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At least 343 records · Page 19

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗

Optimization of simulated high-field side lower hybrid current drive coupling using machine learning predictions of scrape-off layer density

Lower hybrid current drive (LHCD) is a potential source of non-inductive off-axis current drive (CD) for tokamaks. Although LHCD has been successfully deployed on a number of tokamaks, it is highly sensitive to the scrape-off layer (SOL) conditions local to the LHCD launcher. Large gaps between the launcher and plasma core, SOL turbulence, or edge density perturbations due to edge-localized modes can hamper CD or cause large reflected power. These coupling issues in part motivated the installation of an LHCD launcher on the high-field side (HFS) of DIII-D. On the HFS, the SOL is less turbulent and more controllable compared to the low-field side. This quiescence may result in more predictable edge conditions and thus a more predictable CD. Here, in this work, HFS SOL reflectometry measurements are predicted from global plasma parameters using machine learning models. The SOL predictions coupled with the full-wave simulation of the LHCD launcher allow for the prediction of reflected power, directivity, and arcing risk before the discharge. Launcher performance is then optimized using multi-objective Bayesian optimization, finding the shot parameters that result in an optimal SOL density that maximizes CD while minimizing the risk of arcing. The predictions and optimizations of LHCD performance are then accelerated using a surrogate model of the full-wave LHCD simulation.

Bayesian optimization↗

TEM Approaches for Microstructure-Informed Prediction of Mechanical Properties in Structural Alloys

Predicting the mechanical performance of structural alloys from their evolving microstructure remains a major challenge in materials science, particularly for nuclear structural materials, where irradiation-induced defects span multiple types and length scales and interact through complex mechanisms. The dispersed barrier hardening (DBH) [1] and Friedel–Kroupa–Hirsch (FKH) [2,3] models have been widely used to evaluate the hardening contributions of individual obstacles and to estimate tensile strength from quantified microstructures; however, when multiple size-dependent obstacles coexist and evolve, predicting temperature-dependent tensile strength becomes significantly more complex, and a fully consistent hardening model is still lacking. Transmission electron microscopy (TEM) plays a central role in refining hardening models and enabling predictive assessments of tensile strength evolution by providing quantitative characterization of dislocations, irradiation-induced defects (e.g., dislocation loops and cavities), precipitates, and grain structure (Fig. 1.). These experimentally measured defect densities are incorporated into physically based hardening models with size- and shape- dependent obstacle strengths [4], using root-sum-square superposition for obstacles of comparable strength and linear superposition for dissimilar ones [5]. In addition, recent advances in TEM [6-8], including high-resolution imaging, 4D-STEM strain mapping, EDS/EELS elemental analysis, and flash-polishing-based TEM specimen preparation and extraction-replica methods (Fig. 2), further improve the accuracy of microstructural quantification. By comparison with prior studies as well as our own results, we show that when TEM-derived microstructural information is carefully integrated with physically grounded hardening models, yield strength (or irradiation-induced hardening) measured at room temperature can be predicted with good quantitative agreement across multiple alloy classes. In-situ TEM combined with high-temperature mechanical testing represents an important next step for refining hardening models by directly probing dislocation–obstacle interactions across varying irradiation doses and temperatures [9]. Because the barrier strength factor (α) depends on both temperature and obstacle size, it should not be treated as a constant fitting parameter; rather, it must be explicitly evaluated to achieve physically meaningful predictions of mechanical behaviour at operating temperatures. This presentation therefore discusses why all strengthening contributions (e.g., Peierls stress, solid-solution strengthening, voids, bubbles, dislocation loops, dislocation lines, and grain boundaries) must be considered collectively, why appropriate superposition methods are essential when obstacles possess different barrier strength factors, how hardness measurements can be meaningfully related to tensile properties, and how TEM-derived microstructural information can be systematically incorporated into hardening models. More broadly, it outlines a pathway toward microstructure-informed prediction of mechanical properties and supports the goal of establishing science-based tools for evaluating structural materials in extreme environments [10].

