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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Dry-Season Greening and Water Stress in Amazonia: The Role of Modeling Leaf Phenology

Large uncertainties on the sensitivity of Amazon forests to drought exist. Even though water stress should suppress photosynthesis and enhance tree mortality, a green-up has been often observed during the dry season. This interplay between climatic forcing and forest phenology is poorly understood and inadequately represented in most of existing dynamic global vegetation models calling for an improved description of the Amazon seasonal dynamics. Recent findings on tropical leaf phenology are incorporated in the state-of-the-art eco-hydrological model Thetys & Chloris. The new model accounts for a mechanistic light-controlled leaf development, synchronized dry-season litterfall, and an age-dependent leaf photosynthetic capacity. Simulation results from 32 sites in the Amazon basin over a 15-year period successfully mimic the seasonality of gross primary productivity; evapotranspiration (ET); as well as leaf area index, leaf age, and leaf productivity. Representation of tropical leaf phenology reproduces the observed dry-season greening, reduces simulated gross primary productivity, and does not alter ET, when compared with simulations without phenology. Tolerance to dry periods, with the exception of major drought events, is simulated by the model. Deep roots rather than leaf area index regulation mechanisms control the response to short-term droughts, but legacy effects can exacerbate multiyear water stress. Our results provide a novel mechanistic approach to model leaf phenology and flux seasonality in the tropics, reconciling the generally observed dry-season greening, ET seasonality, and decreased carbon uptake during severe droughts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Enhancing the representation of water management in global hydrological models

Abstract. This study enhances an existing global hydrological model (GHM), Xanthos, by adding a new water management module that distinguishes between the operational characteristics of irrigation, hydropower, and flood control reservoirs. We remapped reservoirs in the Global Reservoir and Dam (GRanD) database to the 0.5∘ spatial resolution in Xanthos so that a single lumped reservoir exists per grid cell, which yielded 3790 large reservoirs. We implemented unique operation rules for each reservoir type, based on their primary purposes. In particular, hydropower reservoirs have been treated as flood control reservoirs in previous GHM studies, while here, we determined the operation rules for hydropower reservoirs via optimization that maximizes long-term hydropower production. We conducted global simulations using the enhanced Xanthos and validated monthly streamflow for 91 large river basins, where high-quality observed streamflow data were available. A total of 1878 (296 hydropower, 486 irrigation, and 1096 flood control and others) out of the 3790 reservoirs are located in the 91 basins and are part of our reported results. The Kling–Gupta efficiency (KGE) value (after adding the new water management) is ≥ 0.5 and ≥ 0.0 in 39 and 81 basins, respectively. After adding the new water management module, model performance improved for 75 out of 91 basins and worsened for only 7. To measure the relative difference between explicitly representing hydropower reservoirs and representing hydropower reservoirs as flood control reservoirs (as is commonly done in other GHMs), we use the normalized root mean square error (NRMSE) and the coefficient of determination (R2). Out of the 296 hydropower reservoirs, the NRMSE is > 0.25 (i.e., considering 0.25 to represent a moderate difference) for over 44 % of the 296 reservoirs when comparing both the simulated reservoir releases and storage time series between the two simulations. We suggest that correctly representing hydropower reservoirs in GHMs could have important implications for our understanding and management of freshwater resource challenges at regional-to-global scales. This enhanced global water management modeling framework will allow the analysis of future global reservoir development and management from a coupled human–earth system perspective.

13 HYDRO ENERGY↗
DOE OSTI2018

PtWOX11 acts as master regulator conducting the expression of key transcription factors to induce de novo shoot organogenesis in poplar

