are often studied independently using different accelerometer types and body locations. Understanding whether accelerometers designed for monitoring each behavior can provide similar sleep parameter estimates may help determine whether one device can be used to measure both behaviors. Three hundred and thirty one adults (70.7 ± 13.7 years) from the Baltimore Longitudinal Study of Aging wore the ActiGraph GT9X Link and the Actiwatch 2 simultaneously on the non-dominant wrist for 7.0 ± 1.6 nights. Total sleep time (TST), wake after sleep onset (WASO), sleep efficiency, number of wake bouts, mean wake bout length, and sleep fragmentation index (SFI) were extracted from ActiGraph using the Cole–Kripke algorithm and from Actiwatch using the software default algorithm. These parameters were compared using paired t-tests, Bland–Altman plots, and Deming regression models. Stratified analyses were performed by age, sex, and body mass index (BMI). Compared to the Actiwatch, the ActiGraph estimated comparable TST and sleep efficiency, but fewer wake bouts, longer WASO, longer wake bout length, and higher SFI (all p < .001). Both devices estimated similar 1-min and 1% differences between participants for TST and SFI (β = 0.99, 95% CI: 0.95, 1.03, and 0.91, 1.13, respectively), but not for other parameters. These differences varied by age, sex, and/or BMI. The ActiGraph and the Actiwatch provide comparable absolute and relative estimates of TST, but not other parameters. The discrepancies could result from device differences in movement collection and/or sleep scoring algorithms. Further comparison and calibration is required before these devices can be used interchangeably.

Liu, Fangyu (ORCID:0000000315541478)↗

DOE OSTI2021

New Approach Methodology for Assessing Inhalation Risks of a Contact Respiratory Cytotoxicant: Computational Fluid Dynamics-Based Aerosol Dosimetry Modeling for Cross-Species and In Vitro Comparisons

Regulatory agencies are considering alternative approaches to assessing inhalation toxicity that utilizes in vitro studies with human cells and in silico modeling in lieu of additional animal studies. In support of this goal, computational fluid-particle dynamics models were developed to estimate site-specific deposition of inhaled aerosols containing the fungicide, chlorothalonil, in the rat and human for comparisons to prior rat inhalation studies and new human in vitro studies. Under bioassay conditions, the deposition was predicted to be greatest at the front of the rat nose followed by the anterior transitional epithelium and larynx corresponding to regions most sensitive to local contact irritation and cytotoxicity. For humans, simulations of aerosol deposition covering potential occupational or residential exposures (1–50 µm diameter) were conducted using nasal and oral breathing. Aerosols in the 1–5 µm range readily penetrated the deep region of the human lung following both oral and nasal breathing. Under actual use conditions (aerosol formulations >10 µm), the majority of deposited doses were in the upper conducting airways. Beyond the nose or mouth, the greatest deposition in the pharynx, larynx, trachea, and bronchi was predicted for aerosols in the 10–20 µm size range. Only small amounts of aerosols >20 µm penetrated past the pharyngeal region. Using the ICRP clearance model, local retained tissue dose metrics including maximal concentrations and areas under the curve were calculated for each airway region following repeated occupational exposures. These results are directly comparable with benchmark doses from in vitro toxicity studies in human cells leading to estimated human equivalent concentrations that reduce the reliance on animals for risk assessments.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2026

Error quantification and comparison of binary neutron star gravitational waveforms from numerical relativity codes

Future gravitational wave detections of merging binary neutron star systems have the possibility to tightly constrain the equation of state of dense nuclear matter. In order to extract such constraints, gravitational waveform models need to be calibrated to accurate numerical relativity simulations of the late inspiral and merger. In this work, we take an essential step toward classifying the error and potential systematics in current generation numerical relativity simulations of merging binary neutron stars. To this end, we perform a direct comparison of two codes (fil, spec), which differ in many aspects, including the numerical methods and discretizations used and equations solved. We find that despite these different approaches, the codes are—within current numerical resolution bounds—fully consistent, and broadly comparable in cost for a given accuracy level. Our results indicate that the error in the waveforms is primarily dominated by the hydrodynamic evolution, consistent with earlier findings in the literature. Finally, we also discuss current limitations and cost estimates for numerical relativity simulations to reach the accuracies required in the era of next-generation gravitational detectors.

gravitational waves↗

DOE OSTI2026

Fault-tolerant resource comparison of qudit and qubit encodings for diagonal quadratic operators

