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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Distributed non-negative matrix factorization with determination of the number of latent features

The holistic analysis and understanding of the latent (that is, not directly observable) variables and patterns buried in large datasets is crucial for data-driven science, decision making and emergency response. Such exploratory analyses require devising unsupervised learning methods for data mining and extraction of the latent features, and non-negative matrix factorization (NMF) is one of the prominent such methods. NMF is based on compute-intense non-convex constrained minimization, which, for large datasets requires fast and distributed algorithms. However, current parallel implementations of NMF fail to estimate the number of latent features. In practice, identifying these features is both difficult and significant for pattern recognition and latent feature analysis, especially for large dense matrices. Here, we introduce a distributed NMF algorithm coupled with distributed custom clustering followed by a stability analysis on dense data, which we call DnMFk, to determine the number of latent variables. The results on synthetic data and the classical Swimmer data set demonstrate the accuracy of model determination while scaling nearly linearly across multiple processors for large data. Further, we employ DnMFk to determine the number of hidden features from a terabyte matrix.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. Here, we observe and discuss systematic map quality deterioration as result of data incompleteness.

Hydrogen bond↗
DOE OSTI2021

Rapid determination of supercritical CO 2 and brine relative permeability using an unsteady-state flow method

In this study, relative permeability of supercritical CO 2 (scCO 2 ) and brine was determined in reactive and non-reactive rock cores using a combination of unsteady-state methodology and computed tomography. Experiments were conducted using a medical grade CT scanner to determine saturation using a custom Python script. The saturation and differential pressure across the core were then used to derive four empirical constants to calculate relative permeability. This methodology increases temporal efficiency while reducing experimental complexity. Additionally, we show that the method can be used to determine scCO 2 relative permeability in a wide range of lithologies and flow rates, and with the ability to account for matrix dissolution during scCO 2 flooding.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Determination of the 161 Tb half-life

There is significant interest in the use of terbium radioisotopes for applications in cancer therapy and diagnosis. Of these, 161 Tb, a medium energy beta- and prolific auger emitter, is being investigated as a potential alternative to 177 Lu. The higher proportion of conversion electron and Auger electron emissions, and variety of low-energy gammas make 161 Tb an attractive targeted theranostic. As a product of nuclear fission, 161 Tb is also of importance to nuclear forensics. The current evaluated half-life of 6.89(2) d has a standard uncertainty that contributes significantly to the standard uncertainty of decay calculated activity determination. Furthermore, the accuracy of this evaluated half-life has been called into question by measurements reported recently at the Institute of Radiation Physics (IRP), Switzerland. In this work, the half-life of 161 Tb was measured at three independent laboratories located in the United Kingdom and United States of America for a total of five determinations using three independent measurement techniques. In conclusion, the half-life determined for 161 Tb of 6.9637(29) d confirms the observed 1 % relative increase observed by IRP, though the reported half-lives in this work and at IRP are significantly different (ζ-score = 3.1).

half-life↗
DOE OSTI2023

Accurate activity determination of a californium neutron source

Accurately counting analog events requires constructing an electronics chain that produces one count for each input pulse. Here, in this work, we review the use of Nuclear Instrumentation Module electronic units for counting neutron capture events in a 3He tube. We identify two unique types of false trigger events in a leading-edge discriminator and show how a dual timer module can be used to produce a veto window to exclude these events. We use the constructed electronics chain to build an apparatus to measure neutron pulses from a 252 Cf neutron source. We compare the measurements with a Monte Carlo N-Particle (MCNP) model to determine the activity of the neutron source. Furthermore, by making additional measurements with borated polyethylene attenuators between the source and detector, we are able to determine the boron concentration of the polyethylene. This technique provides accurate determination of the source activity to a precision of 2.8% at the k=1 level. The method used is simple, inexpensive, and requires no additional calibrated instruments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Influence of cementation on the yield surface of rocks numerically determined from digital microstructures

