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

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Evaluation of Data Catalog Software for Hanford Site Environmental Datasets

Environmental information and data underpin achievement of the U.S. Department of Energy (DOE) Office of Environmental Management (EM) mission at the Hanford Site. The Hanford Environmental Data Management (HEDM) Program is the DOE Richland Operations Office (RL) approach to develop and implement a formal program for managing environmental data and the associated records, materials, and systems at the Hanford Site. The current project, contract, organization, and contractor-specific efforts at managing environmental data sets are insufficient to provide orderly, long-term, site-wide access. A vital element to be created within the HEDM program plan is a catalog of data sources, called the Hanford Environmental Information and Data Index (HEIDI), that will enable long-term access and retrievability for the multiple independent sources of data that might otherwise be difficult to discover. This report compares leading open source and commercial data catalog platforms using criteria to assess the functionality needed to develop the HEIDI catalog of Hanford data sources that connects and exchanges data with established Hanford Local Area Network (HLAN) enterprise information technology systems. Proprietary platforms evaluated included ArcGIS Enterprise Sites, Junar, OpenDataSoft, and Socrata, and non-proprietary platforms included Energy Data eXchange (EDX), Comprehensive Knowledge Archive Network (CKAN), and DKAN (a Drupal-based open data portal based on CKAN). Capabilities supporting data discoverability, retrieval, and archival, as well as metadata standard requirements and integration into the HLAN were rated as either failing to meet requirements (F), meeting requirements (M), or exceeding requirements by delivering additional desired features (E). The lowest rating for any capability area was assigned as the overall rating for the platform. These findings enable DOE-RL and the contractors implementing the HEDM plan to focus on candidate tools likely to meet the requirements for implementing HEIDI. All of the platforms receiving an overall rating of ‘F’ were unable to be deployed on Hanford infrastructure or within dedicated cloud resources. A propriety software-as-a-service (SaaS) model of delivering a data catalog (e.g., found in software such as Junar and OpenDataSoft) favors consistency across customers at the expense of customization and configurable roles that are needed for Hanford work. Hosting data on a shared commercial platform places limits on dataset size (maximum of 240 Mb for OpenDataSoft), a significant limitation for HEIDI implementation. EDX, a government data catalog based on CKAN, received the ‘F’ rating due to an inability to incorporate authentication from HLAN into the system. Among platforms rated ‘M’ or ‘E’, only the Socrata platform had a SaaS delivery model. In contrast to other SaaS platforms, Socrata provided custom roles and gateways that allow local datasets to be incorporated into an online catalog. Socrata also complies with the Federal Risk and Authorization Management Program, a significant benefit for cloud-based management of Hanford data. The other platforms rated ‘M’ or ‘E’, ArcGIS Enterprise Sites, CKAN, and DKAN, provide fully self-hosted options, allowing for greater control and flexibility with the HEIDI catalog. These widely used tools have supportive communities of practice, extensive customization options, and demonstrated deployments that provide evidence that they can meet requirements, often deliver additional desired features, and work well with federal government systems. Completely customized alternatives built on a collection of applications were not evaluated because achieving similar performance to CKAN or DKAN requires substantial resources, especially in the absence of the active communities that have grown to support these tools. ArcGIS Enterprise Sites, Socrata, CKAN, and DKAN were evaluated as strong candidates for successful implementation with HEIDI.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Real-Time Partitioning of Diurnal Stem CO 2 Efflux into Local Stem Respiration and Xylem Transport Processes

The apparent respiratory quotient (ARQ) of tree stems, defined as the ratio of net stem CO 2 efflux (E S_CO2 ) to net stem O 2 influx (E S_O2 ), offers insights into the balance between local respiratory CO 2 production and CO 2 transported via the xylem. Traditional static chamber methods for measuring ARQ can introduce artifacts and obscure natural diurnal variations. Here, we employed an open flow-through stem chamber with ambient air coupled with cavity ring-down spectrometry, which uses the molecular properties of CO 2 and O 2 molecules to continuously measure E S_CO2 , E S_O2 , and ARQ, at the base of a California cherry tree (Prunus ilicifolia) during the 2024 growing season. Measurements across three stem chambers over 3–11-day periods revealed strong correlations between E S_CO2 and E S_O2 and mean ARQ values ranging from 1.3 to 2.9, far exceeding previous reports. Two distinct diurnal ARQ patterns were observed: daytime suppression with nighttime recovery, and a morning peak followed by gradual decline. Partitioning E S_CO2 into local respiration and xylem-transported CO 2 indicated that the latter can dominate when ARQ exceeds 2.0. Furthermore, transported CO 2 exhibited a higher temperature sensitivity than local respiration, with both processes showing declining temperature sensitivity above 20 °C. These findings underscore the need to differentiate stem CO 2 flux components to improve our understanding of whole-tree carbon cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fluid-Kinetic Coupling: Advanced Discretizations for Simulations on Emerging Heterogeneous Architectures (LDRD FY20-0643)