Finite local Hilbert-space truncations arise naturally in quantum simulations of lattice field theories and motivate qudit encodings, but their fault-tolerant advantage over qubit encodings remains unclear. We compare the non-Clifford cost of implementing quadratic diagonal evolutions, exemplified by 𝑈 = 𝑒$^{−𝑖⁢𝑡⁢𝜙^2_𝑥}$ in a uniform field-amplitude discretization of a real scalar field, using either one logical 𝑑-level qudit or 𝑛 𝑏 = ⌈log 2⁡ 𝑑⌉ logical qubits. We analyze two standard settings: product-formula simulation and linear combination of unitaries (LCU) per block encoding, taking the resource metric to be the number of non-Clifford gates after synthesis into a discrete logical gate set. Because tight synthesis bounds for general single-qudit rotations are not known, we express the qudit constructions in terms of embedded two-level SU⁡(2) rotations and derive explicit finite-𝑑 break-even conditions for their synthesis cost; these serve as compiler targets for when qudit encodings can outperform the qubit baseline. Within the constructive models studied here, product-formula implementations would require an exponentially stronger per-primitive synthesis advantage for qudits to win asymptotically, while in the LCU setting the qubit encoding is asymptotically cheaper in 𝑑. Nevertheless, the finite-𝑑 threshold analysis identifies low-dimensional regions in which qudits can yield meaningful constant-factor savings, particularly for LCU-based implementations. As a secondary analysis of the LCU construction, we use an idealized negligible-overhead qubit-qudit code-switching model to give an absolute 𝑇-count comparison and reinterpret the savings as an allowable per-switch overhead budget.

Godwood, Samuel [Univ. of Liverpool (United Kingdo↗

DOE OSTI2023

Comparison of spontaneous emission in trapped-ion multiqubit gates at high magnetic fields

Penning traps have been used for performing quantum simulations and sensing with hundreds of ions and provide a promising route toward scaling up trapped ion quantum platforms because of the ability to trap and control hundreds or thousands of ions in two- and three-dimensional crystals. In both Penning traps and the more common RF Paul traps, lasers are often used to drive multi-qubit entangling operations. A leading source of decoherence in these operations is off resonant spontaneous emission. While many trapped ion quantum computers or simulators utilize clock qubits, other systems, especially those with high magnetic fields such as Penning traps, rely on Zeeman qubits, which require a more complex calculation of this decoherence. We therefore examine theoretically the impacts of spontaneous emission on quantum gates performed with trapped-ion ground state Zeeman qubits in a high magnetic field. In particular, we consider two types of gates—light-shift ($\hat{σ}^z_i$ $\hat{σ}^z_j$) gates and Mølmer-Sørensen ($\hat{σ}^x_i$ $\hat{σ}^x_j$) gates—obtained with laser beams directed approximately perpendicular to the magnetic field (the quantization axis) and compare the decoherence errors in each. Within each gate type, we also compare different operating points with regards to the detunings, polarizations, and required intensity of the laser beams used to drive the gates. Here, we show that both gates can have similar performance at their optimal operating conditions at high magnetic fields and examine the experimental feasibility of various operating points. By examining the magnetic field dependence of each gate, we demonstrate that, when the P state fine structure splitting is large compared to the Zeeman splittings, the theoretical performance of the Mølmer-Sørensen gate is significantly better than that of the light-shift gate. Additionally, for the light-shift gate, we make an approximate comparison between the fidelities that can be achieved at high fields with the fidelities of state-of-the-art two-qubit trapped ion quantum gates. We show that, with regards to spontaneous emission, the achievable fidelity of the current NIST configuration is about an order of magnitude below that of the best low-field gates, but we also discuss several alternative configurations with potential error rates that are comparable with those for state-of-the art trapped ion gates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Measurements of the time-dependent cosmic-ray Sun shadow with seven years of IceCube data: Comparison with the Solar cycle and magnetic field models

