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At least 631 records · Page 35

Effects of HLA single chain trimer design on peptide presentation and stability

MHC class I “single-chain trimer” molecules, coupling MHC heavy chain, β 2 -microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.

59 BASIC BIOLOGICAL SCIENCES↗

Improving Building Footprint Extraction Using NAIP and 3DEP Lidar Derived Features with Deep Learning

Accurate building footprint extraction is critical for applications ranging from population estimation to disaster management. Although optical imagery provides detailed spectral information, it often struggles with shadows, occlusions, and background clutter in dense urban environments. Lidar data, by contrast, offer precise elevation and structural attributes but face challenges such as variable point density and noise. This study integrates multispectral imagery from the U.S. Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) with lidar-derived feature height and intensity from the U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) to improve footprint extraction using a U-Net–based deep learning model. A six-band input stack (RGB, near-infrared, height, intensity) was developed, normalized, and tiled for training and evaluation against Microsoft Global Building Footprints (GBF). Results from the Houston, TX test site show that the six-band model achieved a precision of 0.86, recall of 0.88, F1 score of 0.87, and Intersection-over-Union (IoU) of 0.76, consistently outperforming four-band baselines by reducing false positives while maintaining sensitivity. Predictions on withheld Houston tiles confirmed strong within-region generalization, yielded a precision of 0.78, recall of 0.81, F1 score of 0.79, and IoU of 0.66. Qualitative analysis further revealed limitations stemming from both training label quality and vegetation–building confusion. These findings demonstrate the complementary value of integrating spectral and structural information for robust building footprint extraction and how domain adaptation strategies can be used to enhance cross-regional transferability.

Liu, Jung Kuan [United States Geological Survey (U↗

Mathematical methods for neutrino cross-section extraction

Precise modeling of neutrino-nucleus scattering is becoming increasingly important as accelerator-based oscillation experiments seek definitive answers to open questions about neutrino properties. To guide the needed model refinements, a growing number of experimental collaborations are pursuing a wide-ranging program of neutrino interaction measurements at GeV energies. A key step in most such analyses is cross-section extraction, in which measured event counts are corrected for background contamination and imperfect detector performance to yield cross-section results that are directly comparable to theoretical predictions. In this paper, I review the major approaches to cross-section extraction in the literature using representative examples from the MINERvA, MicroBooNE, and T2K experiments. I then present two mathematical techniques, blockwise unfolding and the conditional covariance background constraint, which overcome some limitations of typical cross-section extraction procedures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Revisiting the Role of Entropy for Charge Separation in 1D Pi-Conjugated Semiconductors

Free carrier generation in organic donor/acceptor heterojunctions and redox-doped organic semiconductors is poorly understood, since assumed tight electron-hole binding conflicts with observed high free carrier yields. Cornerstone analyses that have guided the field for over 15 years predict that entropy can stabilize free charges in 2D and 3D pi-conjugated semiconductors but not in 1D systems. Here, the impact of entropy on charge generation in 1D pi-conjugated semiconductors is revisited by exploiting a greatly simplified system where enthalpy considerations alone should not allow for free charge generation. Noncontact solution-phase microwave conductivity is used to investigate the carrier density-dependent conductivity and dielectric constant in isolated chemically doped semiconducting single-walled carbon nanotubes in a low-dielectric solvent. Dopant chemical structure dramatically influences the carrier density-dependent complex conductivity, with bulky dopants facilitating carrier escape even at carrier densities below one carrier per nanotube. Three distinct numerical calculations show that entropic stabilization dramatically lowers the Gibbs energy barrier for free charge generation, explaining the high yield of free carriers, even in 1D. This renewed understanding of entropy's role in carrier generation has important implications for designing organic electronic devices-such as solar cells and thermoelectric energy harvesters-for enhanced carrier yield, conductivity, and performance.

36 MATERIALS SCIENCE↗

Spatial biases of information influence global estimates of soil respiration: how can we improve global predictions?