Plasma physics simulations are vital for a host of Sandia mission concerns, for fundamental science, and for clean energy in the form of fusion power. Sandia's most mature plasma physics simulation capabilities come in the form of particle-in-cell (PIC) models and magnetohydrodynamics (MHD) models. MHD models for a plasma work well in denser plasma regimes when there is enough material that the plasma approximates a fluid. PIC models, on the other hand, work well in lower-density regimes, in which there is not too much to simulate; error in PIC scales as the square root of the number of particles, making high-accuracy simulations expensive. Real-world applications, however, almost always involve a transition region between the high-density regimes where MHD is appropriate, and the low-density regimes for PIC. In such a transition region, a direct discretization of Vlasov is appropriate. Such discretizations come with their own computational costs, however; the phase-space mesh for Vlasov can involve up to six dimensions (seven if time is included), and to apply appropriate homogeneous boundary conditions in velocity space requires meshing a substantial padding region to ensure that the distribution remains sufficiently close to zero at the velocity boundaries. Moreover, for collisional plasmas, the right-hand side of the Vlasov equation is a collision operator, which is non-local in velocity space, and which may dominate the cost of the Vlasov solver. The present LDRD project endeavors to develop modern, foundational tools for the development of continuum-kinetic Vlasov solvers, using the discontinuous Petrov-Galerkin (DPG) methodology, for discretization of Vlasov, and machine-learning (ML) models to enable efficient evaluation of collision operators. DPG affords several key advantages. First, it has a built-in, robust error indicator, allowing us to adapt the mesh in a very natural way, enabling a coarse velocity-space mesh near the homogeneous boundaries, and a fine mesh where the solution has fine features. Second, it is an inherently high-order, high-intensity method, requiring extra local computations to determine so-called optimal test functions, which makes it particularly suited to modern hardware in which floating-point throughput is increasing at a faster rate than memory bandwidth. Finally, DPG is a residual-minimizing method, which enables high-accuracy computation: in typical cases, the method delivers something very close to the $L^2$ projection of the exact solution. Meanwhile, the ML-based collision model we adopt affords a cost structure that scales as the square root of a standard direct evaluation. Moreover, we design our model to conserve mass, momentum, and energy by construction, and our approach to training is highly flexible, in that it can incorporate not only synthetic data from direct-simulation Monte Carlo (DSMC) codes, but also experimental data. We have developed two DPG formulations for Vlasov-Poisson: a time-marching, backward-Euler discretization and a space-time discretization. We have conducted a number of numerical experiments to verify the approach in a 1D1V setting. In this report, we detail these formulations and experiments. We also summarize some new theoretical results developed as part of this project (published as papers previously): some new analysis of DPG for the convection-reaction problem (of which the Vlasov equation is an instance), a new exponential integrator for DPG, and some numerical exploration of various DPG-based time-marching approaches to the heat equation. As part of this work, we have contributed extensively to the Camellia open-source library; we also describe the new capabilities and their usage. We have also developed a well-documented methodology for single-species collision operators, which we applied to argon and demonstrated with numerical experiments. We summarize those results here, as well as describing at a high level a design extending the methodology to multi-species operators. We have released a new open-source library, MLC, under a BSD license; we include a summary of its capabilities as well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Soil properties and root characteristics across four lowland Panamanian forests from 0 - 1 m soil depths

Objectives:Fine roots significantly influence ecosystem-scale cycling of nutrients, carbon (C), and water, yet there is limited understanding of how fine root traits vary across and within tropical forests, some of Earth's most C-rich ecosystems. The biomass of fine roots can impact soil carbon storage, as root mortality is a primary source of new carbon to soils. A positive relationship has been observed between fine root biomass and soil carbon stocks in Panama (Cusack et al 2018). Beyond biomass, root characteristics like specific root length (SRL) could also influence soil carbon, as roots with higher SRL are less dense and thinner, potentially decomposing more easily or promoting soil aggregation. Understanding the effects of root morphology and tissue quality on soil carbon storage and with soil properties in general can improve predictions of landscape-scale carbon patterns. We aggregated new data of root biomass, morphology and nutrient content at 0-10 cm, 10-20 cm, 20-50 cm and 50-100 cm depth increments across four distinct lowland Panamanian forests and paired with already published datasets (Cusack et al 2018; Cusack and Turner 2020) of soil chemistry from the same sites and soil depths to explore relationship between soil carbon stocks and root characteristics.Datasets included:The datasets provided include .csv and .xlsx files for fine root characteristics and soil chemistry from four different forests across 0-10 cm, 10-20 cm, 20-50 cm, and 50-100 cm depth increments. Root characteristics include live fine root biomass, dead fine root biomass, coarse root biomass, specific root length, root diameter, root tissue density, specific root area, root %N, root %C, and root C/N ratio. Soil chemistry data includes total carbon (TC), dissolved organic carbon (DOC), bulk density, total phosphorus (TP), available phosphorus (AEM Pi), and various Mehlich-extractable elements such as aluminum, calcium, iron, potassium, manganese, phosphorus, and zinc. Nitrogen content measures include ammonium, nitrate, total dissolved nitrogen (TDN), dissolved inorganic nitrogen (DIN), and dissolved organic nitrogen (DON). The dataset also includes total exchangeable bases (TEB) and effective cation exchange capacity (ECEC) in both centimoles of charge per kilogram and micromoles of charge per gram. The soil chemistry data was obtained from Cusack et al (2018) and Cusack and Turner (2020) and paired with root characteristics data for the same depth increments and sites. Additionally, a .kml file is provided with coordinates for all 32 plots included in the study across four forests (n = 8 plots per site). Root data was averaged across these 8 plots per site and soil data was collected in one pit in each site. This dataset serves as baseline data before a throughfall exclusion experiment, Panama Rainforest Changes with Experimental Drying (PARCHED), was implemented. No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Data from: "Moisture rivals temperature in limiting photosynthesis by trees establishing beyond their cold-edge range limit under ambient and warmed conditions"