Observations of the time-dependent cosmic-ray Sun shadow have been proven as a valuable diagnostic for the assessment of solar magnetic field models. Here, seven years of IceCube data are compared to solar activity and solar magnetic field models. A quantitative comparison of solar magnetic field models with IceCube data on the event rate level is performed for the first time. Additionally, a first energy-dependent analysis is presented and compared to recent predictions. We use seven years of IceCube data for the moon and the Sun and compare them to simulations on data rate level. The simulations are performed for the geometrical shadow hypothesis for the moon and the Sun and for a cosmic-ray propagation model governed by the solar magnetic field for the case of the Sun. We find that a linearly decreasing relationship between Sun shadow strength and solar activity is preferred over a constant relationship at the 6.4σ level. We test two commonly used models of the coronal magnetic field, both combined with a Parker spiral, by modeling cosmic-ray propagation in the solar magnetic field. Both models predict a weakening of the shadow in times of high solar activity as it is also visible in the data. We find tensions with the data on the order of 3σ for both models, assuming only statistical uncertainties. The magnetic field model CSSS fits the data slightly better than the PFSS model. This is generally consistent with what is found previously by the Tibet AS-γ Experiment; a deviation of the data from the two models is, however, not significant at this point. Regarding the energy dependence of the Sun shadow, we find indications that the shadowing effect increases with energy during times of high solar activity, in agreement with theoretical predictions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Comparison of the static structure factor at long wavelengths for a dusty plasma liquid and other liquids

Especially small values of the static structure factor S(k) at long wavelengths, i.e., small k, were obtained in an analysis of experimental data, for a two-dimensional dusty plasma in its liquid state. For comparison, an analysis of S(k) data was carried out for many previously published experiments with other liquids. Here, the latter analysis indicates that the magnitude of S(k) at small k is typically in a range 0.02–0.13. In contrast, the corresponding value for a dusty plasma liquid was found to be as small as 0.0139. Another basic finding for the dusty plasma liquid is that S(k) at small k generally increases with temperature, with its lowest value, noted above, occurring near the melting point. Simulations were carried out for the dusty plasma liquid, and their results are generally consistent with the experiment. Since a dusty plasma has a soft interparticle interaction, our findings support earlier theoretical suggestions that a useful design strategy for creating materials having exceptionally low values of S(0), so-called hyperuniform materials, is the use of a condensed material composed of particles that interact softly at their periphery.

2-dimensional systems↗

DOE OSTI2020

Measurement of the Spectral Shape of the $β$-Decay of 137 Xe to the Ground State of 137 Cs in EXO-200 and Comparison with Theory

Herein we report on a comparison between the theoretically predicted and experimentally measured spectra of the first-forbidden nonunique $β$-decay transition 137 Xe ( 7/2 - ) → 137 Cs ( 7/2 + ) . The experimental data were acquired by the EXO-200 experiment during a deployment of an AmBe neutron source. The ultralow background environment of EXO-200, together with dedicated source deployment and analysis procedures, allowed for collection of a pure sample of the decays, with an estimated signal to background ratio of more than 99 to 1 in the energy range from 1075 to 4175 keV. In addition to providing a rare and accurate measurement of the first-forbidden nonunique $β$-decay shape, this work constitutes a novel test of the calculated electron spectral shapes in the context of the reactor antineutrino anomaly and spectral bump.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Design and Comparison of Surface Inset Permanent Magnet Machine and Surface Permanent Magnet Machine without Heavy Rare Earth Magnets for Traction Applications

This paper presents two machine designs: a surface inset permanent magnet (SIPM) machine and a surface permanent magnet (SPM) machine, both without heavy rare-earth magnets, that achieve 50 kW/L active power density and a constant-power speed ratio of 3 for EV traction applications. Compared to surface PM machines, SIPM machines do not require a special containment sleeve to hold the magnets in place at high speeds, provided that the rotor laminations are carefully designed together with the magnet mounting configuration to ensure the rotor’s structural integrity. Comparisons between the SPM and SIPM machines sharing the same stator, same current level, and same power speed envelope are presented. Both deliver very similar performance characteristics, but the SIPM machine’s simpler magnet containment configuration may give it an advantage in terms of reduced material and manufacturing costs.

42 ENGINEERING↗

DOE OSTI2026

Fidelity Comparison of Time-Bin and Fock State Encoding in Hybrid Quantum Systems Under Channel and Transduction Effects

Future quantum networks are expected to integrate a heterogeneous combination of quantum systems, owing to the diverse advantages offered by different physical platforms in terms of scalability, coherence times, and interfacing capabilities. Within the context of this emerging quantum communication paradigm, this paper presents an analytical comparison of two photonic encoding schemes—time-bin and Fock state (single rail)—in hybrid quantum systems where flying qubits are entangled with stationary matter qubits. We evaluate their resilience against fiber channel and quantum transduction effects by calculating the fidelity of the final states relative to their ideal forms. Employing the characteristic function approach, we derive analytical fidelity expressions and investigate their dependence on parameters such as transmissivity, noise levels, fiber length, and source generation success probability. Additionally, we simulate the scenario with a dedicated QuTiP software implementation to verify the validity of the theoretical models. Our findings reveal that due to its inherent single-mode structure, the Fock state encoding consistently outperforms time-bin encoding in fidelity, as this structure significantly minimizes susceptibility to losses compared to the two-mode nature of the time-bin scheme. This analysis offers valuable insights for future hybrid quantum communication and information processing applications.