Soil respiration (Rs), the efflux of CO2 from soils to the atmosphere, is a major component of the terrestrial carbon cycle, but is poorly constrained from regional to global scales. The global soil respiration database (SRDB) is a compilation of in-situ Rs observations from around the globe that has been consistently updated with new measurements over the past decade. It is unclear whether the addition of data to new versions of the SRDB has produced better-constrained global Rs estimates. We compared two versions of the SRDB (v3.0 n=5173 and v5.0 n=10366) to determine how additional data influenced the global sum and uncertainty of Rs as predicted by a quantile regression forest model. A model parameterized using SRDBv3 yielded a global Rs sum of 88.6 Pg C yr-1, and associated uncertainty of 29.9 (mean absolute error) and 57.9 (standard deviation) Pg C yr-1, whereas parameterization using SRDBv5 yielded 96.5 Pg C yr-1 and associated uncertainty of 30.2 (mean average error) and 73.4 (standard deviation) Pg C yr-1. Empirically estimated global heterotrophic respiration (Rh) from v3 and v5 were 49.9-50.2 (mean 50.1) and 53.3-53.5 (mean 53.4) Pg C yr-1, respectively. Interestingly, SRDBv5’s inclusion of new data from underrepresented regions (e.g., Asia, Africa, South America) thus resulted in overall higher model uncertainty. The SRDBv5 is still biased towards northern latitudes and temperate zones, so we tested that an optimized global distribution of Rs measurements resulted in a global sum of 96.4 ± 21.4 Pg C yr-1 and lower model uncertainty. These results support current global estimates of Rs but highlight spatial inconsistencies that influence model parameterization and interpretation that should be addressed to improve regional- to global-scale predictions.

Stell, Emma↗

Machine Learning for Mapping Multipactor Susceptibility in RF Systems: Capabilities and Generalization Constraints

Multipactor is a surface-driven electron avalanche phenomenon that degrades the performance and reliability of radio-frequency (RF) systems in particle accelerator and vacuum electronics applications. Multipactor behavior in a given device structure is conventionally assessed through susceptibility charts, which provide a parameter-space characterization of the instability. In this work, we assess the capabilities of machine-learning (ML) models to learn and predict such susceptibility charts and analyze the constraints governing their generalization across materials. Using a simulation-derived dataset spanning six distinct secondary-electron-yield material profiles in a canonical two-surface planar geometry, we train supervised regression models and artificial neural networks to predict the time-averaged electron growth rate, δavg, across the relevant parameter space. Model performance is evaluated using metrics that explicitly probe the structure of susceptibility charts, including Intersection over Union, Structural Similarity Index, and correlation analysis. Tree-based ensemble models outperform neural-network models in reconstructing susceptibility regions and in generalizing across material domains. Principal-component analysis reveals disjoint material feature distributions, indicating that the piecewise mode structure of multipactor susceptibility is difficult to represent with a single global model and that generalization is constrained by data coverage rather than by model complexity. An exhaustive reduced-coverage study further shows that sparse material-space coverage can yield mean performance in the same general range but producing large variability in the susceptibility-region overlap. These results clarify the capabilities of ML-based surrogate models for parameter-space characterization of multipactor discharge. They also provide guidance for their appropriate use in RF system design.

43 PARTICLE ACCELERATORS↗

Free-field Ground Motion Induced by Underground Explosions at Aqueduct Mesa with Predictions for Physical Experiment One (PE1)

We fit standard power-law models for ground acceleration and particle velocity using scaled ground motion observations from underground nuclear explosions at Aqueduct Mesa on the Nevada National Security Site. The models are then validated using small-scale high-explosive (HE) test data from nearby Rainier Mesa. The comparison between model predictions and observations is good and can be made more favorable if the assumed yield for the HE tests are doubled. Further validation is made with a numerical experiment that additionally shows a transition in ground motion attenuation to elastic propagation (1 = r). An extended model is provided to incorporate the long-range transition in attenuation, which results in increased ground motions at farther range. We then make predictions for the field experiment, Physical Experiment One (PE1), to take place in P-tunnel on Aqueduct Mesa, and suggest that the models could be used in planning various operations for PE1.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

UniverseMachine: Predicting Galaxy Star Formation over Seven Decades of Halo Mass with Zoom-in Simulations

In this work, we apply the empirical galaxy–halo connection model UniverseMachine to dark-matter-only zoom-in simulations of isolated Milky Way (MW)–mass halos, along with their parent cosmological simulations. This application extends UniverseMachine predictions into the ultrafaint dwarf galaxy regime (10 2 M ⊙ ≤ M * ≤ 10 5 M ⊙) and yields a well-resolved stellar mass–halo mass (SMHM) relation over the peak halo mass range of 10 8 –10 15 M ⊙. The extensive dynamic range provided by the zoom-in simulations allows us to assess specific aspects of dwarf galaxy evolution predicted by UniverseMachine. In particular, although UniverseMachine is not constrained for dwarf galaxies with M * ≲ 10 8 M ⊙, our predicted SMHM relation is consistent with that inferred for MW satellite galaxies at z = 0 using abundance matching. However, UniverseMachine predicts that nearly all galaxies are actively star-forming below M * ~ 10 7 M ⊙ and that these systems typically form more than half of their stars at z ≲ 4, which is discrepant with the star formation histories of Local Group dwarf galaxies that favor early quenching.