Digital Rock Physics has reached a level of maturity on the characterisation of primary properties that depend on the microstructure – such as porosity, permeability or elastic moduli – by numerically solving field equations on μCT scan images of rock. After small deformations or at depth though, most rocks eventually reach their limit of elasticity and the complementary plastic properties are needed to describe the full mechanical behaviour. Currently, determination of a rock’s yield surface from its microstructure is often restricted to semi-analytical criteria derived by limit analysis or numerical simulations performed on idealised geometries. Such simplification lacks representativeness, particularly for processes that affect directly the pore-grain interface such as the cementation phenomenon, happening during diagenesis. Eventually, only direct numerical simulation of elasto-plasticity performed on digitalised microstructures can be used to assess the strength of different cemented materials and its evolution with the alteration of the microstructure. In this study, we provide a comprehensive parametric study on the impact of cementation on rock strength for real microstructures of cemented granular materials. Compared to most previous studies, the whole yield surface is determined numerically (using Finite Element Method) in order to assess the influence of cementation for different stress-paths. The previously known tendency of rock to strengthen with increasing cementation volume is verified. New results on the influence of cement property namely Young’s modulus, friction and cohesion on the rock’s yield surface are explored. The envelopes obtained are compared to the ones obtained by experimental data and existing models. Finally, the framework presented in this study showcases the wider possibility of determining any rock’s or porous material’s yield surface from its microstructure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Evaluation of the ring tension test (RTT) for robust determination of material strengths

The ring tension test (RTT) is an experimental method for determining mechanical behavior in a material’s circumferential or hoop direction. It is a crucial test for testing anisotropic materials with tube geometry, such as nuclear fuel cladding or irradiated pipes. Several RTT configurations exist, each with their own advantages and disadvantages. However, this test is significantly more complex than traditional tensile testing and can be especially sensitive to small differences and inconsistencies in the test setup and geometry, ultimately affecting the derived mechanical properties. Previous research has focused on method development, and little work has been done on understanding the subtle differences between an ideal test and experiments, specifically when the tests are performed on highly irradiated materials in hot cells. In this work, a finite element-based investigation of the RTT is conducted to fill this gap. The two most used test configurations are investigated, comparing their ability to determine accurate material strengths through plastic deformation. Several non-ideal conditions and uncontrollable effects which are likely to occur during experimental testing such as machining tolerances, variations of specimen geometry from nominal dimensions, rotation of specimens and fixturing, and other test setup discrepancies are studied. The sensitivity of measured strengths to these conditions is presented. A mechanics-based approach to describing and correcting raw data to determine actual strengths is also included for one of the configurations, resulting in a robust correction method with highly accurate material strength measurements. Finally, based on these analyses, the hemicylindrical mandrel configuration is recommended with a gauge region oriented at a 45° angle.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Determination of neutron irradiation temperatures of SiC using electrical resistivity method

The irradiation temperature of silicon carbide (SiC) was determined post-irradiation by examination of the recovery of the electrical resistivity due to thermal annealing in a rapid heating/cooling optical furnace. High-purity, high-resistivity grade SiC is routinely used as a passive temperature monitor in neutron irradiation studies at the High Flux Isotope Reactor (HFIR), and this paper presents an alternative automated technique for determination of the irradiation temperature the SiC experienced. Neutron collisions with the atoms results in displaced lattice atoms (interstitials) that act as electron donors yielding a significant decrease in electrical resistivity. The irradiation defects become thermodynamically unstable and start to recombine, when annealed above the irradiation temperature, resulting in a recovery of the electrical resistivity. The resistivity is measured at a fixed elevated temperature above ambient, which is below the target irradiation temperature. When the resistivity is plotted as a function of annealing temperatures, a clear increase is observed due to the recovery of irradiation defects. We have demonstrated that this electrical resistivity measurement of SiC is effective to determine irradiation temperature of SiC. In conclusion, energy levels of various defects in SiC were calculated from Arrhenius plots of electrical conductivity versus inverse temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Accurate determination of the electron spin polarization in magnetized iron and nickel foils for Møller polarimetry

