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DOE OSTI2023

Language Barriers in Organismal Biology: What Can Journals Do Better?

Synopsis In the field of organismal biology, as in much of academia, there is a strong incentive to publish in internationally recognized, highly regarded, English-language journals to promote career advancement. This expectation has created a linguistic hegemony in scientific publishing, whereby scholars for whom English is an additional language face additional barriers to achieving the same scientific recognition as scholars who speak English as a first language. Here, we surveyed the author guidelines of 230 journals in organismal biology with impact factors of 1.5 or greater for linguistically inclusive and equitable practices and policies. We looked for efforts that reflect first steps toward reducing barriers to publication for authors globally, including the presence of statements that encouraged submissions from authors of diverse nationalities and backgrounds, policies regarding manuscript rejection based on perceived inadequacies of the English language, the existence of bias-conscious reviewer practices, whether translation and editing resources or services are available, allowance for non-English abstracts, summaries, or translations, and whether journals offer license options that would permit authors (or other scholars) to translate their work and publish it elsewhere. We also directly contacted a subset of journals to verify whether the information on their author guidelines page accurately reflects their policies and the accommodations they would make. We reveal that journals and publishers have made little progress toward beginning to recognize or reduce language barriers. Counter to our predictions, journals associated with scientific societies did not appear to have more inclusive policies compared to non-society journals. Many policies lacked transparency and clarity, which can generate uncertainty, result in avoidable manuscript rejections, and necessitate additional time and effort from both prospective authors and journal editors. We highlight examples of equitable policies and summarize actions that journals can take to begin to alleviate barriers to scientific publishing.

Nolde-Lopez, B.↗

DOE OSTI2020

Constraining level densities through quantitative correlations with cross-section data

The adopted level densities (LD) for the nuclei produced through different reaction mechanisms significantly impact the accurate calculation of cross sections for the different reaction channels. Many common LD models make simplified assumptions regarding the overall behavior of the total LD and the intrinsic spin and parity distributions of the excited states. However, very few experimental constraints are taken into account in these models: LD at neutron separation energy coming from average spacings of s- and p-wave resonances ( D 0 and D 1 , respectively) whenever they have been previously measured, and the sometimes subjective extrapolation of discrete levels. These, however, constrain the LD only in very specific regions of excitation energy, and for specific spins and parities. This work aims to establish additional experimental constraints on LD through quantitative correlations between cross sections and LD. This allows for fitting and the determination of detailed structures in LD. For this we use the microscopic Hartree-Fock-Bogoliubov (HFB) LD as a starting point as the HFB LD provide a more realistic spin and parity distributions than phenomenological models such as Gilbert-Cameron (GC). We then associate variations predicted by the HFB model with the structure observed in double-differential cross sections at low outgoing neutron energy, a region that is dominated by the LD input. We also use (n, p) on 56 Fe , as an example case where angle-integrated cross sections are extremely sensitive to LD. For comparison purposes we also perform calculations with the GC model. With this approach we are able to perform fits of the LD based on actual experimental data, constraining the model and ensuring its consistency. This approach can be particularly useful in extrapolating the LD to nuclei for which high-excited discrete levels and/or values of D 0 or D 1 are unknown. Finally, it also predicts neutron-induced inelastic γ cross sections that in some cases can differ significantly from more standard phenomenological LD models such as GC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Measurement of muon pairs produced via γ γ scattering in nonultraperipheral Pb + Pb collisions at s N N = 5.02 TeV with the ATLAS detector

Results of a measurement of dimuon photoproduction in nonultraperipheral Pb + Pb collisions at √ s NN = 5.02 TeV are presented. The measurement uses ATLAS data from the 2015 and 2018 Pb + Pb data-taking periods at the LHC with an integrated luminosity of 1.94 nb –1 . The γγ → μ + μ – pairs are identified via selections on pair momentum asymmetry and acoplanarity. Differential cross sections for dimuon production are measured in different centrality, average muon momentum, and pair rapidity intervals as functions of acoplanarity and k ⊥ , the transverse momentum kick of one muon relative to the other. Measurements are also made as a function of the rapidity separation of the muons and the angle of the muon pair relative to the second-order event plane to test whether magnetic fields generated in the quark-gluon plasma affect the measured muons. A prior observation of a centrality-dependent broadening of the acoplanarity distribution is confirmed. Furthermore, the improved precision of the measurement reveals a depletion in the number of pairs having small acoplanarity or k ⊥ values in more central collisions. The acoplanarity distributions in a given centrality interval are observed to vary with the mean p T of the muons in the pair, but the k ⊥ distributions do not. Comparisons with recent theoretical predictions are made. The predicted trends associated with effects of magnetic fields on the dimuons are not observed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Adaptive Computing for Scale-Up Problems

