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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality (“greenness”) as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1996

Accurate Predictions of Mean Geomagnetic Dipole Excursion and Reversal Frequencies, Mean Paleomagnetic Field Intensity, and the Radius of Earth's Core Using McLeod's Rule

The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field intensity, and mean geomagnetic dipole power excursion and axial dipole reversal frequencies. We conclude that McLeod's Rule helps unify geo-paleomagnetism, correctly relates theoretically predictable statistical properties of the core geodynamo to magnetic observation, and provides a priori information required for stochastic inversion of paleo-, archeo-, and/or historical geomagnetic measurements.

Voorhies, Coerte V.↗
DOE OSTI2021

Evolutionary inverse design of defects at graphene 2D lateral interfaces

Grain boundaries (GBs) in two-dimensional (2D) materials often have a profound impact on various material properties from mechanical to optical to electronic, yet predicting all possible GB formations is a challenge. Here, we introduce a workflow based on an evolutionary algorithm for exploring possible GBs formed at a lateral 2D interface. In a departure from conventional genetic algorithm based structure optimization methods, we perform genetic operations in the near interface region that allow us to be computationally efficient. We benchmark our method using graphene, which is a well-studied 2D material with a wide range of point defects. An empirical potential was used as the surrogate of the evolutionary search. More than 11.5 × 106 structures in total were evaluated for 128 GB orientations, and for each orientation, the ten best structures are recorded. A subset of low energy GBs predicted by empirical potential based search was relaxed by first-principles calculations and used to validate the energetic rank order. With the validated formation energy, we rank-ordered the best 128 GB structures and performed a detailed statistical analysis of primitive rings to find the correlation between the ring distribution and the formation energy. We found that for low energy GBs (below 0.5eV/Å), Stone–Wales defects will dominate, while structures with a higher energy (0.5–1.1eV/Å) show an increasing population of heptagons and nine-membered rings to form seven-nine defect pairs. For structures with energy higher than 1.1eV/Å, the percentage of octagons and nine-membered rings increases, which indicates that these two types of rings are not energetically favorable. Our proposed methodology is broadly applicable to explore defective low dimensional materials and represents a powerful tool that enables a systematic search of GBs of lateral interfaces for 2D materials.

Zhang, Jianan↗
NASA NTRS2024

Harnessing Collaborative Learning Automata to Guide Multi-objective Optimization based Inverse Analysis for Structural Damage Identification

Structural damage identification based on physical models is often transformed into an optimization problem that minimizes the difference between measurement information of structure being monitored and the model prediction in the parametric space. However, the objective function in this context often exhibits multimodality, involving high-dimensional variables due to the reliance on finite element models for damage identification. These features pose challenges to optimization algorithms, where entrapment in local solutions can lead to false positives and false negatives in damage identification. In this research, we propose a reinforcement learning based multi-swarm optimizer to tackle such challenges in pursuit of a small yet diverse solution set that can capture the true damage scenario as one of the solutions. The proposed method leverages the flexibility of the particle swarm optimizer and incorporates novel strategies of metaheuristics to realize targeted improvement. To enable the particle swarm to adaptively select the appropriate search strategy based on the current environment, we adopt the learning automata technique, which sidesteps the need for reward strategy selection that is usually ad hoc at each step of the search. The integration harnesses the automatic learning and self-adaptation capabilities of learning automata, enabling the particles to navigate based on environmental signals. This leads to accumulated probabilities tied to advantageous movements, fostering an adaptive exploration of particles in the search space. The proposed approach is first validated through implementing into benchmark test cases with comparisons. It is then applied to structural damage identification with piezoelectric admittance experimental signals. `The results highlight the capability of the algorithm to identify a small solution set with high accuracy to match the actual damage scenario.

