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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18
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NASA NTRSDate not supplied

Machine Learning Approach for Aircraft Performance Model Parameter Estimation for Trajectory Prediction Applications

Inaccurate prediction of aircraft trajectory by ground-based decision support tools (DST) is a major concern in air traffic management (ATM). Aircraft trajectory prediction tools rely on a simplified point-mass aircraft performance model (APM) to make their predictions. Even though the performance coefficients and weight of an aircraft are a vital part of the APM’s predictions and accuracy, these coefficients are proprietary in nature and therefore, unavailable to DSTs. Current ATM research focuses on improving the estimate of some APM parameters by freezing all other coefficients. This simplified approach introduces unwanted sources of bias and negatively impacts the accuracy of the performance model. In this paper, we apply machine learning (ML) techniques for the simultaneous prediction of three key APM parameters (two drag coefficients and the initial aircraft weight). To accomplish this, we employ an ordinary differential equation (ODE) fitting approach to generate optimized APM parameter labels customized to each individual flight record. Subsequently, we train ML models to capture the relationship between the historical data and the optimized APM parameters. Two different ML model solutions are applied and APM coefficients are predicted for unseen flights. The results indicate that the ML models are able to capture the relationship between APM parameters and flight-related features with good accuracy.

trajectory prediction, machine learning, aircraft ↗
NASA NTRSDate not supplied

Analysis and Prediction of VFR Vs IFR Traffic Behavior to Support Uncrewed Aircraft Flight Operations at Regional Airports

Uncrewed Aircraft flight operations at a regional airport will be affected by the uncertainty in the Visual Flight Rules traffic around. This paper analyzes Visual Flight Rules traffic behavior, compares it with Instrument Flight Rules traffic and develops traffic prediction methods to support uncrewed aircraft flight operations. The spatio-temporal distribution of traffic operating under Visual Flight Rules and Instrument Flight Rules was analyzed from one month of historical track data around Fort Worth Alliance airport as a representative regional airport. The traffic behavior was visualized as occupancy maps generated at different altitudes. The Instrument Flight Rules traffic was concentrated in fewer regions of the airspace along structured routes where the risk of interacting with one or more flights reached close to fifty percent in some areas. Visual Flight Rules traffic was spread over more regions, mostly segregated from the Instrument Flight Rules regions, and the risk of interaction was lower reaching up to twenty-five percent on average over the month in some regions. The interaction risk was predicted using predictive occupancy maps over multiple time horizons and conditioned on time and partial observation of traffic in the vicinity. The month-to-month predictability of Visual Flight Rules risk was lower than that of the Instrument Flight Rules traffic, consistently over all the conditions analyzed. However, the prediction and its accuracy were demonstrated to be sensitive to the conditions used. The predictive models generated can be used to support both strategic planning and in-flight decision-making by uncrewed aircraft during flight operations while maintaining an acceptable risk of interacting with other traffic.

VFR↗
NASA NTRSDate not supplied

Analysis and Prediction of VFR Vs IFR Traffic Behavior to Support Uncrewed Aircraft Flight Operations at Regional Airports

Uncrewed Aircraft flight operations at a regional airport will be affected by the uncertainty in the Visual Flight Rules traffic around. This paper analyzes Visual Flight Rules traffic behavior, compares it with Instrument Flight Rules traffic and develops traffic prediction methods to support uncrewed aircraft flight operations. The spatio-temporal distribution of traffic operating under Visual Flight Rules and Instrument Flight Rules was analyzed from one month of historical track data around Fort Worth Alliance airport as a representative regional airport. The traffic behavior was visualized as occupancy maps generated at different altitudes. The Instrument Flight Rules traffic was concentrated in fewer regions of the airspace along structured routes where the risk of interacting with one or more flights reached close to fifty percent in some areas. Visual Flight Rules traffic was spread over more regions, mostly segregated from the Instrument Flight Rules regions, and the risk of interaction was lower reaching up to twenty-five percent on average over the month in some regions. The interaction risk was predicted using predictive occupancy maps over multiple time horizons and conditioned on time and partial observation of traffic in the vicinity. The month-to-month predictability of Visual Flight Rules risk was lower than that of the Instrument Flight Rules traffic, consistently over all the conditions analyzed. However, the prediction and its accuracy were demonstrated to be sensitive to the conditions used. The predictive models generated can be used to support both strategic planning and in-flight decision-making by uncrewed aircraft during flight operations while maintaining an acceptable risk of interacting with other traffic.

