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

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A SUMMARY COMPARISON OF DESIGN EVALUATION TECHNIQUES

The United States’ fleet of Nuclear Reactors is considering modernizing their control rooms and instrumentation as an effort to avoid component obsolescence, keep up with competing industries, and cater to a new work force among others. Multiple technologies have potential to improve the control room. In attempts to evaluate the available options researchers employ a variety of measures to ensure the best candidate is used in a modernizing effort. The NRC is in charge of ensuring any new design has been thoroughly vetted before approving a license. Laid out in NUREG-0711 “Human Factors Engineering Program Review Model” is the review criteria for design validation. As there are a variety of measures currently used to evaluate candidate technologies, this paper seeks to identify weaknesses in the common measures used to design and validate technology in control room modernization efforts. Identifying where measurements are not meeting the criteria will help the control room modernization research platform identify where measurement development needs to occur. This will help ensure that current performance measurements are producing as reliable results as possible to select the right technology to integrate into nuclear operating control rooms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Quantifying Impacts of Renewable Electricity Deployment on Air Quality and Human Health in Southeast Asia Based on AIMS III Scenarios

This study augments the ASEAN Interconnection Masterplan Study III (AIMS III) by quantifying changes to air quality and human health that result from its renewable integration and transmission interconnection scenarios. Performing this analysis requires translation of the changes in projected generation from different power sector fuel sources in the AIMS III scenarios to changes in air pollutant emissions, developing what is known as an emissions inventory for each scenario and year evaluated. An emissions inventory represents who emits air pollutants, from where the pollutants are emitted, when, and how much of which air pollutants are emitted. With the assistance of the ASEAN Centre for Energy and leveraging the best available in-region public data sources, the National Renewable Energy Laboratory (NREL) team compiled a detailed inventory of power plants in the ASEAN region, mapping their PM 2.5 , sulfur oxides (SOx), and nitrogen oxides (NOx) emissions. A new, first-of-its-kind, and user-friendly global air quality model, Global InMAP (Thakrar et al. 2022), is then used to transform the inventory of changes in emissions to changes in concentration of fine particulate matter. Global InMAP then maps the location of human populations in ASEAN countries to calculate humans' exposure to PM 2.5 and estimate excess PM 2.5 -caused mortality attributable to thermal generation sources, as modeled in the AIMS III scenarios.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Younger facial looks are associate with a lower likelihood of several age-related morbidities in the middle-aged to elderly

Abstract Background Looking older for one’s chronological age is associated with a higher mortality rate. Yet it remains unclear how perceived facial age relates to morbidity and the degree to which facial ageing reflects systemic ageing of the human body. Objectives To investigate the association between ΔPA and age-related morbidities of different organ systems, where ΔPA represents the difference between perceived age (PA) and chronological age. Methods We performed a cross-sectional analysis on data from the Rotterdam Study, a population-based cohort study in the Netherlands. High-resolution facial photographs of 2679 men and women aged 51.5–87.8 years of European descent were used to assess PA. PA was estimated and scored in 5-year categories using these photographs by a panel of men and women who were blinded for chronological age and medical history. A linear mixed model was used to generate the mean PAs. The difference between the mean PA and chronological age was calculated (ΔPA), where a higher (positive) ΔPA means that the person looks younger for their age and a lower (negative) ΔPA that the person looks older. ΔPA was tested as a continuous variable for association with ageing-related morbidities including cardiovascular, pulmonary, ophthalmological, neurocognitive, renal, skeletal and auditory morbidities in separate regression analyses, adjusted for age and sex (model 1) and additionally for body mass index, smoking and sun exposure (model 2). Results We observed 5-year higher ΔPA (i.e. looking younger by 5 years for one’s age) to be associated with less osteoporosis [odds ratio (OR) 0.76, 95% confidence interval (CI) 0.62–0.93], less chronic obstructive pulmonary disease (OR 0.85, 95% CI 0.77–0.95), less age-related hearing loss (model 2; B = −0.76, 95% CI −1.35 to −0.17) and fewer cataracts (OR 0.84, 95% CI 0.73–0.97), but with better global cognitive functioning (g-factor; model 2; B = 0.07, 95% CI 0.04–0.10). Conclusions PA is associated with multiple morbidities and better cognitive function, suggesting that systemic ageing and cognitive ageing are, to an extent, externally visible in the human face.