De novo shoot regeneration is a prerequisite for propagation and genetic engineering of elite cultivars in forestry. Yet, the regulatory mechanism of de novo organogenesis is poorly understood in tree species. We previously showed that WUSCHEL (WUS)-RELATED HOMEOBOX 11 (PtWOX11) of the hybrid poplar clone 84K ( Populus alba × P. glandulosa ) promotes de novo root formation. Here, we found that PtWOX11 also regulates de novo shoot regeneration in poplar. The overexpression of PtWOX11 enhanced de novo shoot formation, whereas overexpression of PtWOX11 fused with the transcriptional repressor domain ( PtWOX11-SRDX ) or reduced expression of PtWOX11 inhibited this process, indicating that PtWOX11 promotes de novo shoot organogenesis. Although PtWOX11 promotes callus formation, overexpression of PtWOX11 and PtWOX11-SRDX also produced increased and decreased numbers of de novo shoots per unit weight, respectively, implying that PtWOX11 promotes de novo shoot organogenesis partially by regulating the intrinsic mechanism of shoot development. RNA-seq and qPCR analysis further revealed that PtWOX11 activates the expression of PLETHORA1 (PtPLT1) and PtPLT2 , whose Arabidopsis paralogs establish the acquisition of pluripotency, during incubation on callus-inducing medium. Moreover, PtWOX11 activates the expression of shoot-promoting factors and meristem regulators such as CUP-SHAPED COTYLEDON2 (PtCUC2), PtCUC3, WUS and SHOOT MERISTEMLESS to fulfill shoot regeneration during incubation on shoot-inducing medium. These results imply that PtWOX11 acts as a central regulator of the expression of key genes to cause de novo shoot formation. Our studies further provide a possible means to genetically engineer economically important tree species for their micropropagation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Scaling Up metal additive manufacturing process to fabricate molds for composite manufacturing

Direct Energy Deposition (DED) systems are currently used to repair and maintain existing parts in the aerospace and automotive industries. This paper discusses an effort to scale up the DED technique in order to Additively Manufacture (AM) molds and dies used in the composite manufacturing industry. The US molds and dies market has been in a rapid decline over the last decade due to outsourcing to non-US entities. Oak Ridge National Laboratory (ORNL), Wolf Robotics and Lincoln Electric have developed a Metal Big Area Additive Manufacturing (MBAAM) system that uses a high deposition rate and a low-cost wire feedstock material. In this work we used the MBAAM system with a mild steel wire, ER70S-6, to fabricate a compression molding mold for composite structures used in automotive and mass-transit applications. In addition, the mechanical properties of the AM structure were investigated, and it was found that the MBAAM process delivers parts with high planar isotropic behavior. The paper investigates the microstructure and grain of the printed articles to confirm the roots of the observed planar isotropic properties. Here, the manufactured AM mold was used to fabricate 50 composite parts with no observed mold deformations.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Modeling of time-lapse seismic monitoring using CO 2 leakage simulations for a model CO 2 storage site with realistic geology: Application in assessment of early leak-detection capabilities

Time-lapse surface seismic surveys have been widely used at carbon sequestration sites for site characterization, monitoring subsurface CO 2 plume migration, and detecting potential CO 2 leakage from a storage reservoir. Monitoring in the first permeable unit directly above the primary seal is important for early detection of CO 2 leakage. Forward modeling of time-lapse seismic data can be used to assess the utility of the seismic method for CO 2 leakage detection. We develop a workflow for forward modeling of time-lapse seismic data, including constructing seismic velocity models using flow simulation outputs, modeling of pre-stack and post-stack synthetic seismic data following seismic data processing sequence and analysis of processed synthetic time-lapse seismic data. We apply the forward modeling and analysis workflow to assessing the detectability and the earliest detection time of seismic monitoring using the hypothetical CO 2 leakage scenarios for a model geologic storage site with realistic geology. We then derive the detection thresholds using the simulated normalized root-mean-square (NRMS) differences for the no-leakage case at a range of signal-to-noise ratios, representing the background noise levels in seismic data. We then compare NRMS differences triggered by the CO 2 leakage to the detection thresholds at each time step to quantify the detectability and the earliest detection time of seismic monitoring. We analyze the effects of the acquisition parameters and elastic parameters on the produced synthetic seismic data and earliest detection time. Our modeling results indicate that high signal-to-noise ratio is needed to detect the CO 2 leakage at the model site. Minimizing the background noise in seismic data is crucial for improving the detectability of the seismic method. Increasing the shot density or increasing the dominant frequency of the source wavelet is likely to increase the possibility of the leakage detection and reduce the time needed for the detection. The elastic parameters used in the rock physics modeling have significant effects on the resultant seismic velocity models and synthetic seismic data, highlighting their critical roles in understanding and interpreting time-lapse seismic reflection data associated with CO 2 monitoring, verification and accounting activities.