VFR↗
DOE OSTI2026

Deposition Height Prediction in Directed Energy Deposition

Using 316L stainless steel as a model material, reduced-order models are developed to predict capture efficiency, deposition height, and site-specific hardness in directed energy deposition. Capture efficiency is predicted over a 15 to 55 pct range using a dimensionless number derived from processing conditions and thermophysical properties. Deposition height is predicted over a 0.3 to 1.3 mm range without in situ sensing or prior training data, using two models based on the same mass and energy-balance principles. Predictions are compared with machine learning approaches. A quantitative relationship links deposition height, primary dendrite arm spacing (PDAS), and hardness: heights of 0.3 to 1.1 mm correspond to PDAS values of 2.7 to 5.1 µm and Vickers hardness (HV) of 160 to 219. Thinner layers cool more rapidly, producing finer microstructures and higher hardness. Samples fabricated with in situ variations in deposition height exhibited up to 55 HV differences between thick and thin regions, demonstrating that local control of deposition height enables predictive, site-specific hardness within a single build. These results establish deposition height prediction as a pathway for a priori process design and property control in directed energy deposition for 316L stainless steel.

Kunkel, William [Univ. of Wisconsin, Madison, WI (↗
DOE OSTI2026

Thermodynamics and its prediction and CALPHAD modeling: Review, state of the art, and perspectives

Thermodynamics is a science concerning the state of a system, whether it is stable, metastable, or unstable, when interacting with its surroundings. The combined law of thermodynamics derived by Gibbs about 150 years ago laid the foundation of thermodynamics. In Gibbs combined law, the entropy production due to internal processes was not included, and the 2nd law was thus practically removed from the Gibbs combined law, so it is only applicable to systems under equilibrium, thus commonly termed as equilibrium or Gibbs thermodynamics. Gibbs further derived the classical statistical thermodynamics in terms of the probability of configurations in a system in the later 1800's and early 1900's. With the quantum mechanics (QM) developed in 1920's, the QM-based statistical thermodynamics was established and connected to classical statistical thermodynamics at the classical limit as shown by Landau in the 1940's. In 1960's the development of density functional theory (DFT) by Kohn and co-workers enabled the QM prediction of properties of the ground state of a system. On the other hand, the entropy production due to internal processes in non-equilibrium systems was studied separately by Onsager in 1930's and Prigogine and co-workers in the 1950's. In 1960's to 1970's the digitization of thermodynamics was developed by Kaufman in the framework of the CALculation of PHAse Diagrams (CALPHAD) modeling of individual phases with internal degrees of freedom. CALPHAD modeling of thermodynamics and atomic transport properties has enabled computational design of complex materials in the last 50 years. Our recently termed zentropy theory integrates DFT and statistical mechanics through the replacement of the internal energy of each individual configuration by its DFT-predicted free energy. The zentropy theory is capable of accurately predicting the free energy of individual phases, transition temperatures and properties of magnetic and ferroelectric materials with free energies of individual configurations solely from DFT-based calculations and without fitting parameters, and is being tested for other phenomena including superconductivity, quantum criticality, and black holes. Those predictions include the singularity at critical points with divergence of physical properties, negative thermal expansion, and the strongly correlated physics. Furthermore, those individual configurations may thus be considered as the genomic building blocks of individual phases in the spirit of the materials genome®. This has the potential to shift the paradigm of CALPHAD modeling from being heavily dependent on experimental inputs to becoming fully predictive with inputs solely from DFT-based calculations and machine learning models built on those calculations and existing experimental data through newly developed and future open-source tools. Furthermore, through the combined law of thermodynamics including the internal entropy production, it is shown that the kinetic coefficient matrix of independent internal processes is diagonal with respect to the conjugate potentials in the combined law, and the cross phenomena that the phenomenological Onsager flux and reciprocal relationships are due to the dependence of the conjugate potential of a molar quantity on nonconjugate molar quantities and other potentials, which can be predicted by the zentropy theory and CALPHAD modeling.

