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At least 487 records · Page 27

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DOE OSTI2024

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

High-order ( N = 4–6) multiphoton absorption and mid-infrared Kerr nonlinearity in GaP, ZnSe, GaSe, and ZGP crystals

We report a study of high-order multiphoton absorption, nonlinear refraction, and their anisotropy in four notable mid-infrared χ (2) crystals: GaP, ZnSe, GaSe, and ZGP using femtosecond pulses at 2.35 μm with peak intensity in excess of 200 GW/cm 2 . We found that the nonlinear absorption obeys a perturbation model with multiphoton absorption (MPA) orders from N = 4–6, in agreement with the bandgaps of the crystals. A study of the role of free carrier absorption, performed by changing the pulse duration from 30 to 70 fs while maintaining a constant peak intensity, showed that, at our intensity levels, free carriers generated during the MPA process absorb much more strongly than would be expected from their known linear absorption cross section. Possible mechanisms for this anomalous behavior are high-field effects, such as intravalley scattering in the conduction band and absorption to higher lying bands. Nonlinear refractive indices were measured using (i) closed aperture Z-scan and (ii) spectral broadening due to self-phase modulation, both methods agreeing with each other.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Coexistent Quantum Channel Characterization Using Spectrally Resolved Bayesian Quantum Process Tomography

The coexistence of quantum and classical signals over the same optical fiber with minimal degradation of the transmitted quantum information is critical for operating large-scale quantum networks over the existing communications infrastructure. In this work, we systematically characterize the quantum channel that results from simultaneously distributing approximate single-photon polarization-encoded qubits and classical light of varying intensities through fiber-optic channels of up to 15 km. Using spectrally resolved quantum process tomography with a Bayesian reconstruction method that we develop, we estimate the full quantum channel from experimental photon counting data, both with and without classical background. Furthermore, although we find the exact channel description to be a weak function of the pump polarization, we nevertheless show that the coexistent fiber-based quantum channel has high process fidelity with an ideal depolarizing channel when the noise is dominated by Raman scattering. These results provide a basis for the future development of quantum repeater designs and quantum error-correcting codes for real-world channels and inform models used in the analysis and simulation of quantum networks.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Trimeron-phonon coupling in magnetite

Using density functional theory, we study the lattice dynamical properties of magnetite (Fe 3 O 4 ) in the high-temperature cubic and low-temperature monoclinic phases. The calculated phonon dispersion curves and density of states are compared with the available experimental data obtained by inelastic neutron, inelastic x-ray, and nuclear inelastic scattering. We find a very good agreement between the theoretical and experimental results for the monoclinic Cc structure revealing the strong coupling between the charge-orbital (trimeron) order and specific phonon modes. For the cubic phase, clear discrepancies arise due to fluctuation effects, which are not included in the calculation method. Despite this shortcoming, we argue that the main spectral features can be understood assuming that the strong trimeron-phonon coupling is extended above the Verwey transition, with lattice dynamics influenced by the short-range order instead of the average cubic structure. Our results indicate the validity of trimerons (and trimeron-phonon coupling) to explain the physics of magnetite much beyond their original formulation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Medium amplitude parallel superposition (MAPS) rheology. Part 2: Experimental protocols and data analysis

An experimental protocol is developed to directly measure the new material functions revealed by medium amplitude parallel superposition (MAPS) rheology. This protocol measures the medium amplitude response of a material to a simple shear deformation composed of three sine waves at different frequencies, revealing a rich dataset consisting of up to 19 measurements of the third-order complex modulus at distinct three-frequency coordinates. We discuss how the choice of input frequencies influences the features of the MAPS domain studied by the experiment. A polynomial interpolation method for reducing the bias of measured values from spectral leakage and reducing variance due to noise is discussed, including a derivation of the optimal range of amplitudes for the input signal. This leads to the conclusion that conducting the experiment in a stress-controlled fashion possesses a distinct advantage to the strain-controlled mode. The experimental protocol is demonstrated through measurements of the MAPS response of a model complex fluid: a surfactant solution of wormlike micelles. The resulting dataset is indeed large and feature-rich, while still acquired in a time comparable to similar medium amplitude oscillatory shear (MAOS) experiments. We demonstrate that the data represent measurements of an intrinsic material function by studying its internal consistency, compatibility with low-frequency predictions for Coleman–Noll simple fluids, and agreement with data obtained via MAOS amplitude sweeps. Finally, the data are compared to predictions from the corotational Maxwell model to demonstrate the power of MAPS rheology in determining whether a constitutive model is consistent with a material’s time-dependent response.