Adaptive Computing is an application-agnostic outer loop framework to strategically deploy simulations and experiments to guide decision making for scale-up analysis. Resources are allocated over successive batches, which makes the allocation adaptive to some objective such as optimization or model training. The framework enables the characterization and management of uncertainties associated with predictive models of complex systems when scale-up questions lead to significant model extrapolation. A key advancement of this framework is its integration of multi-fidelity surrogate modeling, uncertainty management, and automated orchestration of various computing and experimentation resources into a single integrated software package. This enables efficient multi-fidelity modeling across multiple computing resources by incorporating real-world constraints such as relative queue times and throughput on individual machines into the multi-fidelity sampling decision. We discuss applications of this framework to problems in the renewable energy space, including biofuels production, material synthesis, perovskite crystal growth, and building electrical loads.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

The Geochemistry and Microbial Ecology of Produced Waters from Three Different Unconventional Oil and Gas Regions

One of the most significant challenges associated with predicting reservoir fluid properties is accounting for the effect of microbial activity, which catalyzes chemical reactions that lead to corrosion and sulfide release during or after hydraulic fracturing operations. The current understanding of microbial populations living in hydraulic fracturing systems is based on a limited number of samples and well sites, necessitating additional research efforts to confirm preliminary findings and identify factors driving the microbial ecology. The project objective is to profile the geochemistry and microbiology of three different oil and gas basins to order increase the understanding of how microbial activity affects reservoir fluids.

Lipus, Daniel↗

DOE OSTI2026

Hyperspectral traits (TSWIFT) UC Davis Populus trichocarpa Common Garden

This dataset provides tower-based hyperspectral remote sensing measurements of individualPopulustrees collected with the TSWIFT system to support genetic analyses of canopy photosynthetic traits over time under drought. From 2022-08-18 to 2022-10-18, spectra were repeatedly acquired from the same targeted canopy area of each tree using fixed pointing coordinates. The dataset includes hyperspectral measurements from 400–900 nm and ultraspectral measurements from 730–780 nm. These spectra enable calculation of reflectance-based vegetation indices and other spectral traits, including solar-induced fluorescence (SIF) retrievals from the ultraspectral region. Because measurements were collected exclusively over a drought treatment plot, derived phenotypes are intended for drought-context genetic association and prediction analyses.

09 BIOMASS FUELS↗

DOE OSTI2022

Harnessing Biomineralization Potential of Metal-Sequestering Bacteria for Rare Earth Elements (REE) Material Synthesis

Extremophilic methylotrophs, such as Methylotuvimicrobium alcaliphilum 20ZR are known for their natural ability to carry out REE capture and uptake. It has been predicted that proteins associated with surface layers facilitate transport and homeostasis of essential metals. Indeed, electron microscopic analysis coupled with antibody staining revealed that cell envelop of metal-grown M. alcaliphilum 20ZR contains metal-binding proteins in the base of the cup-shaped structures of S-layers. While less explored, the proteins associated with S-layers are also predicted to contribute to scavenging of other minerals essential for core metabolism. Here, we employed bottom-up proteomic study to compare the protein content of S-layer fractions of M. alcaliphilum 20ZR cultures grown in the presence and absence trace metals to identify putative components REE-scavenging machinery.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Longitudinal genome-wide association study reveals early QTL that predict biomass accumulation under cold stress in sorghum

Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy due to its high biomass yields. However, early growth phases of sorghum are sensitive to cold stress, limiting its planting in temperate environments. Cold adaptability is crucial for cultivating bioenergy and grain sorghum at higher latitudes and elevations, or for extending the growing season. Identifying genes and alleles that enhance biomass accumulation under early cold stress can lead to improved sorghum varieties through breeding or genetic engineering. We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP includes diverse accessions with dense genotyping and varied racial, geographical, and phenotypic backgrounds. Daily, non-destructive imaging allowed temporal analysis of growth-related traits and water use efficiency (WUE). A genome-wide association study (GWAS) was performed to identify genomic intervals and genes associated with cold stress response. The GWAS identified transient quantitative trait loci (QTL) strongly associated with growth-related traits, enabling an exploration of the genetic basis of cold stress response at different developmental stages. This analysis of daily growth traits, rather than endpoint traits, revealed early transient QTL predictive of final phenotypes. The study identified both known and novel candidate genes associated with growth-related traits and temporal responses to cold stress. The identified QTL and candidate genes contribute to understanding the genetic mechanisms underlying sorghum's response to cold stress. These findings can inform breeding and genetic engineering strategies to develop sorghum varieties with improved biomass yields and resilience to cold, facilitating earlier planting, extended growing seasons, and cultivation at higher latitudes and elevations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