79 ASTRONOMY AND ASTROPHYSICS↗

Simulated impact of fill tube geometry on recent high-yield implosions at the National Ignition Facility

Inertial confinement fusion capsules fielded at the National Ignition Facility are filled with deuterium and tritium fuel by means of a fill tube. The fill tube introduces a low-density pathway into the fuel region of the capsule that allows high Z contaminant to invade the hot spot during the course of the implosion. A recent series of nominally identical high-yield implosions on the NIF has exhibited significant variability in performance. We evaluate the impact of the fill tube in these implosions computationally to determine whether variations in fill tube geometry could have contributed to this variability. The main contrast between the fill tube geometry in the six shots was the outer diameter of the capsule bore hole, a conical hole into which the fill tube is inserted. In our simulations, the geometry of the bore hole can play a significant role in the development of nonlinear flows seeded by the fill tube. Additionally, we find that the amount of space between the bore hole and the fill tube is the primary factor that determines the amount of contaminant jetted into the hot spot by the fill tube and, in turn, the level of yield reduction due to the fill tube in our simulations. As a consequence, some capsules with 5 μm fill tubes are predicted to outperform capsules with 2 μm fill tubes. We also find that micrometer-scale changes to bore hole size can impact fusion yields by up to four times near the ignition threshold. Nevertheless, simulation trends do not reproduce experimental yield trends, suggesting that the fill tube geometry was not the primary factor contributing to the observed variability in performance and that the fill tube could be masking sensitivity to other asymmetries such as other micrometer-scale capsule defects like voids that were not included in our simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Predicting ptychography probe positions using single-shot phase retrieval neural network

Ptychography is a powerful imaging technique that is used in a variety of fields, including materials science, biology, and nanotechnology. However, the accuracy of the reconstructed ptychography image is highly dependent on the accuracy of the recorded probe positions which often contain errors. These errors are typically corrected jointly with phase retrieval through numerical optimization approaches. When the error accumulates along the scan path or when the error magnitude is large, these approaches may not converge with satisfactory result. We propose a fundamentally new approach for ptychography probe position prediction for data with large position errors, where a neural network is used to make single-shot phase retrieval on individual diffraction patterns, yielding the object image at each scan point. The pairwise offsets among these images are then found using a robust image registration method, and the results are combined to yield the complete scan path by constructing and solving a linear equation. We show that our method can achieve good position prediction accuracy for data with large and accumulating errors on the order of 10 2 pixels, a magnitude that often makes optimization-based algorithms fail to converge. For ptychography instruments without sophisticated position control equipment such as interferometers, our method is of significant practical potential.

47 OTHER INSTRUMENTATION↗

Redox Potentials for Hydrogen Species in Acetonitrile and Tetrahydrofuran

The properties of the fundamental hydrogen species, proton (H+), hydrogen atom (H•), and hydride anion (H-) are critical to a vast range of chemical processes, yet their thermodynamic properties in nonaqueous solvents are not well established. A hybrid supermolecule-continuum approach is used to predict the Gibbs free energies of solvation (?G°solv) and standard redox potentials (E°) for the 2H+/H2 and H•/H- couples in acetonitrile (MeCN) and tetrahydrofuran (THF) following the approach previously used for water. Gas phase geometry optimizations were done using density functional theory (DFT) with the ?B97XD functional, Møller-Plesset second-order perturbation theory (MP2) with augmented correlation-consistent basis sets and composite-correlated molecular orbital theory (G3MP2 and G3MP2B3). Additional single point calculations in gas phase were performed for H- affinity for MeCN and THF at the coupled cluster CCSD(T) level using MP2 geometries. Solvation was included using the self-consistent reaction field SMD model. For H+, the ?G°solv values are predicted to be -252.2 kcal/mol in MeCN and -261.0 kcal/mol in THF. The redox potentials for the 2H+/H2 couple are +0.49 V in MeCN and +0.11 V in THF relative to the aqueous SHE, consistent with the available experimental data. The ?G°solv for H- is predicted to be -80 kcal/mol in MeCN and -68 in THF, and for H•, ?G°solv is predicted to be -1.3 kcal/mol in THF and -2.0 kcal/mol in MeCN. These solvation energies yield respective calculated redox potentials for the H•/H- couple of -0.14 V in MeCN and -0.68 V in THF relative to the aqueous SHE. H2 solvation is slightly exergonic in MeCN (-3.3 kcal/mol) and near thermoneutral in THF (+1.3 kcal/mol). The pKa(H2) is predicted to be 45.4 in MeCN and 47.8 in THF. The proton-coupled electron transfer (PCET) accounting term CG was evaluated giving values on the ferrocene scale within approximately 2 kcal/mol of literature in both solvents. These results provide benchmarks for hydrogen redox chemistry in MeCN and THF and improve consistency across E°, ?G°solv, pKa, and CG. These results provide benchmarks for hydrogen redox chemistry in nonaqueous media challenging previous estimates based on indirect extrapolations and assumptions.