This archive contains data files that were used to draw conclusions in “Moisture rivals temperature in limiting photosynthesis by trees establishing beyond their cold-edge range limit under ambient and warmed conditions”, by Moyes et al., 2015. All field research was completed in common garden plots set up as part of the Alpine Treeline Warming Experiment (ATWE) on Niwot Ridge, Colorado, USA.There are two main data file formats in this archive: comma-separated values (.csv), and Microsoft Excel (.xls and .xlsx). .xlsx files can be read using Microsoft Excel and Google Sheets, and .csv files can be read using any simple text editor program, such as TextEdit (Mac) and Notepad (Windows). This .pdf data user’s guide can be read using Adobe Acrobat Reader, or any other compatible software. Seedling photographs and their corresponding leaf area-processed images are available in .jpg/.JPG image format, and can be opened using Preview (Mac) and Photos (Windows). To provide additional spatial context, two types of geospatial files are also published in this data package: ESRI shapefiles (.shp) and .kml files. Shapefiles are compatible with any GIS software able to read the file type (such as QGIS or ESRI’s ArcGIS suite), and .kml files can be opened with Google Earth or Google Maps. Figures 3 and 4 in the publication contain data from Moyes et al. 2013. This publication is cited in the References section in this archive, and data files can be accessed via the Alpine Treeline Warming Experiment project portal on ESS-DIVE. ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Climate change is altering plant species distributions globally, and warming is expected to promote uphill shifts in mountain trees. However, at many cold-edge range limits, such as alpine treelines in the western United States, tree establishment may be colimited by low temperature and low moisture, making recruitment patterns with warming difficult to predict.- We measured response functions linking carbon (C) assimilation and temperature- and moisture-related microclimatic factors for limber pine (Pinus flexilis) seedlings growing in a heating × watering experiment within and above the alpine treeline. We then extrapolated these response functions using observed microclimate conditions to estimate the net effects of warming and associated soil drying on C assimilation across an entire growing season.- Moisture and temperature limitations were each estimated to reduce potential growing season C gain from a theoretical upper limit by 15–30% (c. 50% combined). Warming above current treeline conditions provided relatively little benefit to modeled net assimilation, whereas assimilation was sensitive to either wetter or drier conditions.- Summer precipitation may be at least as important as temperature in constraining C gain by establishing subalpine trees at and above current alpine treelines as seasonally dry subalpine and alpine ecosystems continue to warm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Self-Navigating Robotic Assistant for Long-term Wide Area Floor Contamination Monitoring - 18213

For Routine Contamination Testing (RCT) of an operational nuclear facility or one undergoing Decontamination and Decommissioning (D and D), workers utilize specified travel corridors (enclosed hallways or areas designated with tape or rope in open spaces) to minimize the risk of spreading contamination. Radiation health technicians must continually monitor these areas for contamination to minimize worker dose and prevent its spread to uncontrolled areas. For many sites, it is impractical for the technician to adequately survey such areas. The Nuclear Robotics Group (NRG) at UT Austin has developed a self-navigating robotic platform equipped with radiation detectors to augment the technician to improve both survey coverage and frequency. While maintaining a controlled velocity and floor-to-sensor distance, the system takes radiation measurements to identify and/or localize contamination sources. Readings above background levels are reported to a remote workstation to allow technicians to then respond accordingly. The completion of these mundane tasks by a robot allows the trained technicians to focus instead on operational tasks, D and D, or responding to alarms. The robot generates a map using a Lidar range sensor with established Simultaneous Localization and Mapping (SLAM) techniques. Range data is then compared to previously generated maps for robot localization and autonomous navigation. To maximize coverage, the robot executes a Complete Coverage Path Planning (CCPP) algorithm using a static map that is discretized into cells to assure comprehensive yet efficient coverage. As the system executes the generated plan, it builds a radiation map of the area for the technician to validate and verify the results. If contamination is detected, the robot will minimize the spread of contamination by stopping, sounding an alarm, and alerting the remote technician. The proposed system allows for long-term deployment with minimal human intervention. It is robust to both highly dynamic obstacles (i.e. personnel) and low dynamic changes (i.e. temporally stored cart) in the environment. This is accomplished through continuous spatiotemporal updating of the static map, and the utilization of a supervisory controller that allows the system to reliably respond to unexpected events or states (i.e. low battery, closed door, etc.). While the supervisory controller can respond to temporary complications, the system also recognizes the environment can change slowly over time necessitating that the CCPP automatically be updated to account for observed 'permanent' changes to the environment. To do this, the robot uses intermediate probabilistic data to make intelligent planning decisions offline while still maintaining local reactive obstacle avoidance and safety features. The self-updating of the map allows the robot to run longer without the need to remake the map, leading to more consistent monitoring data and less maintenance from the human technician. This paper will review the current system hardware, the CCPP algorithm, the supervisory controller, the probabilistic algorithm for identifying permanent changes, and recent experiments at UT Austin to experimentally validate the reported sensor coverage. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Data from: "Warming and provenance limit tree recruitment across and beyond the elevation range of subalpine forest"