Mekić, Selma↗
DOE OSTI2015

Image-derived and arterial blood sampled input functions for quantitative PET imaging of the angiotensin II subtype 1 receptor in the kidney

Purpose: The radioligand {sup 11}C-KR31173 has been introduced for positron emission tomography (PET) imaging of the angiotensin II subtype 1 receptor in the kidney in vivo. To study the biokinetics of {sup 11}C-KR31173 with a compartmental model, the input function is needed. Collection and analysis of arterial blood samples are the established approach to obtain the input function but they are not feasible in patients with renal diseases. The goal of this study was to develop a quantitative technique that can provide an accurate image-derived input function (ID-IF) to replace the conventional invasive arterial sampling and test the method in pigs with the goal of translation into human studies. Methods: The experimental animals were injected with [{sup 11}C]KR31173 and scanned up to 90 min with dynamic PET. Arterial blood samples were collected for the artery derived input function (AD-IF) and used as a gold standard for ID-IF. Before PET, magnetic resonance angiography of the kidneys was obtained to provide the anatomical information required for derivation of the recovery coefficients in the abdominal aorta, a requirement for partial volume correction of the ID-IF. Different image reconstruction methods, filtered back projection (FBP) and ordered subset expectation maximization (OS-EM), were investigated for the best trade-off between bias and variance of the ID-IF. The effects of kidney uptakes on the quantitative accuracy of ID-IF were also studied. Biological variables such as red blood cell binding and radioligand metabolism were also taken into consideration. A single blood sample was used for calibration in the later phase of the input function. Results: In the first 2 min after injection, the OS-EM based ID-IF was found to be biased, and the bias was found to be induced by the kidney uptake. No such bias was found with the FBP based image reconstruction method. However, the OS-EM based image reconstruction was found to reduce variance in the subsequent phase of the ID-IF. The combined use of FBP and OS-EM resulted in reduced bias and noise. After performing all the necessary corrections, the areas under the curves (AUCs) of the AD-IF were close to that of the AD-IF (average AUC ratio =1 ± 0.08) during the early phase. When applied in a two-tissue-compartmental kinetic model, the average difference between the estimated model parameters from ID-IF and AD-IF was 10% which was within the error of the estimation method. Conclusions: The bias of radioligand concentration in the aorta from the OS-EM image reconstruction is significantly affected by radioligand uptake in the adjacent kidney and cannot be neglected for quantitative evaluation. With careful calibrations and corrections, the ID-IF derived from quantitative dynamic PET images can be used as the input function of the compartmental model to quantify the renal kinetics of {sup 11}C-KR31173 in experimental animals and the authors intend to evaluate this method in future human studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

GIS-Based Modeling of Contaminated Soil Volumes at Multiple Sites in the Formerly Utilized Sites Remedial Action Program - 20149