Duda, Damian P.↗

Sensitivity of Fine‐Resolution Urban Heat Island Simulations to Soil Moisture Parameterization

ABSTRACT Urban areas experience the impact of natural disasters, such as heatwaves and flash floods, disparately in different neighbourhoods across a city. The demand for precise urban hydrometeorological and hydroclimatological modelling to examine this disparity, and the interacting challenges posed by climate change and urbanisation, has thus surged. The Weather Research and Forecasting (WRF) model has served such operational and research purposes for decades. Recent advancements in WRF, including enhanced numerical schemes and sophisticated urban atmospheric‐hydrological parameterizations, have empowered the simulation of urban geophysical processes at high resolution (~1 km), but even this resolution misses significant urban microclimate variability. This study applies the large‐eddy simulations (LES) mode within WRF, coupled with single‐layer urban canopy models (SLUCM), to enable even finer‐scale modelling (150 m) of the Urban Heat Island (UHI) effect in the Baltimore metropolitan area. We run nine scenarios to evaluate various methods of initializing soil moisture and various spinup lead times, and to assess the impact of WRF's Mosaic approach in depicting subgrid‐scale processes. We evaluate the scenarios by comparing the WRF simulated land surface temperature (LST) against Landsat LST and the WRF simulated hourly 2‐m air temperatures (AT) with observations from eight weather stations across the domain. Results underscore the paramount influence of the lead spinup time on the spatiotemporal distribution of simulated soil moisture, consequently shaping WRF's efficacy in predicting the UHI. Furthermore, interpolating soil moisture‐related parameters from the parent for child domain initialization yields a notable reduction in mean and root‐mean‐squared errors. This improvement was particularly evident in simulations with the longest spinup time, affirming the importance of carefully designing the initialization of soil moisture for improved urban temperature predictions.

Talebpour, Mahdad↗

Protein model quality assessment using rotation–equivariant transformations on point clouds

Machine learning research concerning protein structure has seen a surge in popularity over the last years with promising advances for basic science and drug discovery. Working with macromolecular structure in a machine learning context requires an adequate numerical representation, and researchers have extensively studied representations such as graphs, discretized 3D grids, and distance maps. As part of CASP14, we explored a new and conceptually simple representation in a blind experiment: atoms as points in 3D, each with associated features. These features—initially just the basic element type of each atom—are updated through a series of neural network layers featuring rotation-equivariant convolutions. Starting from all atoms, we further aggregate information at the level of alpha carbons before making a prediction at the level of the entire protein structure. We find that this approach yields competitive results in protein model quality assessment despite its simplicity and despite the fact that it incorporates minimal prior information and is trained on relatively little data. As a result, its performance and generality are particularly noteworthy in an era where highly complex, customized machine learning methods such as AlphaFold 2 have come to dominate protein structure prediction.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting demand for hydrogen station fueling

Full function hydrogen stations are a reality; fuel cell electric vehicle drivers can pull up to commercial fueling stations and receive 3–5 kg in less than 5 min, for an approximately 300-mile range. The demand for hydrogen is increasing, driven by an increase in the fueling of public and private fuel cell vehicles. This study describes the development and value of a model that simulates stochastic future demand at a hydrogen filling station. The predictive hydrogen demand model described in this article is trained from mathematical models constructed from actual hydrogen fill count, amount, and frequency data. Future fill probabilities inform the hour-by-hour demand profile and the station state of either “available, ready to fill” or “available, filling”. For example, a prediction for a station generally dispensing 5,000 kg a week on a Friday afternoon at 4 p.m. is 16 fills, totaling 48.7 kg, with a 0.52 proportion of time spent in “available, filling” state yielding 31 min of filling time. This is a first-of-its kind, published study on predicting future hydrogen demand by the time of day (e.g., hour-by-hour intervals) and day of week. This study can be used for hydrogen station requirements and operation and maintenance strategies and to assess the impact of demand variations and scenarios. Finally, this article presents the current status of hydrogen demand, the model development methods, a set of sample results. Discussion and conclusions concentrate on the value and use of the proposed model.