42 ENGINEERING↗
DOE OSTI2025

Transferable predictions of energetic and structural properties for refractory solid solution alloys across chemical compositions

We present a data-efficient approach to train graph neural networks (GNNs) on density functional theory (DFT) data for accurate and transferable predictions of energetic and structural properties of refractory solid solution alloys in the niobium-tantalum-vanadium (Nb-Ta-V) chemical space. We start by training the GNN model only on DFT data that describes refractory binary alloys niobium-tantalum (Nb-Ta), niobium-vanadium (Nb-V), and tantalum-vanadium (Ta-V) to predict formation enthalpy and root mean squared displacement. Once trained, the GNN predictions are tested on DFT data describing refractory ternary alloys Nb-Ta-V. While, unsurprisingly, direct transferability from binary to ternary is not sufficiently accurate, augmenting the training with only 1% of the available ternary data (uniformly distributed across the entire range of chemical compositions) improves significantly the quality of the GNN predictions. For comparison, we assess the transferability in the opposite direction by training GNN models on ternary Nb-Ta-V data and making predictions on binaries Nb-Ta, Nb-V, and Ta-V, which exhibits notably higher predictive errors. The proposed methodology, which favors transferability from lower-component to higher-component alloys, offers an efficient path towards avoiding the curse of dimensionality incurred when collecting DFT data for discovery and design of multi-component disordered alloys.

Density functional theory calculations↗
DOE OSTI2025

CFD modeling of near-wall combustion and unburned methane prediction in natural gas spark ignition engines

Natural gas-powered engines play a critical role in gas drilling, compression, and transmission sectors, but methane (CH 4 ) from engine combustion slip can be significant over their lifespan, contributing to atmospheric pollution and signaling reduced engine efficiency. Here, to address this challenge, computational fluid dynamics (CFD) simulations offer valuable insights into the in-cylinder combustion process, enabling the optimization of combustion strategies and engine designs to minimize unburned CH 4 slip. This study aims to evaluate and improve combustion models for simulating the combustion process and predicting unburned CH 4 concentrations in natural gas spark-ignition (SI) engines, including engines that are part of combined reformer-engine systems. Specifically, the performance of two flamelet-based combustion models—the Extended Coherent Flame Model (ECFM) and the G-equation model—was assessed using experimental engine data collected under varying excess-air ratio (λ) conditions and fuel compositions, including natural gas and syngas blends. In addition, to enhance the predictive capabilities of the G-equation model, a flame-wall interaction (FWI) sub-model was integrated into its framework. The effects of its model parameters, such as quenching and influence distance, on combustion behavior and unburned methane predictions were analyzed in detail. The ECFM tended to predict delayed combustion phasing under diluted mixture conditions, resulting in overprediction of unburned CH 4 concentrations. In contrast, the G-equation model provided reasonable predictions of combustion pressure, while representing higher the CH 4 reduction rate across the operating condition compared to experimental data. Incorporating the FWI sub-model—with the quenching distance calculated based on a pressure-dependent relation (P -0.48 ) and a fixed influence distance of 1.5 mm—further improved the G-equation model’s accuracy in predicting CH 4 reduction rates without compromising its ability to simulate the combustion process.