An overview of wind-energy-production prediction bias, losses, and uncertainties

Abstract. The financing of a wind farm directly relates to the preconstruction energy yield assessments which estimate the annual energy production for the farm. The accuracy and the precision of the preconstruction energy estimates can dictate the profitability of the wind project. Historically, the wind industry tended to overpredict the annual energy production of wind farms. Experts have been dedicated to eliminating such prediction errors in the past decade, and recently the reported average energy prediction bias is declining. Herein, we present a literature review of the energy yield assessment errors across the global wind energy industry. We identify a long-term trend of reduction in the overprediction bias, whereas the uncertainty associated with the prediction error is prominent. We also summarize the recent advancements of the wind resource assessment process that justify the bias reduction, including improvements in modeling and measurement techniques. Additionally, because the energy losses and uncertainties substantially influence the prediction error, we document and examine the estimated and observed loss and uncertainty values from the literature, according to the proposed framework in the International Electrotechnical Commission 61400-15 wind resource assessment standard. From our findings, we highlight opportunities for the industry to move forward, such as the validation and reduction of prediction uncertainty and the prevention of energy losses caused by wake effect and environmental events. Overall, this study provides a summary of how the wind energy industry has been quantifying and reducing prediction errors, energy losses, and production uncertainties. Finally, for this work to be as reproducible as possible, we include all of the data used in the analysis in appendices to the article.

17 WIND ENERGY↗

DOE OSTI2025

PERCEPTIVE: an R shiny $\underline{p}$ipelin$\underline{e}$ for the p$\underline{r}$edi$\underline{c}$tion of $\underline{ep}$igenetic modula$\underline{t}$ors $\underline{i}$n no$\underline{v}$el sp$\underline{e}$cies

Epigenetic processes are central to regulating gene expression, genome stability, and metabolic function across the tree of life; yet, their roles remain underexplored in microalgae, especially as new species continue to be identified and characterized. This is likely due to the cumbersome nature and species-dependent attributes of epigenetic wet-lab methodologies, which preclude the rapid identification of epigenetic modifications and modulators. However, there is high conservation of epigenetic processes from budding yeast to humans; in many cases, one may infer how behavior and function are epigenetically regulated in novel species by identifying epigenetic modulators, or the proteins responsible for conferring epigenetic modifications. Here, to this end, we have developed a graphical software package, titled PERCEPTIVE (pipeline for the prediction of epigenetic modulators in novel species). This platform solely uses the genomic sequence of an algal species, and preexisting information from other model organisms, to predict the epigenetic modulators and associated modifications in algae. Predictions are presented to the user in a graphical interface, which provides literature-based interpretation of results, enabling users to quickly understand potential epigenetic processes in their algal species of interest and plan follow-up experiments. To test PERCEPTIVE, we predicted epigenetic modulators in several feedstock candidate algae species. To validate these predictions, wet-lab studies were performed, including mass spectrometry; these results underscore the high accuracy of PERCEPTIVE predictions. Overall, PERCEPTIVE represents a powerful in silico tool for the research and manipulation of algal species, which does not require a priori knowledge of epigenetics and is accessible to a broad set of investigators.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Resiliency-Driven Proactive Distribution System Reconfiguration With Synchrophasor Data

Measuring and enabling resiliency of electric distribution systems with increasing weather and cyber events are important. Some of the extreme events (e.g. Earthquakes, Hurricanes) and associated paths are predicted and monitored closely in advance and allow to take pre-event proactive control actions. The Distribution Phasor Measurement Units (D-PMUs) provide new opportunities and supporting such proactive actions. Here, a synchrophasor based resiliency driven pre-event reconfiguration can ensure minimizing impact of the expected event on the power distribution system and associated performance. However, the D-PMUs will also face challenges in terms of data quality similar to the transmission PMUs. The focus of this paper is to provide data mining approaches for anomaly detection in D-PMUs and proposing resiliency-driven pre-event reconfiguration with islanding as a proactive mechanisms to minimize the impact of adverse events on system using processed synchrophasors data. Results are validated for real industrial feeders and test cases with satisfactory response

controlled islanding↗

DOE OSTI2022

Bat554: Machine Learning for Accelerated Life Prediction and Cell Design

This presentation describes work associated with the early prediction of life and failure modes using machine learning. Key areas which will be highlighted are the generation of synthetic data, the use of deep learning and other machine learning models and the use of machine learning to train life prediction models.