This data package contains data used to support conclusions drawn in “Warming and provenance limit tree recruitment across and beyond the elevation range of subalpine forest”, by Kueppers et al. 2017. Data were collected in field sites within the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, on the eastern slope of the Colorado Rocky Mountains, USA. Files containing geospatial data are also included, to provide additional locational context.There are four document formats associated with this archive: three comma-separated values (.csv) files, three Microsoft Excel (.xlsx) files, one .pdf data user’s guide, four keyhole markup language (.kml) files, and a compressed folder containing seven ESRI shapefiles (.shp). The .csv files can be opened using any simple text-editor software, R, or Microsoft Excel. The .xlsx files can only be opened using Microsoft Excel. The .kml file can be opened by Google Earth and Google Maps, and the shapefiles can be opened with any GIS application compatible with the file type, such as ESRI’s ArcGIS, and QGIS.We provide two versions of the seedling data file: “PIEN_PIFLseedlings20150522_20150525rev12222020.csv/.xlsx” (hereafter PIEN_PIFLseedlings2015) and “PIEN_PIFLseedlings20160408rev12222020.csv/.xlsx” (hereafter PIEN_PIFLseedlings2016). PIEN_PIFLseedlings2015 contains the data we used in the paper. PIEN_PIFLseedlings2016 contains an updated version of these data that includes sampling from later years. The main differences between the two files lie in the columns titled “k[YEAR],” which describe the number of seedlings that were killed in a particular year. In PIEN_PIFLseedlings2016, there also is an additional year of data for k2015, and k2014 also has additional data input for the 2014 cohort. Additionally, in years 2010-2014, there are minor differences in the number of seedlings killed -- in as few as 0 plots (in 2011) to as many as 5 plots (in 2014) -- due to errors in data input that were rectified in later years.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Upslope range shifts by subalpine tree species are a widely anticipated effect of climate change. Climate niche models predict subalpine forests to expand upslope, given more suitable growing conditions for adult trees. However, these models do not take into account climates required for successful seedling recruitment and establishment, an essential element for expansion. Further, localized upper treeline populations are hypothesized to contain favorable traits for colonizing the alpine. To test these expectations and to expand our knowledge of seedling recruitment under climate change, we designed a common garden, climate-warming experiment spread across an elevation gradient at Niwot Ridge in the Colorado Rocky Mountains. We focus on two widespread Western North American species, Engelmann spruce (Picea engelmannii Parry ex. Engelm) and limber pine (Pinus flexilis James), which occur at treeline. While the former is considered a late-seral species more tolerant of shade, limber pine is a shade-intolerant pioneer species able to establish on infertile sites.Every autumn, seeds of the two species were collected from high- (3370 m–3570 m) and low-provenance (2910–3240 m) sources close to the experimental sites and sown in our plots. A subset of plots were heated and another subset watered over the summer months to offset the effects of warming. Across five years, we found that seeds originating from low elevation recruited more strongly for both species, although this provenance difference diminished by the fourth year for Engelmann spruce, likely due to small sample sizes. Despite the recruitment of low-provenance seed, warming treatments decreased recruitment at all elevations. Combining this with the likeliness and availability of lower-quality, high provenance seed moving upslope at the treeline, tree migration into the alpine may be slowed. Overall, our findings suggest that the hardier limber pine is likely to become a more significant species in subalpine forest communities in the future, while the more sensitive Engelmann spruce may experience range contraction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Numerical Simulations of Geologic Storage Reservoir Management to Support Risk Mitigation Evaluation