Lennon, Kyle R. (ORCID:0000000212515461)↗

DOE OSTI2021

Transverse mode analysis for free-space laser beams using Bayesian analysis

Reliable and rapid assessment of the transverse mode quality of a free-space laser beam has a wide range of applications in laser development, research, and utilization. It has become even more important with recent advances in developing orbital angular momentum photon beams across a broad spectral region. In this work, a general modal analysis method for a free-space multimode laser beam has been developed based on Bayesian analysis. After transforming mode decomposition into a linear system problem, a Gaussian probabilistic model is used to find a closed-form solution. The method is found to be robust with the presence of Gaussian noise. Prior knowledge about the mode content can be incorporated into the method to improve the solution for situations when coherent disturbances or contamination are present in the laser beam. This method can be used to analyze the mode content for laser beams in different bases, such as Hermite–Gaussian (HG) modes and Laguerre–Gaussian (LG) modes. Three applications of this method are presented: a detailed modal analysis of the beam image from the incoherent intensity addition of HG modes and two examples of mode decomposition using the complex wavefront from the coherent superposition of HG and LG modes. The feasibility of this method is demonstrated using various simulation results. Based on digital images of a laser beam recorded without complex wavelength-limiting optics, in principle, this method can be used in a wide wavelength range from infrared to ultraviolet, and possibly x ray.

Liu, Peifan (ORCID:0000000273816153)↗

DOE OSTI2024

A robust spectral element implementation of the $k - τ$ RANS model in Nek5000/NekRS

The $k - ω$ Reynolds Averaged Navier Stokes (RANS) model is one of the industry standard approaches for modeling of turbulent flows. It performs better than the $k - ϵ$ model for low Reynolds number flows and is also more suitable for boundary layers with adverse pressure gradients. Major drawback of the model, however, is that the asymptotic value of $ω$ at the walls is singular, necessitating the use of a contrived “sufficiently” large value for $ω$ as the boundary condition for its transport equation. Here, this invariably leads to the solution being sensitive to near wall grid spacing. While an acceptable solution for low order (finite volume) methods, the excessive near wall gradients lead to persistent numerical stability issues in high order codes. To alleviate the problem, specifically in the context of the high order spectral element code Nek5000, a regularized $k - ω$ approach was formulated in our prior work (Tomboulides et al., 2018). The formulation, however, relies on the use of wall distance and its gradients for modeling the closure terms and can pose problems for simulations in complex geometries. This work presents a novel implementation of the $k - τ$ RANS model in Nek5000, where $τ = 1/ω$, eliminating the need for regularization, owing to the asymptotically bounded behavior of the source terms in the $τ$ transport equation, and also eliminating dependence on wall distance. Robustness and stability of the $k - τ$ model is ensured through implicit treatment of the source terms and their careful numerical implementation and demonstrated through several cases aimed at verification and validation. Studies include both canonical and engineering relevant problems, viz., turbulent channel flow, pipe flow, backward facing step, flow over NACA 0012 airfoil and flow in a T-junction. Results from the $k - τ$ model are shown to be consistent with regularized $k - ω$ model and also with the $k - ω$ SST model in OpenFOAM (for select studies). Comparison with experimental data is also shown, where available, to bolster validation efforts for the $k - τ$ model implementation through prediction of key turbulent quantities of interest.