Lin, Yan-Ru [ORNL] (ORCID:0000000339991473)↗

Accurate machine-learning predictions of coercivity in high-performance permanent magnets

Increased demand for high-performance permanent magnets in the electric vehicle and wind-turbine industries has prompted the search for cost-effective alternatives. Discovering magnetic materials with the desired intrinsic and extrinsic permanent magnet properties presents a significant challenge to researchers because of issues with the global supply of rare-earth elements, material stability, and a low maximum magnetic energy product BH max . While first-principles density functional theory (DFT) predicts materials’ magnetic moments, magnetocrystalline anisotropy constants, and exchange interactions, it cannot compute extrinsic properties such as coercivity (H c ). Although it is possible to calculate H c theoretically with micromagnetic simulations, the predicted value is larger than the experiment by almost an order of magnitude due to the Brown paradox. To circumvent these issues, we employ machine-learning (ML) methods on an extensive database obtained from experiments, DFT calculations, and micromagnetic modeling. The use of a large experimental dataset enables realistic H c predictions for materials such as Ce-doped Nd 2 ⁢Fe 14 ⁢B, comparing favorably against micromagnetically simulated coercivities. Remarkably, our ML model accurately identifies uniaxial magneto-crystalline anisotropy as the primary contributor to H c . With DFT calculations, we predict the Nd-site-dependent magnetic anisotropy behavior in Nd 2 ⁢Fe 14 ⁢B, confirming that Nd 4⁢g sites mainly contribute to uniaxial magnetocrystalline anisotropy, and also calculate the Curie temperature (T c ). Finally, both calculated results are in good agreement with the experiments. The coupled experimental dataset and ML modeling with DFT input predict H c with far greater accuracy and speed than was previously possible using micromagnetic modeling. Further, we reverse engineer the grain-boundary and intergrain exchange coupling with micromagnetic simulations by employing the ML predictions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗

Machine Learning Approaches to Predicting Induced Seismicity and Imaging Geothermal Reservoir Properties

This project developed machine learning (ML) methods, lab data sets, and field data to advance geothermal exploration and geothermal energy production. The work had three focus areas. One involved the development of ML methods to use microearthquakes (MEQs) for imaging geothermal reservoir properties and improving subsurface characterization – most importantly the evolution of permeability within the evolving reservoir. This part of the work included development of ML approaches for automated MEQ location, focal mechanism determination and identification of earthquake precursors. The second area focused on using MEQ signals generated by geothermal exploration and production to predict the relationship between fluid injection and seismicity. Here, we extended to reservoir scale our success in using ML to predict laboratory earthquakes and fault zone stress state. The third focus area was on lab experiments. Here, we developed new ML models for lab earthquake prediction and identification of precursors to failure to improve earthquake forecasting and early warning in geothermal settings. Major outcomes of our work include ML models that learn from MEQ signals during geothermal exploration and production to predict induced seismicity. MEQs occur naturally in connection with drilling and energy production. We developed ML methods to use the seismic waves from these events to characterize the elastic, hydraulic and poromechanical properties of reservoirs. Our work illuminated fracture geometry and the evolution of fracture permeability by incorporating seismic coda wave analysis and ML methods to relate fluid injection and seismicity. We significantly expanded laboratory earthquake prediction to include methods that use both passive measurements of microearthquakes within the lab fault zones and also active source acoustic measurements of fault zone elastic properties. These methods can now predict fault zone stress state, time to failure and the magnitude of lab earthquakes. Our work showed that repetitive stick- slip failure events during frictional sliding (the lab equivalent of earthquakes) are preceded by a cascade of micro-failure events that radiate energy in a manner that foretells unstable failure – manifest as laboratory MEQs. We documented a mapping between fracture properties and statistical attributes of elastic radiation. We extended existing works to geothermal reservoir scale and developed ML methods to determine reservoir permeability, fracture properties, and their evolution during geothermal energy production. An attractive feature of ML algorithms is their ability to handle big datasets and reveal patterns and correlations that may remain invisible to conventional analyses. Our work connected data from field, laboratory and intermediate scales to study permeability, stress, strength, fracture stiffness and geometry. At the field scale we used data from the Newberry Volcano field site, UtahFORGE, EGS Collab, and also the Bedretto underground research lab in Switzerland. These data sets are bridging the gap between the lab scale, theory, and reservoir scale. Our work produced plain language summaries to improve public understanding of DOE research. We also developed openly distributed ML and seismicity datasets for use by all researchers and we published connections between induced seismicity in geothermal areas and reservoir properties including permeability, fracture properties, and stress state. Our models are designed for the large data sets of induced seismicity typically associated with geothermal sites. We produced labeled event catalogs and used them on geothermal data to assess how ML can facilitate geothermal production and exploration. All datasets are available on the GDR Productivity: The project produced 32 publications in peer reviewed journals (two are in review). It supported the work of 6 PhD students, 40 conference presentations, 6 keynote talks at national meetings, and mentoring and professional development for 4 postdoctoral fellows.