This report provides a detailed description of a set of numerical simulations that represent reservoir behavior over time in response to different operational decision scenarios for detection of potential leakage and reduction or avoidance of leakage impact at a hypothetical geological carbon storage (GCS) site. These simulations serve as the basis for a series of GCS leakage risk forecasts that are to be developed using the National Risk Assessment Partnership’s Open-Source Integrated Assessment Model (NRAP-Open-IAM), and a demonstration of a simple decision support workflow for evaluation of mitigation strategies based on results of those system model forecasts. This risk assessment and decision support study is forthcoming. Four injection scenarios were considered: a constant rate carbon dioxide (CO 2 ) injection case (base case), a case with CO 2 injection rate adjustment, a case with early termination of injection operations, and a case with brine extraction. CO 2 injection operations were controlled to ensure that the pressure transient remains below the defined manageable reservoir fracture pressure, with consideration shown to hypothetical locations within the modeled spatial domain where the overburden was weaker and lower transient pressure increases were allowable. Additionally, a brine extraction alternative was considered as a reservoir management and risk mitigation option to reduce reservoir pressure, steer the plume away from any hypothetical geohazard such as fault as needed, and enhance storage capacity. Such operational actions contribute to risk management overtime. This study explores the potential utility of reservoir management for risk reduction at GCS sites. This study shows that the injection design may modify the time to CO 2 breakthrough at a legacy well; in particular, these results show that brine extraction can add value for mitigating risk both by delaying leakage and reducing pressure build-up. For the scenario considered, both pressure plots and pressure distributions demonstrate that pressure build-up was decreased by 3% with brine extraction. Additionally, extraction of brine afforded enhancement of CO 2 storage capacity by 5% compared to the base case. These findings suggest that brine extraction has substantial potential to steer the risk-related reservoir effects away from known geohazards (e.g., faults and legacy wells) by conducting pressure transient effects and CO 2 plume movement toward the production well. Injection rate adjustment scenarios considered in this study show potential value for managing both reservoir pressure transients and CO 2 plume behavior. Operational actions for reducing injection and/or early termination of injection (as compared to the base case), however, require careful design; tailoring both the extent and timing of injection rate adjustment over the injection and post-injection operational period must be thoroughly planned to balance maximizing storage and minimizing subsurface environmental risk. The study also gives preliminary consideration to the effectiveness that monitoring strategy may play in providing useful information to inform reservoir management decisions for risk reduction. Two types of monitoring were considered: 1) pressure build-up or pressure transient; and 2) potential leakage detection from a CO 2 mass or plume. Four hypothetical legacy wells, two plugged and two abandoned, were placed in the model domain. Monitoring along these wells was measured over time in individual stacked reservoir formations and shale formations to support risk mitigation decisions, especially operational decisions that assisted in risk reduction. These simulations will serve as the basis for a series of GCS leakage risk forecasts that are to be developed using NRAP’s Open-IAM, and demonstration of a simple decision support workflow for comparative assessment of mitigation alternatives based on results of those system model forecasts. This risk assessment and decision support study is forthcoming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Expanding the Breeder’s Toolbox for Perennial Grasses

With the increase in world energy demand and the environmental impacts associated with continued fossil fuel use, there is a great need for the development of alternative and sustainable fuel sources. Switchgrass (Panicum virgatum L.), a perennial grass native to North America, is poised to become one of the first dedicated biomass crops deployed on a large scale in the United States in large part due to its inherent high yield, adaptability and perennial nature. Current ‘cultivars’ of switchgrass are essentially undomesticated wild selections from natural populations. Thus, there is considerable potential for improvement of this emerging energy crop. Traditional breeding approaches in switchgrass have been hampered by its self-incompatibility and sensitivity to inbreeding, therefore there is a significant need to develop new tools for improved switchgrass breeding. The proposed research uses a systems biology approach to accelerate switchgrass breeding, to develop its biotechnological improvement through the generation of stress-tolerant varieties, and to establish ways to minimize the potential impact of transgenes on ecosystems. In this proposal, we will develop new breeding tools for perennial grasses and apply these tools toward improving switchgrass. Specifically, we will employ two complementary approaches to overcome the difficulty of breeding a large, polyploid, self-incompatible plant. The first approach will accelerate conventional breeding by developing a method to rapidly create doubled haploid (homozygous) lines for breeding. This approach is based on altering CENH3, a centromere-specific histone, leading to the production of haploid offspring when the centromere mutant is crossed to wild type plants. Subsequent genome doubling results in fully homozygous individuals and overcomes one of the major limitations in breeding self-incompatibile crops. These homozygous lines would allow switchgrass breeders to apply a variety of breeding approaches that have been previously impossible. The second approach is to develop tools and reagents to accelerate the biotechnological improvement of switchgrass including: modules for improved stress tolerance, a test bed to evaluate transgenes in a perennial model grass and a robust gene containment system. In order to maintain a favorable energy balance and avoid competition with food crops, dedicated biomass crops must be grown with minimal inputs (fertilizer and water) on marginal lands that are unsuited to the traditional high input agriculture necessary to produce food. Thus, abiotic stress tolerance and efficient water and nutrient use are of paramount importance. Considerable basic research has been directed at these areas and this knowledge has been used to develop transgenic approaches to greatly improve water and nutrient use efficiency. By applying these approaches to switchgrass we will rapidly increase drought tolerance and nutrient use efficiency. This approach can rapidly introduce these traits in different cultivars allowing breeders to add these traits to their elite germplasm. Since biotechnologically improved switchgrass must ultimately be grown in open fields, they must be designed to minimize the potential impact of the transgenes on non-target ecosystems. The best way to do this is to minimize gene flow from the transgenic plants. Thus, we will develop technology to introduce sterility into the transgenic plants. We will then combine this technology with the stress resistance modules to create switchgrass lines with enhanced resistance to abiotic stresses.

09 BIOMASS FUELS↗
DOE OSTI2021

A trait-based framework for linking microbial communities with carbon transformations under precipitation change