25 ENERGY STORAGE↗

DOE OSTI2022

Analysis of the laser welding keyhole using inline coherent imaging

Laser beam welding is a widely used fusion welding process in many industrial applications such as automotive, aerospace, energy, defense, and medical products. Industry has a fundamental need to model the laser welding process to minimize experimental testing and improve confidence in production welds. However, computational models attempting to predict weld formation are limited by an incomplete understanding of the beam-material interactions. As a consequence, these models do not accurately predict the mechanisms associated with laser weld formation. To improve the current state of prediction capabilities, it is vital to better detect/measure the physical aspects of the weld pool during high energy density welding. In this work, a novel real-time laser weld monitoring device using inline coherent imaging (ICI) was used to provide a fundamental understanding of laser weld formation via vaporization. The objective of this work was to investigate and quantify the relationship relating laser weld parameters and the vapor capillary (keyhole) through a state-of-the-art measurement technique. Bead-on-plate laser beam welds were produced with partial penetration on 304L stainless steel, 2205 duplex stainless steel, and Ti-6Al-4V. Keyhole monitoring was performed using a commercially available ICI system to collect keyhole penetration data in real time. These measurements were reconstructed to generate the vapor capillary shape at different welding parameters. Process parameters significantly influenced the keyhole shape and the keyhole root position relative to the process beam. Finally, the keyhole geometry showed distinct differences between the stainless steel alloys and Ti-6Al-4V.

2205↗

DOE OSTI2023

Subseasonal Representation and Predictability of North American Weather Regimes Using Cluster Analysis

Abstract This study focuses on assessing the representation and predictability of North American weather regimes, which are persistent large-scale atmospheric patterns, in a set of initialized subseasonal reforecasts created using the Community Earth System Model, version 2 (CESM2). The k -means clustering was used to extract four key North American (10°–70°N, 150°–40°W) weather regimes within ERA5 reanalysis, which were used to interpret CESM2 subseasonal forecast performance. Results show that CESM2 can recreate the climatology of the four main North American weather regimes with skill but exhibits biases during later lead times with overoccurrence of the West Coast high regime and underoccurrence of the Greenland high and Alaskan ridge regimes. Overall, the West Coast high and Pacific trough regimes exhibited higher predictability within CESM2, partly related to El Niño. Despite biases, several reforecasts were skillful and exhibited high predictability during later lead times, which could be partly attributed to skillful representation of the atmosphere from the tropics to extratropics upstream of North America. The high predictability at the subseasonal time scale of these case-study examples was manifested as an “ensemble realignment,” in which most ensemble members agreed on a prediction despite ensemble trajectory dispersion during earlier lead times. Weather regimes were also shown to project distinct temperature and precipitation anomalies across North America that largely agree with observational products. This study further demonstrates that unsupervised learning methods can be used to uncover sources and limits of subseasonal predictability, along with systematic biases present in numerical prediction systems. Significance Statement North American weather regimes are large-scale atmospheric patterns that can persist for several days. Their skillful subseasonal (2 weeks or greater) prediction can provide valuable lead time to prepare for temperature and precipitation anomalies that can stress energy and water resources. The purpose of this study was to assess the climatological representation and subseasonal predictability of four key North American weather regimes using a research subseasonal prediction system and clustering analysis. We found that the Pacific trough and West Coast high regimes exhibited higher predictability than other regimes and that skillful representation of conditions across the tropics and extratropics can increase predictability during later lead times. Future work will quantify causal pathways associated with high predictability.

58 GEOSCIENCES↗

DOE OSTI2025

Advancing understanding and predictive capability for fast-ion driven instabilities and associated anomalous transport in NSTX-U

This project advanced predictive capability for the spherical tokamak (ST) by (a) experimental validation of physics models in GTC for simulating fast-ion driven instabilities and their fast-ion and energy transport in the ST, and (b) verification of GTC with linear theory and validation using experimental measurements in the high frequency regime in the ST.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