Yang Zhang↗
DOE OSTI2020

Enhancement of the spin–orbit torque efficiency in W/Cu/CoFeB heterostructures via interface engineering

Here, the spin-torque ferromagnetic resonance signal and the spin Hall magnetoresistance induced by the spin Hall effect of W/Cu/CoFeB heterostructures with different Cu layer thicknesses (t Cu ) have been systemically studied. The effective spin mixing conductance $g^{↑↓}_{eff}$, the interfacial spin transparency T, and the real spin–orbit torque efficiency ( J s J c ) real show a significant increase compared to the W/CoFeB heterostructure. ( J s J c ) real reaches its maximum of ~0.54, increased up to ~50% at the optimized tCu ~ 0.52 nm according to our theoretical prediction. More importantly, the intrinsic spin Hall angle of W, $θ^{int}_{SH}$ ~ 0.79 ± 0.20, has also been obtained after the correction of the inverse spin Hall effect and T. This suggests that the Cu insertion improves the interface quality and, therefore, assists the spin transport in the heterostructures, which potentially improves the performance of next-generation spintronic devices.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Charm meson and charm-meson molecule in an expanding hadron gas

We present our studies on the evolution of charm mesons after the kinetic freeze-out of the expanding hadron gas produced in a heavy-ion collision and the thermal correction to a loosely bound charm-meson molecule in a pion gas. The πD* → πD* reaction rates have t-channel singularities that give contributions inversely proportional to the thermal width of the D. The ratio of the D 0 and D + production rate can differ significantly from those predicted using the measured D* branching fractions. The thermal correction to a loosely bound charm-meson molecule in a pion gas comes primarily from the complex thermal energy shift of the charm-meson constituents.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Status of Cable Aging Knowledge Gaps Identified in the Expanded Materials Degradation Assessment (EMDA)

This report summarizes research relevant to cable aging knowledge gaps identified in NUREG/CR-7153, “Expanded Materials Degradation Assessment (EMDA) Volume 5: Aging of Cables and Cable Systems” (EMDA Vol. 5), performed since the EMDA Vol. 5 was published in 2014. It begins with a discussion of the status of cables in long-term operation of U.S. nuclear power plants (NPPs) and the most common cables found in NPP containment. Next, the major polymer cable insulations, and the mechanisms of concern for degradation of those polymers in service are reviewed. A description of the environmental qualification (EQ) process historically used for safety-related cables is provided as is a review of the potential concerns with that process highlighted in the EMDA Vol. 5. Research addressing each of these is then reviewed. Finally, three potential strategies to support continued safe operation of aging cables are proposed: advanced condition-based verification, targeted material aging studies, and predictive simulation.

42 ENGINEERING↗
NASA NTRS1991

Surface-tension-induced mixing following coalescence of initially stationary drops

The momentumless coalescence of drops of the same liquid, separated by an immiscible host, is studied experimentally. Observations show that for low-viscosity drops of unequal sizes, there is considerable mixing following coalescence, with the smaller drop penetrating the larger drop as a vortex. The extreme case of coalescence of a small drop with the bulk of the same liquid at a flat interface with an immiscible liquid is studied in detail. The penetration depths of small drops (1-5 mm) following coalescence are measured and correlated with theoretical predictions. It is found that in the range of the investigation, the penetration depth is proportional to the 5/4 power of drop diameter and inversely proportional to the square root of the drop viscosity.

Anilkumar, A. V.↗
NASA NTRS1997

The Dissipation Rate Transport Equation and Subgrid-Scale Models in Rotating Turbulence

The dissipation rate transport equation remains the most uncertain part of turbulence modeling. The difficulties arc increased when external agencies like rotation prevent straightforward dimensional analysis from determining the correct form of the modelled equation. In this work, the dissipation rate transport equation and subgrid scale models for rotating turbulence are derived from an analytical statistical theory of rotating turbulence. In the strong rotation limit, the theory predicts a turbulent steady state in which the inertial range energy spectrum scales as k(sup -2) and the turbulent time scale is the inverse rotation rate. This scaling has been derived previously by heuristic arguments.