Droughts are common throughout the world. As the climate changes, droughts may become more frequent and intense. Still, scientists are uncertain about how drought will affect the natural world, particularly the bacteria, fungi, and other microbes that live in soils. These tiny life forms are crucial because they control the Earth’s flows of carbon and essential nutrients. Researchers at the University of California, Irvine, and Lawrence Berkeley National Laboratory teamed up to study how the microbiome, or collection of bacteria and fungi in the soil, deals with drought. Since 2007, the researchers have used shelters with retractable roofs to prevent nearly half of normal rainfall from reaching grass and shrub ecosystems, and their soil microbiomes, in Southern California. The study team discovered that microbes have some clever tricks up their sleeve for surviving drought. When growing on dead grass as a food source, microbes ramp up production of specialized chemicals called osmolytes that keep their cells from drying out. But microbes growing on dead shrubs face another problem. Unlike grass, shrub leaves are a lousy food source. To digest and consume shrub leaves, microbes have to exude more enzymes, which act like biochemical chef knives that chop complex leaf molecules into bite-sized pieces. Carbon is the coin of the microbial realm, earned via enzyme action or slurping up dead plant juices. Microbes growing under normal conditions on tasty dead grass have it easy: they can spend most of their carbon currency on growth. With drought, life gets harder as microbes need to pay up for osmolytes and ramp down their growth. It gets worse with shrub leaves because microbes have to multi-task among growth, enzyme secretion, and osmolyte production. When drought hits, microbes on shrub leaves forgo the osmolytes, probably because losing the carbon revenue from enzyme investment would be a deal-breaker for survival. The next question tackled by the researchers asked how the genes controlling microbial lifestyles sort out across the tree of life. Most microbiologists thought these lifestyles would correspond to rather large branches on the tree. But the study team found that in fact, very closely related microbes differ in important and interesting ways. For example, bacteria that have nearly identical housekeeping genes respond distinctively to warming, rainfall, and plant chemistry. As a result, soil microbiomes are much richer in diversity than originally thought. And studying microbial diversity in much greater detail could open up many more possibilities for how microbial life deals with changing environmental conditions. Trying to understand microbial life without the fine details of genetic diversity is like trying to stream Netflix on a dial-up connection. By looking across the landscape, the researchers revealed that microbial diversity is absolutely critical for maintaining the planet’s flows of carbon and nutrients. The study team designed a new technology—microbial cages—for transplanting intact microbiomes. With the cages, the researchers could move microbiomes to novel environments and compare their ability to cycle carbon and nutrients. In some cases, performance tailed off when microbiomes found themselves in a new environment, but in other cases, performance rivaled or even exceeded that of the resident microbiome. And even the low performers eventually caught up to the native microbiomes if given sufficient time. These findings mean that microbiomes—at least in Southern California—may be resilient to climate shifts due to a high diversity of microbial lifestyles. Coping with heat and drought may literally be in their DNA. The last piece of the research puzzle, and a “Holy Grail” for microbial ecologists, is to forecast the behavior of diverse microbiomes. To meet this challenge, the study team developed new theory and computer models. For the first time, these models account for hundreds of different microbes and how their intricate lifestyles cope with drought. The models are starting to connect the tiniest microbes with the global cycles that sustain Earth’s farms, fields, and forests. With that connection, it will be easier for society to plan for a world with more droughts and other climate disruptions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Uranium-Containing and Thorium-Containing Anions Studied by Photoelectron Spectroscopy