15 GEOTHERMAL ENERGY↗

Predictive Complexity of Quantum Subsystems

We define predictive states and predictive complexity for quantum systems composed of distinct subsystems. This complexity is a generalization of entanglement entropy. It is inspired by the statistical or forecasting complexity of predictive state analysis of stochastic and complex systems theory but is intrinsically quantum. Predictive states of a subsystem are formed by equivalence classes of state vectors in the exterior Hilbert space that effectively predict the same future behavior of that subsystem for some time. As an illustrative example, we present calculations in the dynamics of an isotropic Heisenberg model spin chain and show that, in comparison to the entanglement entropy, the predictive complexity better signifies dynamically important events, such as magnon collisions. It can also serve as a local order parameter that can distinguish long and short range entanglement.

Asplund, Curtis T. (ORCID:0000000305575850)↗

Comparison of Predicted and Experimental Heat-Transfer and Pressure-Drop Results for an Air-Cooled Plug Nozzle and Supporting Struts

A calculational procedure is presented to analyze the heat-transfer and fluid-flow characteristics of a convectively air -cooled plug-nozzle operating on an afterburning turbojet engine. Anderson's method was used to predict hot-gas static pressures in the supersonic stream with fully expanded flow (high nozzle-pressure ratios); the results were excellent. For low nozzle-pressure ratios, the flow was assumed to expand one-dimensionally and isentropically to the plug back pressure. Wall temperatures predicted using this latter pressure distribution agreed well with the wall temperatures predicted using the measured hot-gas pressures (maximum deviation was about 30 K (54 deg R)). Either an in tegral boundary-layer technique or a simple pipe-flow equation may be used to calculate convective heat transfer from the hot gas to the wall. The simple pipeflow equation results in the prediction of slightly higher wall temperatures than does the integral technique. Experimental wall temperatures were generally in good agreement with the two predicted wall temperature distributions. Excellent agreement was noted b etween measured and predicted coolant static-pressure distributions. The plug-coolant temperature rise was generally overpredicted by about 22.2 K (40 deg R); possible explanations are offered. Although an an alysis of the struts, which support the plug, was purposely kept simple, reasonable results were obtained. Potential flow over an ellipse was used to calculate hot-gas static pressure; the results were satisfactory.

Graber, E. J., Jr.↗

Prediction of space shuttle fluctuating pressure environments, including rocket plume effects

Preliminary estimates of space shuttle fluctuating pressure environments have been made based on prediction techniques developed by Wyle Laboratories. Particular emphasis has been given to the transonic speed regime during launch of a parallel-burn space shuttle configuration. A baseline configuration consisting of a lightweight orbiter and monolithic SRB, together with a typical flight trajectory, have been used as models for the predictions. Critical fluctuating pressure environments are predicted at transonic Mach numbers. Comparisons between predicted environments and wind tunnel test results, in general, showed good agreement. Predicted one-third octave band spectra for the above environments were generally one of three types: (1) attached turbulent boundary layer spectra (typically high frequencies); (2) homogeneous separated flow and shock-free interference flow spectra (typically intermediate frequencies); and (3) shock-oscillation and shock-induced interference flow spectra (typically low frequencies). Predictions of plume induced separated flow environments were made. Only the SRB plumes are important, with fluctuating levels comparable to compression-corner induced separated flow shock oscillation.

Plotkin, K. J.↗

Comparison of several methods for predicting separation in a compressible turbulent boundary layer

Several methods for predicting the separation point for a compressible turbulent boundary layer were applied to the flow over a bump on a wind-tunnel wall. Measured pressure distributions were used as input. Two integral boundary-layer methods, three finite-difference boundary-layer methods, and three simple methods were applied at five free-stream Mach numbers ranging from 0.354 to 0.7325. Each of the boundary-layer methods failed to explicitly predict separation. However, by relaxing the theoretical separation criteria, several boundary-layer methods were made to yield reasonable separation predictions, but none of the methods accurately predicted the important boundary-layer parameters at separation. Only one of the simple methods consistently predicted separation with reasonable accuracy in a manner consistent with the theory. The other methods either indicated several possible separation locations or only sometimes predicted separation.

Gerhart, P. M.↗

Interim prediction method for jet noise

A method is provided for predicting jet noise for a wide range of nozzle geometries and operating conditions of interest for aircraft engines. Jet noise theory, data and existing prediction methods was reviewed, and based on this information a interim method of jet noise prediction is proposed. Problem areas are idenified where further research is needed to improve the prediction method. This method predicts only the noise generated by the exhaust jets mixing with the surrounding air and does not include other noises emanating from the engine exhaust, such as combustion and machinery noise generated inside the engine (i.e., core noise). It does, however, include thrust reverser noise. Prediction relations are provided for conical nozzles, plug nozzles, coaxial nozzles and slot nozzles.