The Møller polarimeter in Hall A at Jefferson Lab in Newport News, VA, has provided reliable measurements of electron beam polarization for the past two decades. Past experiments have typically required polarimetry at the 1% level of absolute uncertainty which the Møller polarimeter has delivered. However, the upcoming proposed experimental program including MOLLER and SoLID have stringent requirements on beam polarimetry precision at the level of 0.4% (The MOLLER Collaboration, 2014; The SoLID collaboration, 2019), requiring a systematic re-examination of all the contributing uncertainties. Møller polarimetry uses the double polarized scattering asymmetry of a polarized electron beam on a target with polarized atomic electrons. The target is a ferromagnetic material magnetized to align the spins in a given direction. In Hall A, the target is a pure iron foil aligned perpendicular to the beam and magnetized out of plane parallel or antiparallel to the beam direction. The acceptance of the detector is engineered to collect scattered electrons close to 90° in the center of mass frame where the analyzing power is a maximum (-7/9). One of the leading systematic errors comes from determination of the target foil polarization. Polarization of a magnetically saturated target foil requires knowledge of both the saturation magnetization and g', the electron g-factor which includes components from both spin and orbital angular momentum from which the spin fraction of magnetization is determined. Target foil polarization has been previously addressed in a 1997 publication “A precise target for Møller polarimetry” by de Bever et al. (1997) at a level of precision sufficient for experiments up to this point. Several shortcomings with the previous published value require revisiting the result prior to MOLLER. Here, we utilize the existing world data to provide a best estimate for target polarization for both nickel and iron foils including uncertainties in magnetization, high-field and temperature dependence, and fractional contribution to magnetization from orbital effects. We determine the foil electron spin polarization at 294 K to be 0.08020 ± 0.00018 (@4 T applied field) for iron and 0.018845+/-0.000053 (@2 T applied field) for nickel. Finally, we conclude with a brief discussion of additional systematic uncertainties to Møller polarimetry using this technique.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Experimental determination of critical resolved shear stress for strain-induced phase transformation

The current investigation reports the first attempt to measure the critical resolved shear stress to initiates strain-induced phase transformation in a three-dimensional polycrystalline aggregate using high-energy diffraction microscopy (HEDM). In situ tensile testing was performed on a Fe38.5Mn20Co20Cr15Si5Cu1.5 metastable alloy exhibiting transformation-induced plasticity (TRIP). Grains with a higher propensity for strain-induced phase transformation were tracked using HEDM. A sharp drop in grain specific stress, coinciding with the appearance of a new ε-hcp grain oriented relative to the parent γ-fcc phase, was taken as evidence of grain-specific stress required to trigger phase transformation. The highest resolved shear stress on the potential transformation systems was identified as the critical resolved shear stress (CRSS) for strain-induced phase transformation. For the studied metastable alloy, CRSS for transformation was determined to be 86±3 MPa which was very close to theoretical CRSS value determined using Schmid factor (89±12 MPa) compared to the value determined using Taylor factor (62±7 MPa).

Jain, Roopam↗
DOE OSTI2021

Alpha Shape Analysis (ASA) Framework for Post- Clustering Property Determination in Atom Probe Tomographic Data

While application of clustering algorithms to atom probe tomography data have enabled quantification of solute clusters in terms of number density, size, and subcomposition there exist other properties (e.g., volume, surface area, and composition) that are better determined by defining an interface between the cluster and the surrounding matrix. The limitation in composition results from an ion selection step where the expected matrix ion types are omitted from the cluster search algorithm to enhance the contrast between the matrix and cluster and to reduce the complexity of the search. Previously, composition determination within solute clusters has utilized a secondary envelopment and erosion step on top of conventional methods such as maximum separation. In this work, we present a novel stochastic method that combines the particle identification fidelity of a conventional clustering algorithm with the analytical flexibility of mesh-based approaches through the generation of alpha shapes for each identified cluster. Furthermore, the corresponding mesh accounts for concave components of the clusters and determines the volume and surface area of the clusters; additionally, the mesh boundary is utilized to update the total composition according to the internal ions.