The remediation of hazardous, toxic, and radioactive waste (HTRW) sites produces cost-related risks associated with the estimation of contaminated soil or debris volumes. Historical risk-management techniques include cost contingencies to cover volume uncertainties that affect project budgeting and decision-making. The Buffalo District teamed with project partners to lessen volume uncertainty and reduce project risks at multiple HTRW sites managed under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Historical remedial investigations under FUSRAP commonly identified the presence of radiological material in site media, the associated human health risk, and then areas of remediation. To manage remedial execution and reduce risk, pre-design or remediation-phase sampling essentially 'chased' contamination, which was not conducive to efficient predictive budgeting derived from Feasibility Study (FS) cost analyses. The Buffalo District first optimized their approach to better understand volume uncertainty by utilizing the Argonne National Laboratory's Bayesian Approaches for Adaptive Spatial Sampling (BAASS) software [1]. BAASS processed soft data (e.g., gamma walk-over data) and spatial sampling data to estimate the lateral extent of contaminated soil irrespective of depth (i.e., gross contamination extent) and define areas of contaminant uncertainty. The software performed a binary transformation of contaminant concentrations at all sampling points based upon remedial action goals or a sum of ratios approach (i.e., clean, impacted, or range of impacts in soil). The model produced two-dimensional (horizontal) contaminant probability contours and statistical uncertainty in the sampling coverage and resulting contaminant extents. This method was translated vertically by partitioning the sampling data into depth brackets that produced a stacked representation of contaminant extents and uncertainty in the subsurface (i.e., similar to construction lifts). The results commonly led to a better understanding of project uncertainty and the need for sampling strategies that produce high-confidence soil volumes, which control costs. The BAASS-based delineations were eventually replaced by Empirical Bayesian Kriging (EBK) methods available in ArcGIS Spatial or 3D Analysts [2]. The EBK method calculates contaminant probability zones derived from user-controlled semivariograms of the spatial datasets. The resulting probability zones (e.g., 50% or 80% of contaminant probability) represent the two-dimensional surface delineation of the overall horizontal remedial area, similarly to BAASS. However, unlike BAASS, the vertical sampling data within these probability zones became vertical control points to contour a subterranean surface that connects subsurface points to the land-surface delineations of contamination. The resulting representation of horizontal and vertical impacts within an enclosed envelop (volume) of soil included uncertainty distributions that are used to plan uncertainty-reduction sampling. These data-driven and math-based models of three-dimensional sampling results produced well-bounded remedial volumes for project planning and better uncertainty predictions during project budgeting. The EBK method was applied to several FUSRAP sites managed by the Buffalo District and compared to less rigorously modeled sites previously remediated by the District. The comparison of modeled to actual remediated volumes provide a basis for validating the volume-estimation method. This comparison is important to ensure modeled volumes match physical boundaries of site remediation. FUSRAP sites with denser investigative sampling and lesser volume uncertainty proved useful in remedial planning and contracting. The Buffalo District noted that historical sites with sparser sampling arrays had greater disparity between estimated volumes and final remedial volumes. The benefit achieved over the cost of detailed soil sampling appears positive for FUSRAP projects, especially where impacts vary widely and appear unbounded by investigation-phase sampling. The subsequent Empirical Bayesian Kriging of contamination coupled with vertical contouring for soil estimations reduces uncertainty in soil volumes or indicates where sampling is required to reduce uncertainty, which together optimize remedial planning and budgeting. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Cooling efficiency of a spot-type personalized air-conditioner

Here, this study defined Cooling Efficiency ( CE ) of a Spot-type Personalized Air-Conditioning (SPAC) device as the ratio of the additional sensible heat removal from human body induced by SPAC and the device's cooling capacity. CE enabled the investigation of SPAC performance on the occupant's sensible heat loss (Q s ) and thermal sensation by its quantitative relation with the change of PMV level ( ΔPMV ). Three round nozzles with the diameter of 0.08 m, 0.105 m, and 0.128 m, respectively, discharged air jets at airflow rates from 11.8 L s –1 to 59.0 L s –1 , toward the chest of a seated or standing human body with a clothing of 0.48 clo. This study developed a validated CFD model coupled with the Fanger's thermoregulation model, to calculate Q s in a room of 26 °C ventilated at a rate of 3 ACH. According to the results, Q s , CE and draft risk ( DR ) at face had significant positive linear correlation with the SPAC device's supply airflow rates (R2 >0.96), and a negative linear correlation for ΔPMV. With DR = 20% at face, CE was always under 0.3, and ΔPMV was around -1.0–1.1. Interestingly, both CE and ΔPMV had the least favorable values for the air jet produced by the nozzle with the diameter of 0.105 m independent of body posture. In conclusion, although SPAC could lead to additional Q s by sending air at a higher airflow rate from a smaller nozzle, the improvement in cooling efficiency and thermal sensation had a limit due to draft risk.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Computational Approach for Improving Three-Dimensional Sub-Surface Earth Structure for Regional Earthquake Hazard Simulations in the San Francisco Bay Area