08 HYDROGEN↗

Machine learning approaches for influenza A virus risk assessment identifies predictive correlates using ferret model in vivo data

In vivo assessments of influenza A virus (IAV) pathogenicity and transmissibility in ferrets represent a crucial component of many pandemic risk assessment rubrics, but few systematic efforts to identify which data from in vivo experimentation are most useful for predicting pathogenesis and transmission outcomes have been conducted. To this aim, we aggregated viral and molecular data from 125 contemporary IAV (H1, H2, H3, H5, H7, and H9 subtypes) evaluated in ferrets under a consistent protocol. Three overarching predictive classification outcomes (lethality, morbidity, transmissibility) were constructed using machine learning (ML) techniques, employing datasets emphasizing virological and clinical parameters from inoculated ferrets, limited to viral sequence-based information, or combining both data types. Among 11 different ML algorithms tested and assessed, gradient boosting machines and random forest algorithms yielded the highest performance, with models for lethality and transmission consistently better performing than models predicting morbidity. Comparisons of feature selection among models was performed, and highest performing models were validated with results from external risk assessment studies. Our findings show that ML algorithms can be used to summarize complex in vivo experimental work into succinct summaries that inform and enhance risk assessment criteria for pandemic preparedness that take in vivo data into account.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of ACHILLES and GENIE Observables for DUNE-PRISM and the SBN Program, with New 2p2h Predictions

The DUNE near detector LAr-TPC can be moved to different off-axis positions to sample different neutrino fluxes, which in turn will yield different cross section distributions for observables. Several DUNE ND off axis locations were simulated using GENIE and ACHILLES, and generator differences and FSI contributions were examined for various observables. Additionally, the predictions were compared with those of existing experiments, and it is shown that the DUNE ND 20m off axis predictions are similar to that of MicroBooNE for various observables. Finally, the 2p2h interaction mode was simulated for ACHILLES for the first time for ICARUS, and a preliminary comparison is made to MicroBooNE data and simulations from different event generators.

Dumont, Daniel [Fermilab]↗

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

STRUCTURAL MODELING TO SUPPORT POST-YIELD ACCEPTANCE CRITERIA FOR SPENT NUCLEAR FUEL CLADDING

Spent nuclear fuel (SNF) is evaluated for structural failure during storage and transportation scenarios. The U.S. Department of Energy’s Spent Fuel and Waste Science and Technology (SFWST) program has sponsored significant research in quantifying mechanical loads on SNF during storage and transportation scenarios using experimental and modeling methods. The SFWST program has also performed significant research on measuring the mechanical behavior of irradiated SNF as defueled cladding segments and cladding with fuel pellets to measure composite behavior. This paper considers some of the key material data from the Sibling Pin testing and uses structural modeling and analysis methods that have been informed by testing to consider post-yield acceptance criteria for SNF cladding structural analysis. Test data published by Oak Ridge National Laboratory (ORNL) and Pacific Northwest National Laboratory (PNNL) are the foundation for informing the material behavior of the models developed in this study. In particular, four-point bend (4PB) tests of fueled and defueled cladding segments provide significant information about the bending failure mode of SNF. ORNL’s 4PB test data is on fueled cladding segments, so the composite behavior of SNF is demonstrated. This paper describes PNNL’s coincident beam model that was developed to approximate the composite behavior of SNF. This paper also presents PNNL’s structural dynamic finite element models of a cask tip-over scenario, which is predicted to cause the strongest mechanical loads on SNF of all postulated storage and transportation scenarios. SNF bending loads predicted in the cask tip-over scenario and cladding acceptance criteria beyond yield are considered, with justification based on the Sibling Pin test data. ASME Boiler and Pressure Vessel code stress intensity limits are also considered. The ultimate goal of this work is to aid in the justification of structural acceptance criteria for SNF cladding beyond the cladding’s irradiated yield strength for use in structural analysis of all storage and transportation scenarios.

Klymyshyn, Nicholas A.↗