Fiorini, Francesco [Pisa U.]↗

DOE OSTI2022

An Experiment-based Distribution Level Performance Comparison among PMUs

This paper presents a experiment-based distribution level performance comparison among three Phasor Measurement Units (PMUs). Several evaluation criteria, including the total vector error, the phase angle error, the frequency error, the rate of change of frequency, the response time, the settling time, the overshoot, and the algorithm window size, are selected to compare the static and dynamic performances of the PMUs under steady state and step response test conditions. In order to have a more realistic test environment, a test is setup in which PMUs under evaluation have exactly the same input signals. The quantitative experiment result analysis gives an end-user guideline to the PMU selection regarding distribution level applications.

Yin, He↗

DOE OSTI2019

Field-Aged Glass/Backsheet and Glass/Glass PV Modules: Encapsulant Degradation Comparison

Ethylene vinyl acetate (EVA) is the predominant encapsulant in crystalline-silicon photovoltaic (PV) modules; however, its degradation is a subject of major concern, which causes significant power loss under field conditions. This article presents a comparison of EVA degradation in field-aged PV modules with glass/backsheet (G/B) and glass/glass (G/G) architectures. Modulelevel characterization included UV fluorescence imaging and I-V measurements. Material analytical techniques, including colorimetry, differential scanning calorimetry, thermogravimetric analysis, Fourier transform infrared spectroscopy, and Raman spectroscopy, were performed to correlate the module performance parameters with EVA material properties. An intense EVA discoloration in G/G modules was observed, which was corroborated by higher module Isc and Pmax degradation rates compared with its counterpart G/B modules. Higher power degradation was accompanied by a significant increase in EVA crosslinking, vinyl acetate content, yellowness index, and presence of functional groups containing unsaturated moieties that are linked to degradation products of photothermal reaction, and a higher decrease in the degree of crystallinity. The absence of a polymeric backsheet in hermetically sealed G/G modules, which restricts photobleaching and enhances the entrapment of volatile acetic acid and other degradation by-products, plays a major role in causing higher EVA degradation in G/G modules. This article concludes that EVA might have been a good choice of an encapsulant for the G/B modules over the decades, but it may prove to be an inappropriate choice for the G/G modules because of potential degassing, corrosion, and/or discoloration issues. Ionomers or polyester-based encapsulants like polyolefins could be best suited for G/G modules as it appears to be a current trend in the industry.

14 SOLAR ENERGY↗

DOE OSTI2021

Voltage Loss Comparison in CdSe/CdTe Solar Cells and Polycrystalline CdSeTe Heterostructures

Cd(Se)Te solar cells have considerable headroom to increase voltage. Voltage losses occur due to incomplete absorption above bandgap E_g and band tail absorption below E_g; such losses are quantified using radiative voltage. The largest voltage losses are attributed to nonradiative recombination, which is quantified via carrier lifetime and radiative efficiency. We compare radiative voltage, radiative efficiency, and carrier lifetime for Cu-doped CdSe/CdTe solar cells and for undoped polycrystalline CdSeTe heterostructures passivated with Al_2O_3. Using external quantum efficiency spectrum and a CdSeTe absorption spectrum obtained from absolute photoluminescence (PL), we show that the radiative voltage is greater than 1.1 V. Time-resolved PL experiments and modeling show that a major part of voltage losses can be attributed to recombination in the absorber bulk. The front interface recombination makes a larger impact within the first few nanoseconds after pulsed excitation, and the comparison of time-gated and time-integrated PL can be used to assess relative contributions of front interface and bulk recombination rates.