58 GEOSCIENCES↗
DOE OSTI2021

Lignin-enzyme interaction: A roadblock for efficient enzymatic hydrolysis of lignocellulosics

Efficiently producing second-generation biofuels from biomass is of strategic significance and meets sustainability targets, but it remains a long-term challenge due to the existence of biomass recalcitrance. Lignin contributes significantly to biomass recalcitrance by physically limiting the access of enzymes to carbohydrates, and this could be partially overcome by applying a pretreatment step to directly target lignin. However, lignin typically cannot be completely removed, and its structure is also significantly altered during the pretreatment. As a result, lignin residue in the pretreated materials still significantly hindered a complete conversion of carbohydrate to its monosugars by interacting with cellulase enzymes. The non-productive adsorption driven by hydrophobic, electrostatic, and/or hydrogen bonding interactions is widely considered as the major mechanism of action governing the unfavored lignin-enzyme interaction. One could argue this type of interaction between lignin residue and the activated enzymes is the major roadblock for efficient enzymatic hydrolysis of pretreated lignocellulosics. To alleviate the negative effects of lignin on enzyme performance, a deep understanding of lignin structural transformation upon different types of pretreatments as well as how and where does lignin bind to enzymes are prerequisites. In the last decade, the progress toward a fundamental understanding of lignin-enzyme interaction, structural characterization of lignin during pretreatment and/or conformation change of enzyme during hydrolysis is resulting in advances in the development of methodologies to mitigate the negative effect of lignin. Here in this review, the lignin structural transformation upon different types of pretreatments and the inhibition mechanism of lignin in the bioconversion of lignocellulose to bioethanol are summarized. Some technologies to minimize the adverse impact of lignin on the enzymatic hydrolysis, including chemical modification of lignin, adding blocking additives, and post-treatment to remove lignin were also introduced. The production of liquid biofuels from lignocellulosic biomass has shown great environmental benefits such as reducing greenhouse gas emissions and mitigate climate change. By addressing the root causes of lignin-enzyme interaction and how to retard this interaction, it is our hope that this comprehensive review will pave the way for significantly reducing the high cost associated with the enzymatic hydrolysis process, and ultimately achieving a cost-effective and sustainable biorefinery system.

09 BIOMASS FUELS↗
DOE OSTI2023

Information theory and machine learning illuminate large‐scale metabolomic responses of Brachypodium distachyon to environmental change

SUMMARY Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC‐MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC‐MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ–condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)‐based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML‐based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co‐accumulation analysis further identified condition‐specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio‐Analytic Resource for Plant Biology website ( https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi‐bin/efpWeb.cgi ), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Policy-Driven Sustainable Saline Drainage Disposal and Forage Production in the Western San Joaquin Valley of California