Nek5000↗

DOE OSTI2021

Simultaneous imaging of two-phase velocities in particle-laden flows by two-color optical phase discrimination

In this Letter, we present a particle image/tracking velocimetry (PIV/PTV) technique for simultaneous velocity measurement of both fluid and particle phases, adopting newly developed optical phase discrimination methods and novel optical particles. Spherical acrylic (PMMA) particles of diameter ∼ <#comment/> O ( 100 µ <#comment/> m ) were used as the particle phase, while fine B A M : E u 2 + phosphors of diameter ∼ <#comment/> O ( 1 µ <#comment/> m ) were used as the fluid tracer. Under Nd:YAG 355 nm laser excitation, both the laser-induced fluorescence (LIF) from PMMA and laser-induced phosphorescence (LIP) from B A M : E u 2 + provided sufficiently strong signals for PIV imaging with two non-intensified cameras and were clearly separable for phase discrimination using spectral filters and temporal profiles. The advantages of the PIV/PTV method include the relatively low cost of B A M : E u 2 + phosphors, high sphericity and narrow size distribution of PMMA particles with LIF emission, and direct optical discrimination eliminating artifacts, while requiring much less computational capacity for PIV/PTV processing of complex particle-laden flows.

Bi, Xiaopeng (ORCID:0000000190847325)↗

DOE OSTI2021

Scale-Dependent Bedform Migration and Deformation in the Physical and Spectral Domains

Multi-scale bathymetries observed in laboratory channels and natural rivers have posed several challenges to the description of bedform geometry and kinematics. To better quantify scale-dependent migration velocity, high resolution spatio-temporal bed evolution data are analyzed using three independent methods: (i) a bedform tracking method that identifies individual bedforms in longitudinal bed elevation profiles, (ii) a cross-correlation based, image matching technique in consecutive bathymetry scans similar to Particle Image Velocimetry, and (iii) two-dimensional frequency-wavenumber spectra marking a dispersion relation between bedform period and length, allowing estimation of Fourier-based, scale-dependent migration velocities. The comparative studies show that the spectral and bedform tracking methods present small differences in the migration velocity of medium-large bedforms. However, significant deviations occur in the small bedforms, mostly due to bedform sheltering or amplified exposure to the flow, which also contribute to their enhanced scale-dependent deformation. The analysis also shows that some form of scale separation is needed to extract the large and slowly migrating bedforms as they are masked by secondary features when several bedform orders coexist. Bathymetric Image Velocimetry reasonably estimates the averaged migration velocity and exhibits potential to study relations between spanwise bed surface velocity and local bedform kinematics.

58 GEOSCIENCES↗

DOE OSTI2026

Stochastic equilibrium Raman spectroscopy (STERS)

In this manuscript, we propose a new method for cavity- and surface-enhanced Raman spectroscopy (SERS) with improved temporal resolution in the measurement of stochastic Raman spectral fluctuations. Our approach combines Fourier spectroscopy and photon correlation to decouple the integration time from the temporal resolution. Using statistical optics Monte Carlo simulations, we establish the relationship between time resolution and Raman signal strength, revealing that typical Raman spectral fluctuations, commensurate with molecular conformational dynamics, can theoretically be resolved on micro- to millisecond timescales. The method can further extract average single-molecule dynamics from small sub-ensembles, thereby potentially mitigating challenges in achieving strictly single-molecule isolation on SERS substrates.