14 SOLAR ENERGY↗

DOE OSTI2020

Comparison of simulated and experimentally measured detector impulse responses to pulsed x-rays

The Gamma Array Simulation Toolkit (GAST) is a multi-physics software stack comprised of Geant4, MATLAB, and experimentally measured photomultiplier tube (PMT) impulse response waveforms that is used to model and inform the end-toend performance of radiation detector systems. In order to validate the ability of GAST to predict the impulse response of a modeled detector configuration operated in current mode, experimental measurements using the Nevada National Security Site Transformational Diagnostics and Imaging 2 MeV endpoint energy electron linear accelerator (linac) with a tungsten target were performed. Seven different detector configurations consisting of unique combinations of scintillator material, size, reflectivity conditions, presence or absence of light guide, and PMT were evaluated. The resultant impulse response of each detector configuration was recorded and compared to a GAST simulation that emulated the respective linac experiment conditions. The comparison of the experimental and simulated detector impulse responses indicated that GAST can reliably predict detector impulse responses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Accurate Efficiency Measurements for Emerging PV: A Comparison of NREL's Steady-State Performance Calibration Protocol Between Conventional and Emerging PV Technologies

Emerging PV technologies (e.g. Perovskite, and Quantum Dot) are commonly known to possess challenges for accurate performance measurement under the existing IEC 60904 series of standards, which were developed for conventional Si solar cells. Potential performance artifacts depending on scan rates and directions and light bias exposure history are often seen in those emerging solar cells. To avoid these artifacts and provide an unbiased and reliable efficiency measurement, NREL's Cell and Module Performance (CMP) Group has developed a steady-state performance calibration protocol - the asymptotic P MAX method. In this paper, we applied this procedure to four PV cell technologies, Si, CIGS, perovskite, and Quantum Dot (QD), and compared their performance variations between the transient and the steady-state conditions. By comparison, we found that the performance parameters ( i.e. V OC , I SC , FF, ..eta..) measured between fast I-V scans (and the asymptotic method (steady-state) change significantly for perovskite and QD cells. These changes do not happen for Si and CIGS cells. Furthermore, the statistical performance analysis on nearly 100 emerging cells received globally (including OPV, Perovskite, and QD) shows that over 70 % of the fast I-V scans have a relative performance deviation larger than 1% compared to those determined using the asymptotic P MAX scan. Given the complex dynamic behavior observed in emerging PV devices, the CMP group at NREL thus only certifies their steady steady-state performance using the Asymptotic P MAX method. We highly recommend similar steady-state performance calibration protocol for all researchers in emerging PV because accuracy in reported efficiencies is critical to the long-term success of those promising new PV technologies.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2023

Comparison of Multi-Scale Nonlinear and Conventional Linear Methods for Stress Analysis of Nb 3 Sn Superconducting Magnets

Here this is an extension of the work on a multi-scale nonlinear procedure that demonstrated how to conduct nonlinear stress analysis of Nb 3 Sn superconducting accelerator magnets. The nonlinear procedure uses measured stress-strain curves of annealed copper, Nb 3 Sn strands and coil samples as inputs, which reduces the number of assumptions made for material properties—key uncertainties of any engineering analysis. The results from nonlinear analysis, semi-nonlinear analysis, and linear analysis of the same QFFB2 Nb 3 Sn quadrupole magnet under the same temperature and loads, were compared and discussed. The comparison illustrates that nonlinear stress analysis is significantly more accurate than other methods. As the superconducting coil block is a complex, composite material, it would be inadequate to assume the whole coil block to be linear, either isotropic or orthotropic. It is imperative to conduct nonlinear analysis by simulating the superconducting coil to the level of detail of the individual cables and individual strands. The nonlinear stress analysis procedure can be used to simulate not only Nb 3 Sn magnets, but also NbTi and HTS magnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Comparison of Power System Current Sensors via Playback of Electrical Disturbances

The need to accurately measure high-frequency content in power system voltage and current phenomena is increasingly becoming more of a priority. As the amount of distributed energy resources (DER) and nonlinear loads penetrating the grid increases, so do challenges associated with traditional measurement and metering applications. In this paper, three commercially-available medium-voltage-level current sensors are characterized in terms of their harmonic amplitude and phase performance against reference signals that are “played back” through the sensors through the use of an arbitrary waveform generator. It is shown that none of the three sensors studied are able to faithfully replicate all of the input signals completely, though there are advantages and disadvantages to each in terms of noise, resonance, and induced phase drift. Additionally, the Goodness-of-Fit metric, typically used for PMU model validation, is used to generate side-by-side comparisons of sensor accuracy over a small window around the events under study.

Wilson, Aaron↗