In our Exascale Computing Project (ECP) we seek to simulate earthquake ground motions at much higher frequency than is currently possible. Previous simulations in the SFBA were limited to 0.5-1 Hz or lower (Aagaard et al. 2008, 2010), while we have recently simulated the response to 5 Hz. In order to improve confidence in simulated ground motions, we must accurately represent the three-dimensional (3D) sub-surface material properties that govern seismic wave propagation over a broad region. We are currently focusing on the San Francisco Bay Area (SFBA) with a Cartesian domain of size 120 x 80 x 35 km, but this area will be expanded to cover a larger domain. Currently, the United States Geologic Survey (USGS) has a 3D model of the SFBA for seismic simulations. However, this model suffers from two serious shortcomings relative to our application: 1) it does not fit most of the available low frequency (< 1 Hz) seismic waveforms from moderate (magnitude M 3.5-5.0) earthquakes; and 2) it is represented with much lower resolution than necessary for the high frequency simulations (> 5 Hz) we seek to perform. The current model will serve as a starting model for full waveform tomography based on 3D sensitivity kernels. This report serves as the deliverable for our ECP FY2017 Quarter 4 milestone to FY 2018 “Computational approach to developing model updates”. We summarize the current state of 3D seismic simulations in the SFBA and demonstrate the performance of the USGS 3D model for a few selected paths. We show the available open-source waveform data sets for model updates, based on moderate earthquakes recorded in the region. We present a plan for improving the 3D model utilizing the available data and further development of our SW4 application. We project how the model could be improved and present options for further improvements focused on the shallow geotechnical layers using dense passive recordings of ambient and human-induced noise.

58 GEOSCIENCES↗
DOE OSTI2016

Building America Case Study: Columbia County Habitat for Humanity Passive Townhomes, Hudson, New York

Columbia County (New York) Habitat for Humanity built a pair of townhomes to Passive House criteria with the purpose of exploring approaches for achieving Passive House performance and to eventually develop a prototype design for future projects. The project utilized a 2x6 frame wall with a structural insulated panel curtain wall and a ventilated attic over a sealed OSB ceiling air barrier. Mechanical systems include a single head, wall mounted ductless mini-split heat pump in each unit and a heat recovery ventilator. Costs were $26,000 per unit higher for Passive House construction compared with the same home built to ENERGY STAR version 3 specifications, representing about 18 percent of total construction cost. This report discusses the cost components, energy modeling results and lessons from construction. Two alternative ventilation systems are analyzed: a central system; and, a point-source system with small through-wall units distributed throughout the house. The report includes a design and cost analysis of these two approaches.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2019