42 ENGINEERING↗
DOE OSTI2020

Rapid Determination of Uranium Isotopic Abundance from Cotton Swipes: Direct Extraction via a Planar Surface Reader and Coupling to a Microplasma Ionization Source

The collection of solid particulates and liquids from surfaces by the use of cloth swipes is fairly ubiquitous. In such methods, there is a continuous concern regarding the ability to locate and quantitatively sample the analyte species from the material. In this effort, we demonstrate the initial coupling of an Advion Plate Express plate reader to a liquid sampling–atmospheric pressure glow discharge (LS-APGD) microplasma ionization source with an Orbitrap mass spectrometer to perform uranium isotopic analyses of solution residues on cotton swipes. The Plate Express employs a sampling probe head to engage and seal against the swipe surface. Subsequentially, the analyte residues are desorbed and transported within a 2% HNO 3 electrolyte flow to the ionization source. Quantitative recoveries were observed following a single 30 s extraction step, with the absolute mass sampled per extraction being ~100 ng. While the intrasample variability in the analytical responses for triplicate sampling of the same swipe yield ~30% RSD, this lack of precision is offset by the ability to determine isotope ratios for enriched uranium specimens with a precision of better than 10% RSD. Pooled, intersample precision ( n = 9) was found to be <5%RSD across the various sample compositions. Finally, 235 U/ 238 U determinations (ranging from 0.053 to 1.806) were accurate with errors of <10%, absolute. The 234 U- and 236 U-inclusive ratios were determined with similar accuracy in enriched samples. While the driving force for the effort is in the realm of nuclear nonproliferation efforts, the ubiquitous use of cloth swipes across many application areas could benefit from this convenient approach, including the use of versatile, reduced-format mass spectrometer systems.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Determining the N -Representability of a Reduced Density Matrix via Unitary Evolution and Stochastic Sampling

The N-representability problem consists in determining whether, for a given p-body matrix, there exists at least one N-body density matrix from which the p-body matrix can be obtained by contraction, that is, if the given matrix is a p-body reduced density matrix (p-RDM). The knowledge of all necessary and sufficient conditions for a p-body matrix to be N-representable allows the constrained minimization of a many-body Hamiltonian expectation value with respect to the p-body density matrix and, thus, the determination of its exact ground state. However, the number of constraints that complete the N-representability conditions grows exponentially with system size, and hence, the procedure quickly becomes intractable for practical applications. This work introduces a hybrid quantum-stochastic algorithm to effectively replace the N-representability conditions. The algorithm consists of applying to an initial N-body density matrix a sequence of unitary evolution operators constructed from a stochastic process that successively approaches the reduced state of the density matrix on a p-body subsystem, represented by a p-RDM, to a target p-body matrix, potentially a p-RDM. The generators of the evolution operators follow the well-known adaptive derivative-assembled pseudo-Trotter method (ADAPT), while the stochastic component is implemented by using a simulated annealing process. The resulting algorithm is independent of any underlying Hamiltonian, and it can be used to decide whether a given p-body matrix is N-representable, establishing a criterion to determine its quality and correcting it. We apply the proposed hybrid ADAPT algorithm to alleged reduced density matrices from a quantum chemistry electronic Hamiltonian, from the reduced Bardeen–Cooper–Schrieffer model with constant pairing, and from the Heisenberg XXZ spin model. In all cases, the proposed method behaves as expected for 1-RDMs and 2-RDMs, evolving the initial matrices toward different targets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

In this work, we have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å 2 , a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (S CD ) profiles calculated from the simulations were in relatively good agreement with S CD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å 2 resulted in good agreement between the simulation and experimental scattering form factors, but not with S CD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Orientation and Conformation of Proteins at the Air–Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. Here in this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2022

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Mass Spectrometric Determination of Site-Specific O -Acetylation in Rhamnogalacturonan I Oligomers

O-acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify O-acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses smaller sample amounts, faces challenges due to O-acetyl migration between monosaccharide positions. The multiple steps in pectin sample analysis can further promote O-acetyl migration, especially near free hydroxyl groups. Moreover, during tandem MS, O-acetyl groups may detach, complicating the accurate tracking. This study presents an approach to lock O-acetyl groups by introducing trideuteroacetyl and propionyl substituents onto free hydroxyls of RG-I or partially acetylated RG-I. By combining matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization (ESI) MS with MS/MS or tandem mass spectrometry (MSn), we devised a way to determine the monosaccharide sequence in the oligomer and the precise positions of O-acetyl groups in partially acetylated RG-I. This method enables the study of the regiospecificity of recombinant pectin O-acetyltransferases and can be applied to other oligosaccharides to determine acyl positions.

O-acetylation↗