Cobb-Bruno, Colburn [University of California, Ber↗

DOE OSTI2025

First Measurement of Z Opacity Sample Evolution near Solar Interior Conditions Using Time-Resolved Spectroscopy

Opacity model differences with Fe opacity measurements at high temperature (T>1⁢8⁢0 eV ) and high electron density (𝑛 𝑒 >3×10 22 cm −3 ) at nearly solar interior conditions have remained unresolved [Bailey et al., Nature 517, 56 (2015) and Nagayama et al., Phys. Rev. Lett. 122, 235001 (2019)]. Systematic errors from temporal gradients are one hypothesis for the discrepancy. Past data recorded on x-ray film provided spectral measurements over a time determined by the 2.8-ns backlighter duration. Here, we present the first measurements of opacity sample temporal evolution using novel hCMOS ultrafast x-ray camera technology. The measured conditions, measured backlighter time history, and modeled opacities are used to show that temporal gradients do not resolve the model-data discrepancy. The methods demonstrated provide potential advantages, including opacities at more extreme conditions, spectral line shift measurements, and improved measurements at other facilities.

atomic spectra↗

DOE OSTI2021

Feed-forward spectral calibration methodology for line-scanned tunable laser absorption spectroscopy

A generalized feed-forward method for accurate tunable laser absorption spectroscopy includes generating a laser beam. The generated laser beam is directed down a reference path and a test/sample path. One or more parameters are extracted from the reference path. The one or more parameters, extracted from the reference path, are used as feed-forward, to adjust spectral analysis of the test/sample path to detect a composition and/or concentration of an analyte gas within the test/sample path. The extraction of the one or more parameters from the reference path and the spectral analysis of the test/sample path are performed substantially concurrently.

Green, William↗

DOE OSTI2022

Evaluation of an LED Simulator for Single- and Multi-Junction PV Cell Performance Testing

We present the evaluation of a solar simulator comprising a Light Emitting Diode (LED) array as its light source. While multiple applications can be envisioned for such a light source, here we focus on its use for performance testing of solar cells at Standard Test Conditions. With this in mind, we present characterization of the spatial uniformity of the irradiance and its temporal stability as well as the spectral range and spectral class. For a multisource simulator, the spectral uniformity across the test plane should also be evaluated and we discuss a method for performing this evaluation that is well suited to a solar cell performance testing application. One major advantage of this simulator is the ability to easily adjust the spectral output as needed in multijunction PV cell measurements and we also discuss this application here.

LED↗

DOE OSTI2026

Deep Learning enabled spectral energy conversion for in situ exposure measurements

A detector-specific deep learning (DL) approach is presented for spectra-to-exposure conversion using large-format sodium iodide (NaI(Tl)) detectors deployed for in situ environmental radiation measurements in emergency response scenarios. Accurate determination of exposure from NaI spectra is challenging due to poor energy resolution, partial energy absorption, and the strong sensitivity of traditionally deployed analytical conversion methods to calibrated source geometry and pre-deployment assumptions. Here, to address these limitations, a multi-layer perceptron model was trained on a hybrid in situ /Monte Carlo dataset constructed to span a broad range of photon energies, spatial extents, and realistic deployment variability, representative of general in situ emergency response conditions. The DL model was evaluated against commonly fielded analytical approaches under matched simulation conditions, including a single-factor method, a G-function method, and a modeled pressurized ion chamber (PIC) baseline. This study was intentionally computational in scope to enable controlled, like-for-like comparisons between conversion techniques while minimizing confounding real-world variability. Comparison to the modeled PIC provides contextual benchmarking and is not intended as a field inter-comparison with deployed instruments. Across the evaluated 20 keV to 3 MeV energy range, the DL approach consistently exhibited higher accuracy and reduced variance relative to the analytical methods against a deterministically calculated exposure. This may indicate improved robustness to spectral complexity without reliance on source-, geometric-, or spectral region-specific optimization. While results do not represent real-world validation, the presented work demonstrates that deep learning may effectively learn the nonlinear detector response-to-exposure relationship for asymmetric NaI(Tl) detectors and offers a promising pathway for improving in situ exposure estimation using spectroscopic systems already integrated into initial real-time emergency response operations.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