A Salt Repository Concept for CSNF in 21-PWR Size Canisters

The most straightforward concept for disposal of large, heavy packages containing commercial spent nuclear fuel (CSNF) in a repository in bedded salt, would be to emplace them directly on the floor in emplacement tunnels. In-tunnel axially aligned horizontal emplacement would minimize excavated volume and avoid drilling of large-diameter emplacement boreholes. A similar concept was proposed in Germany for direct disposal of POLLUX ® canisters. The repository would be constructed at a depth of 500 to 1,000 m for isolation from the surface, and for sufficient overburden stress to ensure creep reconsolidation of repository openings. It could entail modular panels of emplacement tunnels arranged on headings oriented in cardinal directions from a central core, to accommodate the estimated 140,000 MTU total U.S. CSNF inventory. To do so, the overall area of the repository layout would be approximately 20 km 2 . Many layouts are possible, but the approach should be modular, excavation should be deferred for as long as possible to avoid maintenance, and the emplacement areas should share support facilities and shafts. Vertical shafts would be used in accordance with mining practice in sedimentary basins. Large diameter shafts would be needed for ventilation exhaust and waste transport, with smaller shafts for waste salt removal, men & materials, and ventilation intake. The spacing between disposal tunnels as estimated from thermal modeling, seeks to limit the maximum average areal thermal load in the panels to 11 W/m 2 to control long-term heat buildup in the host rock. Peak salt temperature would occur within a few years and would be dominated by each waste package locally, simplifying thermal management. There would be some flexibility to decrease the package spacing or increase the emplacement thermal power limit Backfilling emplaced waste packages immediately with mine-run crushed salt would provide shielding and expedite reconsolidation. This arrangement would isolate adjacent waste packages from one another by the intervening backfill, especially after it reconsolidates and its properties approach those of intact salt. After the repository is fully loaded and the performance confirmation program is complete, activities to permanently close the repository would be initiated. During closure operations all openings in the host salt would be backfilled, then shafts would be sealed, and boreholes plugged. Plans for the Waste Isolation Pilot Plant (WIPP) show how sealing and plugging could be done. A monitoring program could continue for 50 years or longer after repository closure. With an emplacement thermal power limit of 10 kW per waste package, nearly all the CSNF that is projected to be produced by the current fleet of reactors in the U.S. could be emplaced over a period of approximately 50 years starting in calendar 2048. No barriers to implementation in a reasonable timeframe have been identified from this generic analysis. Engineering challenges include: 1) shaft construction; 2) a very-large capacity shaft hoist; 3) overpack design; 4) a transport-emplacement-vehicle (TEV) for transporting waste packages once they are underground and emplacing them remotely; and 5) remotely operated equipment for emplacing backfill. The method of shaft construction would depend on site-specific conditions, and could involve freezing the subsurface. A shaft hoist with payload capacity of 175 MT seems technically and economically feasible based on development work in Germany, and it would be the largest hoist of its kind. The function of disposal overpacks would be to provide reliable containment during repository operations, which could be accomplished using a corrosion allowance material such as a low-carbon steel. Development effort would be needed to determine overpack thickness (e.g., 7 to 20 cm) that can resist corrosion and loading from salt creep, to rovide containment throughout the repository operational period. The transport-emplacement vehicle (TEV) would be similar to previous concepts, particularly one option proposed for a Yucca Mountain repository. It would move over a rough salt floor on independently driven and steered wheels, and carry heavy shielding in addition to a waste package. By analogy to the safety case for the WIPP in New Mexico, human intrusion is likely to be the dominant mode of radionuclide release from the repository. Treatment of human intrusion for a CSNF repository in salt could depend on promulgation of site-specific changes in the regulations. Radionuclide release and migration would be quite limited for undisturbed conditions. There may be opportunities for improved understanding of salt performance with waste heating, based on future in situ testing in an underground salt research laboratory. This report also discusses a developing area of salt rock mechanics that involves low-stress, low strain-rate creep that might cause large, heavy waste packages to slowly sink. Site-specific sampling, testing, and modeling would be used to determine if the mechanism is important enough to merit consideration in design, or inclusion in performance assessment. Part of engineering design and postclosure safety assessment for a CSNF repository in salt would be to implement a methodology to show that the probability of a criticality event in the repository, when waste packages eventually breach and are flooded, is less than the probability screening threshold for performance assessment. In the methodology, a criticality analysis would be performed for waste packages in the repository, incorporating measures that could be introduced as needed to limit reactivity, for example using fuel selection and loading rules, and crediting the absorption of thermal neutrons by natural chlorine in the environment. A similar analysis has been underway for CSNF stored in dual-purpose canisters. Ideally the strategy would be developed prior to actually loading SNF assemblies into canisters used in waste packages for disposal.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Columbia County Habitat for Humanity Passive Townhomes

Columbia County (New York) Habitat for Humanity built a pair of townhomes to Passive House criteria with the purpose of exploring approaches for achieving Passive House performance and to eventually develop a prototype design for future projects. The project utilized a 2x6 frame wall with a structural insulated panel curtain wall and a ventilated attic over a sealed OSB ceiling air barrier. Mechanical systems include a single head, wall mounted ductless mini-split heat pump in each unit and a heat recovery ventilator. Costs were $26,000 per unit higher for Passive House construction compared with the same home built to ENERGY STAR version 3 specifications, representing about 18% of total construction cost. This report discusses the cost components, energy modeling results and lessons from construction. Two alternative ventilation systems are analyzed: a central system; and, a point-source system with small through-wall units distributed throughout the house. The report includes a design and cost analysis of these two approaches.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Stratigraphic Identification with Airborne Electromagnetic Methods at the Hanford Site, Washington