An in-depth knowledge of actinide chemistry is fundamental to many aspects of nuclear science and technology, including the synthesis and processing of materials and the remediation of waste disposal sites. Among the actinides, the chemical bonding behaviors of actinium and thorium resemble those of the transition metals; the 5f-electrons of protactinium, uranium, neptunium, and plutonium often play important roles in their bonding; and among the still heavier elements, their bonding tends to mimic the lanthanide elements in terms of electron shielding and their f-electron contributions. Bonding that involves 5f-electrons, however, is especially important, in part because of the significance of uranium and plutonium, but also because these elements are among the few where f-electron participation in bonding is relatively common. This work focused on studying uranium-containing and thorium-containing anions in the gas phase using negative ion photoelectron spectroscopy. Since this technique directly probed valence electrons, it was uniquely positioned to address open questions regarding molecular bonding and electron configurations. A particularly important issue concerned how bonding in actinide-containing molecules was affected by modifications to their actinide atoms’ environment, i.e., due to their interaction with ligands. A closely related question was how actinide atoms’ suborbitals were qualitatively reordered and their energies quantitatively shifted as a result of their ligated environments. These were especially relevant issues in regard to uranium due to it having multiple possible oxidation states (OS) and the potential for 5f electron participation in bonding. The effects of ligands on oxidation states and 5f-orbital energies in uranium bonding was expected to be pronounced. Both ligands and excess electrons were seen as probes of actinide atoms within actinide-containing molecules. Our strategy for advancing knowledge of chemical bonding in the actinide-containing species utilized the synergy between experiments and theory, where in some cases experimental results validated theory and where in others computational results assisted in interpreting experiments. Calculations on actinide systems are terrifically challenging due to large spin-orbit interactions, relativistic effects, and just the sheer number of electrons involved. Even in the simplest species, e.g., U and U2, the most sophisticated, modern calculations carried out by the most experienced theorists often only approximate experimentally-measured values, such as electron affinities. For theory to provide confident predictions that can be used to solve real problems it needed an iterative and ultimately corrective mechanism by which its methods can develop further. Experiments can be used to identify when theory has failed; whereupon the subsequent process of using the experiment-theory interplay can be used to find the cause of the failure. Upon fixing it in one case, different test species can be proposed and studied by the experiment-theory combination to determine whether the problem has been corrected. Thus, experiments not only measure the values of molecular properties, they also provide navigational 3 beacons that keep computations off the reefs in an otherwise dark sea with few reference points. Experimental measurements in the actinide field are not only important, they are in actuality essential to computational progress. While it was not always possible to compare the theoreticallydetermined quantity of interest directly with the same experimentally-measured observable, it was usually possible to compare consequential properties that are both calculable and measurable. In the work completed here electron affinities and electronic state spacings were often sensitive consequential parameters. Reasonable agreement between measured and computational values signaled that a calculation that was very likely to be on-track. We had established collaborative relationships with five computational groups, all of which have expertise in computational actinide chemistry. Their PI’s are L. Cheng, D. Dixon, L. Gagliardi, K. Peterson, and B. Vlaisavljevich. Our close interaction with our theory partners led to us suggesting systems to them and them to us. This reciprocal interaction between our experimental and their computational results was among the most important strengths of this work and was a thread woven throughout. Even though anion photoelectron spectroscopic studies are conducted on anions, much of the information that they provide, pertains to the electronic structure of the neutral counterparts of those anions; among these are electron affinities and electronically excited state spacings. Our experimental tools included several specialized ion sources for forming the anionic species of interest, a mass spectrometer for identifying and mass-selecting them, and an anion photoelectron spectrometer for determining their electron affinities (EA) and characterizing the electronic states of the selected anions’ neutral counterparts. Anion photoelectron spectroscopy is conducted by crossing a mass-selected beam of anions with a fixed-frequency laser beam and energy-analyzing the resultant photodetached electrons. The photodetachment process is governed by the energyconserving relationship: hν = EBE + EKE, where hν is the photon’s energy, EBE is the electron binding (photodetachment transition) energy, and EKE is the electron’s kinetic energy. In our apparatus mass-selection is accomplished via time-of-flight mass spectrometry (TOF-MS), electron energy analysis is achieved with either a magnetic bottle or by velocity mapped imaging. Photodetachment of electrons from anions is implemented via either Nd:YAG or excimer lasers. The photodetachment transition energy, i.e., the EBE, between the ground vibrational and electronic state of an anion and the ground vibrational and electronic state of that anion’s neutral counterpart is the adiabatic electron affinity (EA) of that neutral molecule. Likewise, photodetachment transitions between the ground vibrational and electronic state of an anion and the various electronically-excited states of that anion’s corresponding neutral map the electronic spectrum of that neutral species, i.e., the spectral spacings in the photoelectron spectrum are a mirror image of the neutral’s electronic spectrum. It was, of course, crucial to be able to form the anionic species of interest. There, we had a particularly broad field of anion sources from which to choose. These included several variants of pulsed laser vaporization (LV), laser photoemission, infrared desorption plus photoemission, pulsed arc discharge (PACIS), electrospray ionization (ESI), and Rydberg electron transfer (RET). Each of these anion sources were readily combined with, i.e., connected to, the anion photoelectron spectroscopic portion of our apparatus as described above. Among the sources that utilize lasers, visible light for LV sources as well as IR for desorption sources are provided by Nd:YAG lasers. Ultraviolet photons are provided by both Nd:YAG and excimer lasers, whereas the excitation wavelengths for RET experiments come from two Nd:YAG-pumped dye lasers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Materials laboratories of the future for alloys, amorphous, and composite materials

In alignment with the Materials Genome Initiative and as the product of a workshop sponsored by the US National Science Foundation, we define a vision for materials laboratories of the future in alloys, amorphous materials, and composite materials; chart a roadmap for realizing this vision; identify technical bottlenecks and barriers to access; and propose pathways to equitable and democratic access to integrated toolsets in a manner that addresses urgent societal needs, accelerates technological innovation, and enhances manufacturing competitiveness. Spanning three important materials classes, this article summarizes the areas of alignment and unifying themes, distinctive needs of different materials research communities, key science drivers that cannot be accomplished within the capabilities of current materials laboratories, and open questions that need further community input. Here, we provide a broader context for the workshop, synopsize the salient findings, outline a shared vision for democratizing access and accelerating materials discovery, highlight some case studies across the three different materials classes, and identify significant issues that need further discussion.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Air-coupled tsunamis generated from impacts and airbursts: Our understanding before Hunga-Tonga Hunga-Ha'apai