Combustion model↗
DOE OSTI2025

Utilizing machine learning to predict tensile ductility and yield strength of CoNiV-based multi-principal elements alloys

This study explores the use of machine learning (ML) as a computational tool to accelerate the design of multi-principal element alloys (MPEAs) with improved tensile elongation. An ML model was trained using available experimental data from the literature along with theoretically derived features to predict yield strength (YS) and ductility. A subset of ML-predicted compositions—CoNiVFe, CoNiVTi, CoNiVTiFe, and CoCrNiVTi—was synthesized and evaluated through tensile testing. The ML model underpredicted YS by approximately 20–30 % and overpredicted ductility by 60–70 % for Ti-containing alloys. Microstructural analysis revealed that Ti segregation at interdendritic regions contributed to early fracture, leading to discrepancies in ductility predictions. Ti segregation at these regions likely drives the increased YS due to segregation strengthening. In contrast, the CoNiVFe alloy showed good agreement with both experimental YS and elongation, with prediction errors of ∼10.2 % and ∼20.7 %, respectively. Microstructural characterization revealed minimal segregation in this alloy, suggesting that the ML model can reliably predict the properties of alloys with little to no segregation. These findings highlight the capability of ML in predicting YS with good accuracy but underscore its limitations in capturing defect-driven failure mechanisms such as segregation-induced embrittlement.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Multiphysics simulation of TRISO fuel compacts and the effects of homogenization on silver release predictions

This work studies the impact of explicit and homogenized modeling approaches on the multiphysics simulation of TRistructural ISOtropic (TRISO) fuel compacts in prismatic High Temperature Gas Reactors (HTGRs) and the silver release predictions. TRISO fuel compacts exhibit complex double heterogeneity that significantly affects heat conduction, neutron transport, and fission products release. In this work, we use Cardinal, a multiphysics tool based on the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, to couple neutron transport and heat conduction. OpenMC is used for neutron transport and the MOOSE heat transfer module is used for the heat conduction. Then, we use BISON for the silver release predictions. Two different modeling approaches—explicit modeling of individual TRISO particles and homogenized representation using effective thermal properties—are compared at high TRISO packing fractions (20% and 40%) across varying power densities. Results demonstrate that homogenization significantly under-predicts peak temperatures, for the case of high power/TRISO, there is a difference of 83.73 K in the maximum temperature. Additionally, homogenization underestimates the silver release predictions compared to explicit modeling. Specifically, the temperature and power density differences lead to significant differences in silver release predictions. This work demonstrates the importance of accurately modeling heterogeneity of the TRISO particles to reliably predict fission product release and assess reactor safety margins.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

A novel peridynamics-based approach to predict pharmaceutical tablet robustness

The pharmaceutical drug product development process can be greatly accelerated through the use of modeling and simulation techniques to predict the manufacturability and performance of a given formulation. The anticipation and possible mitigation of tablet damage due to manufacturing stresses represents a specific area of interest in the pharmaceutical industry for predicting formulation and tableting performance. While the finite element method (FEM) has been extensively used for predicting the mechanical behavior of powder material in the compaction processes, a shortcoming of the approach is the inherent difficulty to predict discontinuities (e.g., damage or cracking) within a tablet as FEM is a continuum-based approach. In this work, we propose a novel method utilizing peridynamics (PD), a numerical method that can capture discontinuities such as tablet fracture, to predict the evolution of damage and breakage in pharmaceutical tablets. The approach links (1) the finite element method – to elucidate the behavior of powders during die compaction – with (2) the peridynamics modeling technique – to model the discontinuous nature of damage and predict tablet breakage during the critical stages of unloading and ejection from the compression die. This short communication presents a proof of concept including a workflow to calibrate the linked FEM-PD simulation models. Further, it demonstrates promising results from a preliminary experimental validation of the approach. Following further development, this approach could be used to guide the optimization of compression processes through targeted changes to formulation material properties, compression process conditions, and/or tooling geometries to deliver improved process efficiency and tablet robustness.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Univariate Prediction of Hammett Parameters and Select Relative Reaction Rates Using Loewdin Atomic Charges