Stratigraphic units can influence the fate and transport of subsurface contaminants within groundwater. Units having coarse-grained sediments act as preferential flow pathways, and therefore can accelerate the transport of contaminants to reach human and ecological receptors. At legacy waste sites, detailed knowledge of subsurface stratigraphy can be used for effective monitoring and remediation planning to help minimize risk to human health and the environment. Airborne electromagnetic (AEM) methods can non-invasively provide information on kilometer-scale or larger subsurface stratigraphic features and fill informational gaps in directly sampled data from sparsely located boreholes. In this paper, we present inversion results of a 412 line-km frequency-domain AEM survey to delineate subsurface stratigraphic features at the Hanford Site, located in southeastern Washington State. The inversion was performed using a massively parallel 3D electromagnetic modeling and inversion code, where the modeling is based on solving frequency-domain Maxwell’s equations using an unstructured-mesh finite-element method and the inversion employs a Gauss-Newton optimization scheme. The results are compared to an underlying geologic framework model (GFM), built by interpolating contact depths of stratigraphic units interpreted from site borehole datasets. In areas with good borehole coverage, the inversion results show a good match with the GFM to a depth of about 60 m. Outside of these areas, the inversion results exhibit inconsistencies from the assumptions made to create the GFM, demonstrating that the AEM survey results can be used to improve the understanding of the geological conceptual model.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Automated Construction of Artificial Lattice Structures with Designer Electronic States

Manipulating matter with a scanning tunneling microscope (STM) enables the creation of atomically defined artificial structures that host designer quantum states. However, the time-consuming nature of the manipulation process, coupled with the sensitivity of the STM tip, constrains the exploration of diverse configurations and limits the size of the designed features. In this study, we present a reinforcement learning (RL)-based framework for creating artificial structures by spatially manipulating carbon monoxide (CO) molecules on a copper substrate by using the STM tip. The automated workflow combines molecule detection and manipulation, employing deep-learning-based object detection to locate CO molecules and linear assignment algorithms to allocate these molecules to designated target sites. We initially perform molecule maneuvering based on randomized parameter sampling for sample bias, tunneling current set point, and manipulation speed. This data set is then structured into an action trajectory used to train an RL agent. The model is subsequently deployed on the STM for real-time fine-tuning of the manipulation parameters during structure construction. Our approach incorporates path-planning protocols coupled with active drift compensation to enable atomically precise fabrication of structures with significantly reduced human input while realizing larger-scale artificial lattices with the desired electronic properties. Furthermore, using our approach, we demonstrate the automated construction of an extended artificial graphene lattice and confirm the existence of a characteristic Dirac point in its electronic structure. Further challenges regarding the RL-based structural assembly scalability are discussed.

Algorithms↗
DOE OSTI2016

An ensemble model of QSAR tools for regulatory risk assessment

Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used for chemical risk assessment for protection of human and environmental health, which makes them interesting to regulators, especially in the absence of experimental data. For compatibility with regulatory use, QSAR models should be transparent, reproducible and optimized to minimize the number of false negatives. In silico QSAR tools are gaining wide acceptance as a faster alternative to otherwise time-consuming clinical and animal testing methods. However, different QSAR tools often make conflicting predictions for a given chemical and may also vary in their predictive performance across different chemical datasets. In a regulatory context, conflicting predictions raise interpretation, validation and adequacy concerns. To address these concerns, ensemble learning techniques in the machine learning paradigm can be used to integrate predictions from multiple tools. By leveraging various underlying QSAR algorithms and training datasets, the resulting consensus prediction should yield better overall predictive ability. We present a novel ensemble QSAR model using Bayesian classification. The model allows for varying a cut-off parameter that allows for a selection in the desirable trade-off between model sensitivity and specificity. The predictive performance of the ensemble model is compared with four in silico tools (Toxtree, Lazar, OECD Toolbox, and Danish QSAR) to predict carcinogenicity for a dataset of air toxins (332 chemicals) and a subset of the gold carcinogenic potency database (480 chemicals). Leave-one-out cross validation results show that the ensemble model achieves the best trade-off between sensitivity and specificity (accuracy: 83.8 % and 80.4 %, and balanced accuracy: 80.6 % and 80.8 %) and highest inter-rater agreement [kappa (κ): 0.63 and 0.62] for both the datasets. The ROC curves demonstrate the utility of the cut-off feature in the predictive ability of the ensemble model. In conclusion, this feature provides an additional control to the regulators in grading a chemical based on the severity of the toxic endpoint under study.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Active Learning for Rapid Targeted Synthesis of Compositionally Complex Alloys