The effort to prevent or mitigate the effects of an impact on Earth is known as planetary defense. A significant component of planetary defense research involves risk assessment. Much of our understanding of the risk from near-Earth objects comes from the geologic record in the form of impact craters, but not all asteroid impacts are crater-forming events. Small asteroids explode before reaching the surface, generating an airburst, and most impacts into the ocean do not penetrate the water to form a crater in the sea floor. The risk from these non-crater-forming ocean impacts and airbursts is difficult to quantify and represents a significant uncertainty in our assessment of the overall threat. We are currently working to better understand impact scenarios that can generate dangerous tsunamis. One of the suggested mechanisms for the production of asteroid–generated tsunamis is by direct coupling of the pressure wave to the water, analogous to the means by which a moving weather front can generate a meteotsunami. To test this hypothesis, we ran a series of airburst simulations and provided time-resolved pressure and wind profiles to use as source functions for tsunami models. We used the CTH hydrocode to model the various airburst scenarios to compare to the results of other simulations and provide time dependent boundary conditions as input to shallow-water wave propagation codes. The strongest and most destructive meteotsunamis are generated by atmospheric pressure oscillations with amplitudes of only a few hPa1 (mbar), corresponding to changes in sea level of a few cm. The resulting wave is strongest when there is a resonance between the ocean and the atmospheric forcing. A Proudman resonance takes place when the atmospheric disturbance’s translational speed (U) equals the longwave phase speed $\sqrt{gh}$ of shallow water wave. Coupling is strongest when the Froude number (Fr=U/c) is unity. A weather front propagates much slower than the speed of sound, so meteotsunamis are most common and dangerous in shallow bodies of water such as the Mediterranean Sea or Lake Michigan. By contrast, the blast wave from an airburst or crater-forming impact propagates at a speed faster than a tsunami in the deepest ocean, and a Proudman resonance cannot be achieved even though the overpressures are orders of magnitude greater. However, blast wave profiles are N-waves in which a sharp shock wave leading to overpressure is followed by a more gradual rarefaction to a much longer-duration underpressure phase. Even though the blast outruns the water wave it is forcing, the tsunami should continue to be driven by the out-of-resonance gradient associated with the suction phase, which may depend strongly on the details of the airburst or impact scenario. The open question is whether there are any conditions under which such an airburst-driven tsunami can be dangerous enough to contribute to the overall impact risk. We have also identified other potential mechanisms for airburst-generated tsunamis: 1) reaction force at the surface from the plume ejected into space, which carries significant momentum, 2) expanding toroidal vortices at the surface, which travel more slowly than the shock wave and can generate a Proudman resonance in relatively shallow ocean (such as continental shelf), and 3) steam explosion from seawater ablation by a “Type II” (Libyan Desert Glass-type) airburst in which the hot vapor jet descends to the surface. On January 15, 2022, the Hunga-Tonga Hunga-Ha’apai volcano, located approximately 60 km north of Tongatapu, the main island of Tonga, violently erupted with a powerful explosion, culminating the period of volcanic activity that started in December of 2021. This event and resulting tsunamis provided an existence proof for the air pressure wave coupling mechanism we proposed. It also suggests that it can be stronger and more significant over much greater distances than we contemplated, leading to global tsunamis associated with impact events on land as well as in the water. Large atmospheric explosions generate global Lamb waves with larger amplitudes, longer periods, and slower speeds than the local and regional blast waves we modeled prior to that event. This paper reviews our analysis and modeling of airburst-driven tsunamis prior to the 2022 Hunga-Tonga Hunga-Ha’apai tsunami, which was the subject of two presentations at the 2023 Planetary Defense Conference and is the subject of another paper currently in preparation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Status and future plans for C 3 R&D

C 3 is an opportunity to realize an e + e - collider for the study of the Higgs boson at √s = 250 GeV, with a well defined upgrade path to 550 GeV while staying on the same short facility footprint. C 3 is based on a fundamentally new approach to normal conducting linear accelerators that achieves both high gradient and high efficiency at relatively low cost. Given the advanced state of linear collider designs, the key system that requires technical maturation for C 3 is the main linac. This paper presents the staged approach towards a facility to demonstrate C 3 technology with both Direct (source and main linac) and Parallel (beam delivery, damping ring, ancillary component) R&D. The primary goal of the C 3 Demonstration R&D Plan is to reduce technical and cost risk by building and operating the key components of C 3 at an adequate scale. This R&D plan starts with the engineering design, and demonstration of one cryomodule and will culminate in the construction of a 3 cryomodule linac with pre-production prototypes. This R&D program would also demonstrate the linac rf fundamentals including achievable gradient and gradient stability over a full electron bunch train and breakdown rates. It will also investigate beam dynamics including energy spread, wakefields, and emittance growth. This work will be critical to confirm the suitability of the C 3 beam parameters for the physics reach and detector performance in preparation for a Conceptual Design Report (CDR), as well as for follow-on technology development and industrialization. The C 3 Demonstration R&D Plan will open up significant new scientific and technical opportunities based on development of high-gradient and high-efficiency accelerator technology. It will push this technology to operate both at the GeV scale and mature the technology to be reliable and provide high-brightness electron beams. The timeline for progressing with C 3 technology development will be governed by practical limitations on both the technical progress and resource availability. It consists of four stages: Stage 0) Ongoing fundamental R&D on structure prototypes, damping and vibrations. Stage 1) Advancing the engineering maturity of the design and developing start-to-end simulations including space-charge and wakefield effects. This stage will include testing of strucutres operating at cryogenic temperatures. Beam tests would be performed with high beam current to test full beam loading. Stage 2) Production and testing of the first cryomodule at cryogenic temperatures. This would provide sufficient experimental data to compile a CDR and it is anticipated for Stage 2 to last 3 years and to culminate with the transport of photo-electrons through the first cryomodule. Stage 3) Updates to the engineering design of the cryomodules, production of the second and third cryomodule and their installation. Lower charge and lower emittance beams will be used to investigate emittance growth. The successful full demonstration of the 3 cryomodules to deliver up to a 3 GeV beam and achieve the C 3 five gradient will allow a comprehensive and robust evaluation of the technical design of C 3 as well as mitigate technical, schedule, and cost risks required to proceed with a Technical Design Report (TDR).

radiation hardened magnets↗