Loewdin charges from density functional theory calculations were used here to obtain general, univariate linear correlations for the prediction of experimental Hammett parameters and relative reaction rates. While previous studies have established that Hirshfeld and CM5 charges perform strongly as univariate predictors, the near-ubiquitous Loewdin charges have not yet been evaluated. To this end, we assess the predictive capability of Loewdin charges for three chemical systems. First, we show that Loewdin charges outperform Hirshfeld and CM5 charges for Hammett parameter prediction. Second, we see that Loewdin charges generally perform comparably to Hirshfeld charges for predicting the relative rates of olefin cleavage by photoexcited nitroarenes. The single case of poor correlation, between relative rates and the Loewdin charges on nitrogen sites, is ameliorated when considering the net charge on the NO 2 group. Third, we show that Loewdin, Hirshfeld, and CM5 charges all perform very well for generating correlations for relative reaction rates for C–H activation of 9-(4-X-phenyl)-9H-fluorene substrates by a transition metal catalyst. The equations generated throughout the study enable the prediction of Hammett parameters and relative reaction rates. Finally, these tools can accelerate synthetic and experimental studies by enabling the in silico prediction of uncharacterized chemical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Leveraging Natural Language Processing and Generative Models in Molecular Chemistry: Property Prediction and Novel Compound Generation

The accurate prediction of molecular properties is important for the rational design and the advancement of green chemistry and sustainable materials research. However, the predictive power of traditional computational chemistry methods is limited due to computational restrictions. Here, in this study, we examine an alternative approach to the accurate prediction of properties of organic compounds: natural language processing (NLP)-based molecular embedding. Using viscosity, partition coefficient (log P), and enthalpy of vaporization as test properties through a survey of comprehensive datasets comprising 5695 data points for viscosity, 25 870 data points for log P, and 2296 data points for enthalpy of vaporization. These are important properties for the design of greener, safer, and sustainable chemical processes. Models were trained using NLP methods such as Mol2vec and fine-tuned ChemBERTa, and results were compared with traditional input featurization techniques such as Morgan fingerprints and quantum chemistry derived sigma profiles and DFT features. Among the various machine learning models, Mol2vec demonstrated superior predictive capabilities, achieving the highest correlation coefficient (R 2 = 0.945) and lowest RMSE (0.106 mPa s) for viscosity, as well as high accuracy for log P and enthalpy of vaporization predictions. These findings establish the Mol2vec featurization technique, graph-convolutional neural networks (GCNN), and fine-tuned ChemBERTa model as powerful tools for predictive modeling of organic compounds properties, offering a significant improvement over previously used featurization techniques and opening up strategies for very-high-throughput computational screening. Finally, we integrated ML models with hybrid language-model-based generative adversarial networks (LM-GAN) to generate novel molecular sequences with desirable properties for different research applications. The ability to computationally design solvents with lower viscosity, lower log P, and lower enthalpy of vaporization offers a data-driven route to accelerating the discovery of sustainable alternatives to traditionally toxic solvents.