Environmental policies to address water quality impairments in the San Joaquin River of California have focused on the reduction of salinity and selenium-contaminated subsurface agricultural drainage loads from westside sources. On 31 December 2019, all of the agricultural drainage from a 44,000 ha subarea on the western side of the San Joaquin River basin was curtailed. This policy requires the on-site disposal of all of the agricultural drainage water in perpetuity, except during flooding events, when emergency drainage to the River is sanctioned. The reuse of this saline agricultural drainage water to irrigate forage crops, such as ‘Jose’ tall wheatgrass and alfalfa, in a 2428 ha reuse facility provides an economic return on this pollutant disposal option. Irrigation with brackish water requires careful management to prevent salt accumulation in the crop root zone, which can impact forage yields. The objective of this study was to optimize the sustainability of this reuse facility by maximizing the evaporation potential while achieving cost recovery. This was achieved by assessing the spatial and temporal distribution of the root zone salinity in selected fields of ‘Jose’ tall wheatgrass and alfalfa in the drainage reuse facility, some of which have been irrigated with brackish subsurface drainage water for over fifteen years. Electromagnetic soil surveys using an EM-38 instrument were used to measure the spatial variability of the salinity in the soil profile. The tall wheatgrass fields were irrigated with higher salinity water (1.2–9.3 dS m -1 ) compared to the fields of alfalfa (0.5–6.5 dS m -1 ). Correspondingly, the soil salinity in the tall wheatgrass fields was higher (12.5 dS m -1 –19.3 dS m -1 ) compared to the alfalfa fields (8.97 dS mm -1 –14.4 dS mm -1 ) for the years 2016 and 2017. Better leaching of salts was observed in the fields with a subsurface drainage system installed (13–1 and 13–2). The depth-averaged root zone salinity data sets are being used for the calibration of the transient hydro-salinity computer model CSUID-ID (a one-dimensional version of the Colorado State University Irrigation Drainage Model). This user-friendly decision support tool currently provides a useful framework for the data collection needed to make credible, field-scale salinity budgets. In time, it will provide guidance for appropriate leaching requirements and potential blending decisions for sustainable forage production. This paper shows the tie between environmental drainage policy and the role of local governance in the development of sustainable irrigation practices, and how well-directed collaborative field research can guide future resource management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

UV DRIVEN EVAPORATION OF CLOSE-IN PLANETS: ENERGY-LIMITED, RECOMBINATION-LIMITED, AND PHOTON-LIMITED FLOWS

We have investigated the evaporation of close-in exoplanets irradiated by ionizing photons. We find that the properties of the flow are controlled by the ratio of the recombination time to the flow timescale. When the recombination timescale is short compared to the flow timescale, the flow is in approximate local ionization equilibrium with a thin ionization front where the photon mean free path is short compared to the flow scale. In this “recombination-limited” flow the mass-loss scales roughly with the square root of the incident flux. When the recombination time is long compared to the flow timescale the ionization front becomes thick and encompasses the entire flow with the mass-loss rate scaling linearly with flux. If the planet's potential is deep, then the flow is approximately “energy-limited”; however, if the planet's potential is shallow, then we identify a new limiting mass-loss regime, which we term “photon-limited.” In this scenario, the mass-loss rate is purely limited by the incoming flux of ionizing photons. We have developed a new numerical approach that takes into account the frequency dependence of the incoming ionizing spectrum and performed a large suite of 1D simulations to characterize UV driven mass-loss around low-mass planets. We find that the flow is “recombination-limited” at high fluxes but becomes “energy-limited” at low fluxes; however, the transition is broad occurring over several orders of magnitude in flux. Finally, we point out that the transitions between the different flow types do not occur at a single flux value but depend on the planet's properties, with higher-mass planets becoming “energy-limited” at lower fluxes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A machine learning method of modern urban building energy modeling: A case study of Chicago

Urban-scale building energy modeling is vital for urban planning. However, it can be challenging to assimilate reliable non-geometry building data for urban-scale modeling without extensive investment. Here, this study introduces a novel approach to developing modern urban-scale building energy stock data using geographic information systems and machine learning algorithms without necessarily requiring pre-supplied non-geometric metadata. The proposed framework integrates building footprint and height data to estimate gross floor areas, and matches each building to a pool of candidate records from ComStock or ResStock—filtered to the same county and ranked by geometric similarity—demonstrate a proof-of-concept case study in Chicago for predicting energy use intensity (EUI) using scalable datasets. The model achieved a mean bias error (MBE) of 0.08 kWh/m² and root mean square error (RMSE) of 14.84 kWh/m² under full metadata input for EUI prediction. With only location inputs, the model captured 69.2 % of EUI within predicted ranges. These results demonstrate the model’s potential to support early-stage urban planning, identify candidates for energy-efficient retrofits. By removing the dependency on detailed pre-surveys or extensive building metadata, the approach overcomes a key barrier in traditional urban-scale building energy modeling, illustrating a pathway toward broader and more cost-effective application, though further multi-city validation and improved treatment of pre-1925 buildings are needed.