A Bayesian Deep Learning Approach to Near-Term Climate Prediction

Since model bias and associated initialization shock are serious shortcomings that reduce prediction skills in state-of-the-art decadal climate prediction efforts, we pursue a complementary machine-learning-based approach to climate prediction. The example problem setting we consider consists of predicting natural variability of the North Atlantic sea surface temperature on the interannual timescale in the pre-industrial control simulation of the Community Earth System Model. While previous works have considered the use of recurrent networks such as convolutional LSTMs and reservoir computing networks in this and other similar problem settings, we currently focus on the use of feedforward convolutional networks. In particular, we find that a feedforward convolutional network with a Densenet architecture is able to outperform a convolutional LSTM in terms of predictive skill. Next, we go on to consider a probabilistic formulation of the same network based on Stein variational gradient descent and find that in addition to providing useful measures of predictive uncertainty, the probabilistic (Bayesian) version improves on its deterministic counterpart in terms of predictive skill. Finally, we characterize the reliability of the ensemble of machine learning models obtained in the probabilistic setting by using analysis tools developed in the context of ensemble numerical weather prediction.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Dominant Controls on Preferential Flow and Their Implications for Future Soil Water Fluxes

Abstract Soil water flow, particularly preferential flow (PF), is a critical control on hydrological and biogeochemical processes, including groundwater recharge, contaminant transport, and carbon cycling. However, it remains challenging to predict PF occurrence across large environmental gradients. Here, we developed a deep learning (DL) model to estimate event‐scale soil water flow velocity and the probability of PF occurrence using high‐frequency soil moisture and precipitation data from 33 sites across the National Ecological Observatory Network. The model demonstrated high skill in predicting the binary occurrence of PF (91% F1‐score; 85% accuracy) but the performance was limited in predicting soil water velocity ( R 2 = 0.31). We found that precipitation characteristics (duration, volume, and intensity) were the most important predictors for soil water velocity. Among the non‐precipitation event variables, sand content showed relatively high predictive skill, though differences among non‐event climate variables were generally modest. Lower sand content was associated with increased predicted soil water velocity, a finding that highlights the role of soil structure in producing more non‐uniform flow, which contrasts with traditional uniform flow models. Projecting a reduced DL model under both moderate and high‐emissions future climate scenarios (2060–2099 Representative Concentration Pathways 4.5 and 8.5), we found ∼7.3% increase under RCP4.5 and ∼15% under RCP8.5 of soil water velocities compared to the historical simulation, while modeled likelihood of PF changed little. These findings suggest climate change is not making PF more frequent, but it is making existing PF pathways more efficient with important consequences for associated nutrient and contaminant transport under climate change. Plain Language Summary Water movement in soil is critical for water quality. While often modeled as a uniform flow process, in reality water moves rapidly through cracks and burrows in what is called “preferential flow” (PF), which limits natural filtration and can transport pollutants. We developed a deep learning model, trained on data from 33 U.S. sites, to predict when and how fast this PF occurs based on precipitation, soil, and climate data. The model showed that precipitation characteristics (duration, intensity, volume) were the most important predictors of PF. Lower soil sand content/higher clay content was associated with faster water flow, likely due to clay soils forming aggregates and cracks that water moves through rather than infiltrating uniformly. Further analyses based on climate projections suggest that the speed at which PF occurs will become more rapid under future climate scenarios compared to historical simulation. This highlights the need to represent PF in soil water models when assessing future water quality. Key Points The effect of precipitation peak intensity on soil water velocities declined with increasing precipitation intensity Antecedent soil moisture failed to predict preferential flow (PF), contrasting the high predictive power of sand content Climate predictions suggest that soil water velocities through PF paths will increase ∼15% by 2099

Li, Bonan↗

DOE OSTI2023

Analysis of the rotationally-resolved infrared spectrum of CD 3 79 Br and CD 3 81 Br between 900 and 1400 cm -1

We report the infrared spectrum of CD 3 79 Br and CD 3 81 Br between 900 cm -1 and 1400 cm -1 has been analyzed at high resolution. In this region, two fundamental vibrational states, v 2 = 1 and v 5 = 1, an overtone state, v 3 = 2, and a combination state, v 3 = v 6 = 1, have been analyzed for both isotopologues. As found in other halomethane molecules, strong Coriolis resonances couple the v 2 = 1 state to the v 5 = 1 state, and similar resonances were also used to describe the coupling found between the v 5 = 1 state to the v 3 = 2 state. A new determination of the K-dependent constant A 0 was performed for each isotopologue through the use of perturbation-allowed transitions. The values for A 0 determined from the analysis are 2.6001898(26) and 2.6001905(27) for CD 3 79 Br and CD 3 81 Br, respectively. Ab initio calculations were performed to examine the efficacy of high-level theoretical calculations to accurately predict spectroscopic constants. The ab initio calculations had variable success with the largest errors associated with the prediction of the ΔB rotational constants of the interacting states

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