ChemBERTa↗
DOE OSTI2024

Envisioning U.S. Climate Predictions and Projections to Meet New Challenges

In the face of a changing climate, the understanding, predictions, and projections of natural and human systems are increasingly crucial to prepare and cope with extremes and cascading hazards, determine unexpected feedbacks and potential tipping points, inform long-term adaptation strategies, and guide mitigation approaches. Increasingly complex socio-economic systems require enhanced predictive information to support advanced practices. Such new predictive challenges drive the need to fully capitalize on ambitious scientific and technological opportunities. These include the unrealized potential for very high-resolution modeling of global-to-local Earth system processes across timescales, reduction of model biases, enhanced integration of human systems and the Earth Systems, better quantification of predictability and uncertainties; expedited science-to-service pathways, and co-production of actionable information with stakeholders. Enabling technological opportunities include exascale computing, advanced data storage, novel observations and powerful data analytics, including artificial intelligence and machine learning. Looking to generate community discussions on how to accelerate progress on U.S. climate predictions and projections, representatives of Federally-funded U.S. modeling groups outline here perspectives on a six-pillar national approach grounded in climate science that builds on the strengths of the U.S. modeling community and agency goals. This calls for an unprecedented level of coordination to capitalize on transformative opportunities, augmenting and complementing current modeling center capabilities and plans to support agency missions. Tangible outcomes include projections with horizontal spatial resolutions finer than 10 km, representing extremes and associated risks in greater detail, reduced model errors, better predictability estimates, and more customized projections to support next generation climate services.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Selecting Appropriate Model Complexity: An Example of Tracer Inversion for Thermal Prediction in Enhanced Geothermal Systems

Abstract A major challenge in the inversion of subsurface parameters is the ill‐posedness issue caused by the inherent subsurface complexities and the generally spatially sparse data. Appropriate simplifications of inversion models are thus necessary to make the inversion process tractable and meanwhile preserve the predictive ability of the inversion results. In this study, we investigate the effect of model complexity on fracture aperture inversion and thermal performance prediction in a field‐scale EGS model. Principal component analysis was used to map the aperture field to a low‐dimensional latent space. The complexity of the inversion model was quantitatively represented by the percentage of total variance in the original aperture fields preserved by the latent space. Tracer, pressure and flow rate data were used to invert for fracture aperture through an ensemble‐based inversion method, and the inferred aperture field was used to predict thermal performance. With an over‐simplified aperture model, ensemble collapse occurred. The inverted aperture models failed to resolve necessary flow and transport features, leading to a biased thermal performance prediction. A complex aperture model involved excessive features and was prone to overinterpreting the inversion data. Both the tracer/pressure/flow rate data reproduction and thermal prediction showed significant uncertainties, making it difficult to properly estimate long‐term thermal performance. Fortunately, our results indicate that there exists an appropriate model complexity which can simultaneously match inversion data and predict thermal performance with an acceptable uncertainty. The quality of the fit of tracer data appears to be a useful indicator of such an appropriate model complexity.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

On the Prediction of Aerosol-Cloud Interactions Within a Data-Driven Framework

Aerosol-cloud interactions (ACI) pose the largest uncertainty for climate projection. Among many challenges of understanding ACI, the question of whether ACI can be deterministically predicted has not been explicitly answered. Here we attempt to answer this question by predicting cloud droplet number concentration N c from aerosol number concentration N a and ambient conditions using a data-driven framework. We use aerosol properties, vertical velocity fluctuations, and meteorological states from the ACTIVATE field observations (2020–2022) as predictors to estimate N c . We show that the campaign-wide N c can be successfully predicted using machine learning models despite the strongly nonlinear and multi-scale nature of ACI. However, the observation-trained machine learning model fails to predict N c in individual cases while it successfully predicts N c of randomly selected data points that cover a broad spatiotemporal scale. This suggests that, within a data-driven framework, the N c prediction is uncertain at fine spatiotemporal scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Uncertainty quantification in multivariable regression for material property prediction with Bayesian neural networks

With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including multi-scale and multi-physics nature of materials, intricate interactions between numerous factors, limited availability of large curated datasets, etc. In this work, we introduce a physics-informed Bayesian Neural Networks (BNNs) approach for UQ, which integrates knowledge from governing laws in materials to guide the models toward physically consistent predictions. To evaluate the approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of creep tests demonstrates that this method produces point predictions and uncertainty estimations that are competitive or exceed the performance of conventional UQ methods such as Gaussian Process Regression. Additionally, we evaluate the suitability of employing UQ in an active learning scenario and report competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2025

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↗