Rubinstein, Robert↗
NASA NTRS1998

Euler Calculations at Off-Design Conditions for an Inlet of Inward Turning RBCC-SSTO Vehicle

The inviscid performance of an inward turning inlet design is calculated computationally for the first time. Hypersonic vehicle designs based on the inward turning inlets have been shown analytically to have increased effective specific impulse and lower heat load than comparably designed vehicles with two-dimensional inlets. The inward turning inlets are designed inversely from inviscid stream surfaces of known flow fields. The computational study is performed on a Mach 12 inlet design to validate the performance predicted by the design code (HAVDAC) and calculate its off-design Mach number performance. The three-dimensional Euler equations are solved for Mach 4, 8, and 12 using a software package called SAM, which consists of an unstructured mesh generator (SAMmesh), a three-dimensional unstructured mesh flow solver (SAMcfd), and a CAD-based software (SAMcad). The computed momentum averaged inlet throat pressure is within 6% of the design inlet throat pressure. The mass-flux at the inlet throat is also within 7 % of the value predicted by the design code thereby validating the accuracy of the design code. The off-design Mach number results show that flow spillage is minimal, and the variation in the mass capture ratio with Mach number is comparable to an ideal 2-D inlet. The results from the inviscid flow calculations of a Mach 12 inward turning inlet indicate that the inlet design has very good on and off-design performance which makes it a promising design candidate for future air-breathing hypersonic vehicles.

Takashima, N.↗
NASA NTRS2010

Validation of a Polyimide Foam Model for Use in Transmission Loss Applications

The work described in this paper was focused on the use of a new polyimide foam in a double wall sound transmission loss application. Recall that polyimide foams are functionally attractive, compared to polyurethane foams, for example, owing to their fire resistance. The foam considered here was found to have a flow resistivity that was too high for conventional acoustical applications, and as a result, it was processed by partial crushing to lower the flow resistivity into an acceptable range. Procedures for measuring the flow resistivity and Young s modulus of the material have been described, as was an inverse characterization procedure for estimating the remaining Biot parameters based on standing wave tube measurements of transmission loss and absorption coefficient. The inverse characterization was performed using a finite element model implementation of the Biot poro-elastic material theory. Those parameters were then used to predict the sound transmission loss of a double panel system lined with polyimide foam, and the predictions were compared with full-scale transmission loss measurements. The agreement between the two was reasonable, especially in the high and low frequency limits; however, it was found that the SEA model resulted in an under-prediction of the transmission loss in the mid-frequency range. Nonetheless, it was concluded that the performance of polyimide foam could be predicted using conventional poro-elastic material models and that polyimide foam may offer an attractive alternative to other double wall linings in certain situations: e.g., when fire resistance is a key issue. Future work will concentrate on reducing the density of the foam to values similar to those used in current aircraft sidewall treatments, and developing procedures to improve the performance of the foam in transmission loss applications.

Hong, Kwanwoo↗
NASA NTRS2014

A Predictive Bubble Point Pressure Model for Porous Liquid Acquisition Device Screens

This article presents a simplified model for porous screen channel liquid acquisition devices based on a maximum bubble point pressure method from Adamson and Gast (1997). To validate the model, three 304 stainless steel (325 × 2300, 450 × 2750, and 510 × 3600) mesh samples were tested in methanol, acetone, isopropyl alcohol, and water. Screen pores are estimated based on analysis from scanning electron microscopy, historical data, and current test data. Results show that the bubble point pressure is proportional to the surface tension of the fluid only when accounting for nonzero contact angles. The previous assumption that bubble point pressure scales inversely with effective pore diameter is shown to be invalid, as the second finest 450 × 2750 produced the highest bubble point of the three screens. The simplified bubble point model can be used to make predictions for any pure fluid when pore diameters are based on bubble point tests and not SEM analysis.