Axisymmetric hydrodynamics in numerical relativity using a multipatch method

In this paper, we describe a method of implementing the axisymmetric evolution of general-relativistic hydrodynamics and magnetohydrodynamics through modification of a multipatch grid scheme. In order to ease the computational requirements required to evolve the post-merger phase of systems involving binary compact massive objects in numerical relativity, it is often beneficial to take advantage of these system's tendency to rapidly settle into states that are nearly axisymmetric, allowing for 2D evolution of secular timescales. We implement this scheme in the spectral Einstein code and show the results of application of this method to four test systems including viscosity, magnetic fields, and neutrino radiation transport. Our results show that this method can be used to quickly allow already existing 3D infrastructure that makes use of local coordinate system transformations to be made to run in axisymmetric 2D with the flexible grid creation capabilities of multipatch methods. Our code tests include a simple model of a binary neutron star postmerger remnant, for which we confirm the formation of a massive torus which is a promising source of post-merger ejecta.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Spectral gaps of two- and three-dimensional many-body quantum systems in the thermodynamic limit

We present an expression for the spectral gap, opening up new possibilities for performing and accelerating spectral calculations of quantum many-body systems. We develop and demonstrate one such possibility in the context of tensor network simulations. Our approach requires only minor modifications of the widely used simple update method and is computationally lightweight relative to other approaches. We validate it by computing spectral gaps of the 2D and 3D transverse-field Ising models and find strong agreement with previously reported perturbation theory results. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

A practical method for modeling temporally-averaged ocean wave frequency-directional spectra for characterizing wave energy climates

Wave energy resource characterization investigations have been hindered because frequency-directional wave spectra are not broadly available for many coastal regions due to the insufficient spatial coverage of buoy observation networks and spectral wave model hindcast outputs. We address this problem by developing and validating a practical method for approximating temporally-averaged frequency-directional wave spectra averaged over periods of months or years from bulk wave parameters, which are available at a much greater coverage and resolution than frequency-directional wave spectra. While the temporally averaged frequency-directional wave spectrum over these periods cannot be used for analyzing a single sea state, it aggregates multiple sea states, identifies dominant wave energy systems representing wave climate, and resolves their spectral characteristics. Therefore, modelling temporally averaged frequency-directional wave spectra is of great value for planning and designing wave energy projects, e.g., resource characterization, site assessment, and conceptual design of wave energy converters. Temporally-averaged frequency-directional wave spectra and related important wave energy parameters approximated using this method are found to be more accurate than commonly used parametric wave spectrum models. This method can be applied to a wide range of wave climates given its universality and high accuracy. Also, the availability of bulk wave parameters from multi-decade high-resolution wave model hindcasts is increasing.

16 TIDAL AND WAVE POWER↗

DOE OSTI2025

Demonstration of an AI-driven workflow for dynamic x-ray spectroscopy

X-ray absorption near edge structure (XANES) spectroscopy is a powerful technique for characterizing the chemical state and symmetry of individual elements within materials, but requires collecting data at many energy points which can be time-consuming. While adaptive sampling methods exist for efficiently collecting spectroscopic data, they often lack domain-specific knowledge about the structure of XANES spectra. Here we demonstrate a knowledge-injected Bayesian optimization approach for adaptive XANES data collection that incorporates understanding of spectral features like absorption edges and pre-edge peaks. We show this method accurately reconstructs the absorption edge of XANES spectra using only 15–20% of the measurement points typically needed for conventional sampling, while maintaining the ability to determine the x-ray energy of the sharp peak after the absorption edge with errors less than 0.03 eV, the absorption edge with errors less than 0.1 eV; and overall root-mean-square errors less than 0.005 compared to traditionally sampled spectra. Our experiments on battery materials and catalysts demonstrate the method’s effectiveness for both static and dynamic XANES measurements, improving data collection efficiency and enabling better time resolution for tracking chemical changes. This approach advances the degree of automation in XANES experiments, reducing the common errors of under- or over-sampling points near the absorption edge and enabling dynamic experiments that require high temporal resolution or limited measurement time.

Bayesian optimization↗