Stone, J. R.↗

Aircraft flyover noise prediction

A review is conducted of the prediction techniques for CTOL aircraft noise sources which are presently implemented in the NASA Aircraft Noise Prediction Program (ANOPP). The sources considered include jet noise, fan noise, combination noise, and airframe noise. Questions related to propagation prediction methods, source shielding, atmospheric attenuation, and ground attenuation are also described. It is pointed out that ANOPP is designed to make predictions of varying degrees of complexity, or amounts of detail, depending on the needs of the user. These different degrees of complexity are called levels of prediction. The prediction methods being used imply a similarity law for aircraft noise. Propulsion noise is proportional to mass flow for a selected engine cycle and, since thrust is also proportional to mass flow, aircraft with a fixed thrust-to-weight ratio will have their propulsion noise proportional to weight.

Zorumski, W. E.↗

Wind-tunnel/flight correlation study of aerodynamic characteristics of a large flexible supersonic cruise airplane (XB-70-1). 3: A comparison between characteristics predicted from wind-tunnel measurements and those measured in flight

A program was undertaken by NASA to evaluate the accuracy of a method for predicting the aerodynamic characteristics of large supersonic cruise airplanes. This program compared predicted and flight-measured lift, drag, angle of attack, and control surface deflection for the XB-70-1 airplane for 14 flight conditions with a Mach number range from 0.76 to 2.56. The predictions were derived from the wind-tunnel test data of a 0.03-scale model of the XB-70-1 airplane fabricated to represent the aeroelastically deformed shape at a 2.5 Mach number cruise condition. Corrections for shape variations at the other Mach numbers were included in the prediction. For most cases, differences between predicted and measured values were within the accuracy of the comparison. However, there were significant differences at transonic Mach numbers. At a Mach number of 1.06 differences were as large as 27 percent in the drag coefficients and 20 deg in the elevator deflections. A brief analysis indicated that a significant part of the difference between drag coefficients was due to the incorrect prediction of the control surface deflection required to trim the airplane.

Arnaiz, H. H.↗

Radio propagation prediction services in Japan

Japanese prediction services for HF radio communications are outlined in relation to prediction method, performance and evaluation. The current prediction is based on the CCIR interim method with some modifications matching to a computer system. The principal service is the monthly median prediction issued regularly three months in advance for various communication circuits. A daily prediction for short distance circuits is being prepared by using real time ionospheric sounding data. An evaluation theory and practice is expected to be introduced in the future prediction service.

Maeda, R.↗

Comparison of theoretically predicted lateral-directional aerodynamic characteristics with full-scale wind tunnel data on the ATLIT airplane

An analytical method is presented for predicting lateral-directional aerodynamic characteristics of light twin engine propeller-driven airplanes. This method is applied to the Advanced Technology Light Twin Engine airplane. The calculated characteristics are correlated against full-scale wind tunnel data. The method predicts the sideslip derivatives fairly well, although angle of attack variations are not well predicted. Spoiler performance was predicted somewhat high but was still reasonable. The rudder derivatives were not well predicted, in particular the effect of angle of attack. The predicted dynamic derivatives could not be correlated due to lack of experimental data.

Griswold, M.↗

Space vehicle acoustics prediction improvement for payloads

The modal analysis method was extensively modified for the prediction of space vehicle noise reduction in the shuttle payload enclosure, and this program was adapted to the IBM 360 computer. The predicted noise reduction levels for two test cases were compared with experimental results to determine the validity of the analytical model for predicting space vehicle payload noise environments in the 10 Hz one-third octave band regime. The prediction approach for the two test cases generally gave reasonable magnitudes and trends when compared with the measured noise reduction spectra. The discrepancies in the predictions could be corrected primarily by improved modeling of the vehicle structural walls and of the enclosed acoustic space to obtain a more accurate assessment of normal modes. Techniques for improving and expandng the noise prediction for a payload environment are also suggested.

Dandridge, R. E.↗

Prediction of absolute infrared intensities for the fundamental vibrations of H2O2

Absolute infrared intensities are predicted for the vibrational bands of gas-phase H2O2 by the use of a hydrogen atomic polar tensor transferred from the hydroxyl hydrogen atom of CH3OH. These predicted intensities are compared with intensities predicted by the use of a hydrogen atomic polar tensor transferred from H2O. The predicted relative intensities agree well with published spectra of gas-phase H2O2, and the predicted absolute intensities are expected to be accurate to within at least a factor of two. Among the vibrational degrees of freedom, the antisymmetric O-H bending mode nu(6) is found to be the strongest with a calculated intensity of 60.5 km/mole. The torsional band, a consequence of hindered rotation, is found to be the most intense fundamental with a predicted intensity of 120 km/mole. These results are compared with the recent absolute intensity determinations for the nu(6) band.

Rogers, J. D.↗