Liquid Acquisition Device↗
NASA NTRS2013

Thick Galactic Cosmic Radiation Shielding Using Atmospheric Data

NASA is concerned with protecting astronauts from the effects of galactic cosmic radiation and has expended substantial effort in the development of computer models to predict the shielding obtained from various materials. However, these models were only developed for shields up to about 120 g!cm2 in thickness and have predicted that shields of this thickness are insufficient to provide adequate protection for extended deep space flights. Consequently, effort is underway to extend the range of these models to thicker shields and experimental data is required to help confirm the resulting code. In this paper empirically obtained effective dose measurements from aircraft flights in the atmosphere are used to obtain the radiation shielding function of the earth's atmosphere, a very thick shield. Obtaining this result required solving an inverse problem and the method for solving it is presented. The results are shown to be in agreement with current code in the ranges where they overlap. These results are then checked and used to predict the radiation dosage under thick shields such as planetary regolith and the atmosphere of Venus.

Youngquist, Robert C.↗
DOE OSTI2026

Imaging surface topography with coherent x-ray reflectivity: Theory, kinematics, and simulations

A theoretical formalism is described for understanding coherent x-ray reflectivity (CXR) from the surface of a semi-infinite crystal having a variable surface topography, described by the height profile ℎ(𝑥,𝑦). The surface topography is imaged as a complex “effective density,” obtained from the phasing and inversion of the coherent x-ray reflectivity data, measured through a rocking scan centered at a vertical momentum transfer 𝑄$^{0}_{𝑧}$ and a vertical range Δ⁢𝑄 𝑧 . The formalism predicts that the effective density has an amplitude with a maximum located at the surface height for each position within the surface plane. The phase of the effective density has a lateral variation that is controlled by the surface height and a vertical variation that reflects a combination of the interfacial structure and specific choice of measurement conditions. This understanding enables direct observation of nanometer-scale interfacial topography, i.e., ℎ⁡(𝑥,𝑦)⁢𝑐 𝑠 (where 𝑐 𝑠 is the vertical substrate lattice parameter) with Å-scale sensitivity to surface height. Numerical simulations illustrate and confirm the theoretical results. These results show how the interpretation of the interfacial density phase obtained by CXR data inversion (i.e., surface topography with respect to a flat surface) is conceptually similar to that previously known for Bragg coherent diffraction imaging (BCDI) measurements of isolated nanoparticles (i.e., lattice displacements with respect to an ideal crystal lattice). This suggests that CXR can be thought of as a form of dark field imaging with respect to the bright field BCDI approach. An implication of these results is that interfacial imaging may bypass some of the significant challenges associated with BCDI imaging of multiple particles having different orientations.

X-ray imaging↗
DOE OSTI2020

Learning to Predict Crystal Plasticity at the Nanoscale: Deep Residual Networks and Size Effects in Uniaxial Compression Discrete Dislocation Simulations

The density and configurational changes of crystal dislocations during plastic deformation influence the mechanical properties of materials. These influences have become clearest in nanoscale experiments, in terms of strength, hardness and work hardening size effects in small volumes. The mechanical characterization of a model crystal may be cast as an inverse problem of deducing the defect population characteristics (density, correlations) in small volumes from the mechanical behavior. In this work, we demonstrate how a deep residual network can be used to deduce the dislocation characteristics of a sample of interest using only its surface strain profiles at small deformations, and then statistically predict the mechanical response of size-affected samples at larger deformations. As a testbed of our approach, we utilize high-throughput discrete dislocation simulations for systems of widths that range from nano- to micro- meters. We show that the proposed deep learning model significantly outperforms a traditional machine learning model, as well as accurately produces statistical predictions of the size effects in samples of various widths. By visualizing the filters in convolutional layers and saliency maps, we find that the proposed model is able to learn the significant features of sample strain profiles.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Multi-scale experimental study of creep-fatigue failure initiation in a 709 Stainless Steel alloy using high resolution digital image correlation. Final report