Energy Use Intensity↗
DOE OSTI2022

Thermal modeling of directed energy deposition additive manufacturing using graph theory

Purpose: The purpose of this paper is to develop, apply and validate a mesh-free graph theory–based approach for rapid thermal modeling of the directed energy deposition (DED) additive manufacturing (AM) process. Design/methodology/approach: Here, the authors develop a novel mesh-free graph theory–based approach to predict the thermal history of the DED process. Subsequently, the authors validated the graph theory predicted temperature trends using experimental temperature data for DED of titanium alloy parts (Ti-6Al-4V). Temperature trends were tracked by embedding thermocouples in the substrate. The DED process was simulated using the graph theory approach, and the thermal history predictions were validated based on the data from the thermocouples. Findings: The temperature trends predicted by the graph theory approach have mean absolute percentage error of approximately 11% and root mean square error of 23°C when compared to the experimental data. Moreover, the graph theory simulation was obtained within 4 min using desktop computing resources, which is less than the build time of 25 min. By comparison, a finite element–based model required 136 min to converge to similar level of error. Research limitations/implications: This study uses data from fixed thermocouples when printing thin-wall DED parts. In the future, the authors will incorporate infrared thermal camera data from large parts. Practical implications: The DED process is particularly valuable for near-net shape manufacturing, repair and remanufacturing applications. However, DED parts are often afflicted with flaws, such as cracking and distortion. In DED, flaw formation is largely governed by the intensity and spatial distribution of heat in the part during the process, often referred to as the thermal history. Accordingly, fast and accurate thermal models to predict the thermal history are necessary to understand and preclude flaw formation. Originality/value: This paper presents a new mesh-free computational thermal modeling approach based on graph theory (network science) and applies it to DED. The approach eschews the tedious and computationally demanding meshing aspect of finite element modeling and allows rapid simulation of the thermal history in additive manufacturing. Although the graph theory has been applied to thermal modeling of laser powder bed fusion (LPBF), there are distinct phenomenological differences between DED and LPBF that necessitate substantial modifications to the graph theory approach.

42 ENGINEERING↗
DOE OSTI2018

New developments in calorimetric particle detection

In nuclear, particle and astroparticle physics experiments, calorimeters are used to measure the properties of particles with kinetic energies that range from a fraction of 1 eV to 10 20 eV or more. These properties are not necessarily limited to the energy carried by these particles, but may concern the entire four-vector, including the particle mass and type. In many modern experiments, large calorimeter systems play a central role, and this is expected to be no different for experiments that are currently being planned/designed for future accelerators. In this paper, the state of the art as well as new developments in calorimetry are reviewed. The latter are of course inspired by the perceived demands of future experiments, and/or the increasing demands of the current generation of experiments, as these are confronted with, for example, increased luminosity. These demands depend on the particles to be detected by the calorimeter. In electromagnetic calorimeters, radiation hardness of the detector components is a major concern. The generally poor performance of the current generation of hadron calorimeters is considered inadequate for future experiments, and a lot of the R&D in the past decade has focused on improving this performance. The root causes of the problems are investigated and different methods that have been exploited to remedy this situation are evaluated. Over the past two decades, experiments in astroparticle physics have started to make major contributions to our fundamental understanding of physics and of a variety of processes that are inaccessible in laboratory experiments here on Earth. These experiments typically make use of calorimetric particle detection. At the extreme low end of the energy spectrum, ingenious instruments are used to study phenomena involving energy transfers of the order of 1 eV using calorimetric methods. In separate sections, some salient aspects of this work are reviewed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Multiscale porous elastomer substrates for multifunctional on-skin electronics with passive-cooling capabilities

In addition to mechanical compliance, achieving the full potential of on-skin electronics needs the introduction of other features. For example, substantial progress has been achieved in creating biodegradable, self-healing, or breathable, on-skin electronics. However, the research of making on-skin electronics with passive-cooling capabilities, which can reduce energy consumption and improve user comfort, is still rare. Herein, we report the development of multifunctional on-skin electronics, which can passively cool human bodies without needing any energy consumption. This property is inherited from multiscale porous polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene (SEBS) supporting substrates. The multiscale pores of SEBS substrates, with characteristic sizes ranging from around 0.2 to 7 µm, can effectively backscatter sunlight to minimize heat absorption but are too small to reflect human-body midinfrared radiation to retain heat dissipation, thereby delivering around 6 °C cooling effects under a solar intensity of 840 W∙m -2 . Other desired properties, rooted in multiscale porous SEBS substrates, include high breathability and outstanding waterproofing. The proof-of-concept bioelectronic devices include electrophysiological sensors, temperature sensors, hydration sensors, pressure sensors, and electrical stimulators, which are made via spray printing of silver nanowires on multiscale porous SEBS substrates. The devices show comparable electrical performances with conventional, rigid, nonporous ones. Also, their applications in cuffless blood pressure measurement, interactive virtual reality, and human–machine interface are demonstrated. Notably, the enabled on-skin devices are dissolvable in several organic solvents and can be recycled to reduce electronic waste and manufacturing cost. Such on-skin electronics can serve as the basis for future multifunctional smart textiles with passive-cooling functionalities.

42 ENGINEERING↗
DOE OSTI2023

Simulations Supporting the Development of Northstar's Indirect Beam Parameters Monitoring System

NorthStar Medical Radioisotopes, LLC is planning to produce the important medical radioisotope molybdenum-99 (Mo-99), the parent of technetium-99m (Tc-99m), through photonuclear reactions in molybdenum-100 (Mo-100). In this approach, a target comprising multiple thin disks of enriched molybdenum metal is bombarded with a 40-MeV electron beam. Electrons impinged on the molybdenum target produce bremsstrahlung X-rays that cause the nuclear reaction. Because enriched Mo-100 is expensive, there is a desire to utilize as much beam power as possible to achieve maximum production yield and minimize the size of the target. This requirement leads to very high beam power density (and heat deposition in the target), which creates challenging requirements for the cooling of the target. The critical part of the target is the target window. It separates the high-pressure helium cooled target from the vacuum beamline and the subject of structural and thermal stress. The temperature of the target window is proportional to the energy density deposited by the beam, so it is critical to maintain the desired beam profile on the target window. The feasibility of indirectly monitoring the maximum energy density of the beam on the beam window through beam losses at the main collimator (Collimator) before the production target was verified. A model of the NorthStar beam transport line was constructed for this purpose using MAD-X and Tao/Bmad codes. Beam optics were computed for the standard operational scenario, followed by an investigation involving approximately 400 cases with parameter variations in the last tuning quadrupoles. This was done to assess the correlation between losses in the collimator and the peak energy density on the target. We developed a model to explore the potential application of Optical transition radiation (OTR) for controlling beam parameters in the NorthStar beam delivery system. This model was based on a generic formula derived from the fundamental solution of the inhomogeneous wave equation of the vector potential, and allowed us to consider various surfaces, even those with irregular or random features, using numerical integration. We applied the model to OTR generated by relativistic electrons impacting an Inconel® 718 beam window. We examined cases with different levels of the window’s surface roughness, ranging from 0.5 to 3.0 microns of root square mean (RMS) deviation. The results of the OTR simulations provided distributions of OTR photons that can be used to study the limitations of optical systems for controlling beam parameters.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

47 OTHER INSTRUMENTATION↗
DOE OSTI2015

Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0.28 ± 0.03 mm, and 1.06 ± 0.40 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the premolar were 37.95 ± 10.13 mm{sup 3}, 92.45 ± 2.29%, 0.29 ± 0.06 mm, 0.33 ± 0.10 mm, and 1.28 ± 0.72 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the molar were 52.38 ± 17.27 mm{sup 3}, 94.12 ± 1.38%, 0.30 ± 0.08 mm, 0.35 ± 0.17 mm, and 1.52 ± 0.75 mm, respectively. The computation time of the proposed method for segmenting CBCT images of one subject was 7.25 ± 0.73 min. Compared with two other methods, the proposed method achieves significant improvement in terms of accuracy. Conclusions: The presented tooth segmentation method can be used to segment tooth contours from CT images accurately and efficiently.

60 APPLIED LIFE SCIENCES↗