This report discusses the efforts made towards the multi-scale study of the creep-fatigue response of stainless steel 709. Multiple experimental techniques, including digital image correlation (DIC) and electron backscatter diffraction (EBSD), were used in assessing the evolution of damage accumulation during fatigue, creep-fatigue, and thermomechanical fatigue of alloy 709. The role of microstructural features, hold times, temperature, and loading profiles were quantified and the interchangeability of temperature and time was investigated. Finally, a thermomechanical fatigue model was shown to predict well the failure of samples with varying loading profiles. Results indicate that strain accumulation in 709 steel happens primarily near grain boundaries (GBs) with the strains around GBs being inversely proportional to their measured residual burgers vector. Furthermore, hot-spots for strain accumulation were shown to be the locations of eventual microcrack nucleation. The introduction of hold times to the periodic loading cycle increases the damage accumulation rate and thus shortens the fatigue life of samples–this was true for both room temperature and high temperature. Thermomechanical cycling was shown to have little effect on the end life of samples, with the damage accumulation rate for in-phase and out-of-phase cycling being similar to isothermal fatigue. The interchangeability of time and temperature was shown to be possible within the studied load, time, and temperature ranges, since deformation mechanisms driving strain accumulation did not change with temperature (up to 650°C). The Neu-Sehitoglu thermomechanical fatigue model, with constants obtained from the literature and in part from our experimental results, was applied to predict failure of isothermal creep-fatigue samples. The main objectives of this work were to:(a) Perform high-resolution digital image correlation measurements (HiDIC) for alloy 709; (b) Quantify and assess damage accumulation at the microstructure under fatigue, TMF, and creep-fatigue conditions of 709; (c) Study of the role of hold times, i.e., adding a creep component, to: Room temperature cycling, High temperature cycling, Failure; (d) Study the mechanisms of thermomechanical fatigue in this alloy; (e) Investigate the existence of a time-temperature interchangeability criterion to aid in accelerated creep-fatigue testing; (f) Establish the validity of a combined creep-fatigue model for life prediction for 709. This report is structured with each subsequent section detailing the efforts, results, and conclusions related to each of the objectives described, mostly in chronological order.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Polaritonic Chern Insulators in Monolayer Semiconductors

Systems with strong light-matter interaction open up new avenues for studying topological phases of matter. Examples include exciton polaritons, mixed light-matter quasiparticles, where the topology of the polaritonic band structure arises from the collective coupling between matter wave and optical fields strongly confined in periodic dielectric structures. Distinct from light-matter interaction in a uniform environment, the spatially varying nature of the optical fields leads to a fundamental modification of the well-known optical selection rules, which were derived under the plane wave approximation. Here, in this study, we identify polaritonic Chern insulators by coupling valley excitons in transition metal dichalcogenides to photonic Bloch modes in a dielectric photonic crystal slab. We show that polaritonic Dirac points, which are markers for topological phase transition points, can be constructed from the collective coupling between valley excitons and photonic Dirac cones in the presence of both time-reversal and inversion symmetries. Lifting exciton valley degeneracy by breaking time-reversal symmetry leads to gapped polaritonic bands with nonzero Chern numbers. Through numerical simulations, we predict polaritonic chiral edge states residing inside the topological gaps. Our Letter paves the way for the further study of strong exciton-photon interaction in nanophotonic structures and for exploring polaritonic topological phases and their practical applications in polaritonic devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Limits on Astrophysical Antineutrinos with the KamLAND Experiment

Abstract We report on a search for electron antineutrinos ( ν ¯ e ) from astrophysical sources in the neutrino energy range 8.3–30.8 MeV with the KamLAND detector. In an exposure of 6.72 kton-year of the liquid scintillator, we observe 18 candidate events via the inverse beta decay reaction. Although there is a large background uncertainty from neutral current atmospheric neutrino interactions, we find no significant excess over background model predictions. Assuming several supernova relic neutrino spectra, we give upper flux limits of 60–110 cm −2 s −1 (90% confidence level, CL) in the analysis range and present a model-independent flux. We also set limits on the annihilation rates for light dark matter pairs to neutrino pairs. These data improve on the upper probability limit of 8 B solar neutrinos converting into ν ¯ e , P ν e → ν ¯ e < 3.5 × 10 − 5 (90% CL) assuming an undistorted ν ¯ e shape. This corresponds to a solar ν ¯ e flux of 60 cm −2 s −1 (90% CL) in the analysis energy range.

79 ASTRONOMY AND ASTROPHYSICS↗