The next generation of advanced materials is tending toward increasingly complex compositions. Synthesizing precise composition is time-consuming and becomes exponentially demanding with increasing compositional complexity. An experienced human operator does significantly better than a novice but still struggles to consistently achieve precision when synthesis parameters are coupled. The time to optimize synthesis becomes a barrier to exploring scientifically and technologically exciting compositionally complex materials. This investigation demonstrates an active learning (AL) approach for optimizing physical vapor deposition synthesis of thin-film alloys with up to five principal elements. We compared AL-based on Gaussian process (GP) and random forest (RF) models. The best performing models were able to discover synthesis parameters for a target quinary alloy in 14 iterations. We also demonstrate the capability of these models to be used in transfer learning tasks. RF and GP models trained on lower dimensional systems (i.e., ternary, quarternary) show an immediate improvement in prediction accuracy compared to models trained only on quinary samples. Furthermore, samples that only share a few elements in common with the target composition can be used for model pre-training. We believe that such AL approaches can be widely adapted to significantly accelerate the exploration of compositionally complex materials.

Chemistry↗
DOE OSTI2018

Analyzing urban ecosystem variation in the City of Dongguan: A stepwise cluster modeling approach

Highlights: • A stepwise cluster modeling approach is proposed for urban ecosystem simulation. • Nonlinear relationship is established among NDVI and multiple drivers. • Vegetation conditions get better gradually from the north to the south of Dongguan. • Ecosystem in the east of Dongguan is sensitive to growth of economy and population. In this study, a stepwise cluster modeling approach (SCMA) is developed for analyzing urban ecosystem variation via Normalized Difference Vegetation Index (NDVI). NDVI is an indicator of vegetation growth and coverage and useful in reflecting urban ecosystem. SCMA is established on a cluster tree that can characterize the complex relationship between independent and dependent variables. SCMA is applied to the City of Dongguan for simulating the urban NDVI and identifying associated drivers of human activity, topography and meteorology without specific functions. Results show that SCMA performances better than conventional statistical methods, illustrating the ability of SCMA in capturing the complex and nonlinear features of urban ecosystem. Results disclose that human activities play negative effects on NDVI due to the destruction of green space for pursuing more space for buildings. NDVI reduces gradually from the south part to the north part of Dongguan due to increased gross domestic product and population density, indicating that the ecosystem in Dongguan is better in the south part. NDVI in the northeast part (dominated by agriculture) is sensitive to the growth of economy and population. More attention should be paid to this part for sustainable development, such as increasing afforestation, planting grass and constructing parks. Precipitation has a positive effect on NDVI due to the promotion of soil moisture that is beneficial to plants’ growth. Awareness of these complexities is helpful for sustainable development of urban ecosystem.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Kip, Version 1.0

This high-performance ray tracing library provides very fast rendering, compact code, type flexibility via C++ 'generic programming' techniques, and ease of use through an application programming interface (API) that functions independently of any GUI, on-screen display, or other enclosing application. Kip supports constructive solid geometry models based on any of several built-in shapes and operators and allows for new, user-defined shapes and operators. Additional features include basic texturing, input/output of models using a simple human-readable file format with full error checking and detailed diagnostics, and support for shared data parallelism. Kip is written in pure, ANSI Standard C++, is entirely platform independent, and is very easy to use, as it requires no build system, configuration or installation scripts, wizards, special preprocessing, makefiles, or external libraries.

Staley, Martin↗
DOE OSTI2023

An extended focused assessment with sonography in trauma ultrasound tissue-mimicking phantom for developing automated diagnostic technologies

Medical imaging-based triage is critical for ensuring medical treatment is timely and prioritized. However, without proper image collection and interpretation, triage decisions can be hard to make. While automation approaches can enhance these triage applications, tissue phantoms must be developed to train and mature these novel technologies. Here, we have developed a tissue phantom modeling the ultrasound views imaged during the enhanced focused assessment with sonography in trauma exam (eFAST). The tissue phantom utilized synthetic clear ballistic gel with carveouts in the abdomen and rib cage corresponding to the various eFAST scan points. Various approaches were taken to simulate proper physiology without injuries present or to mimic pneumothorax, hemothorax, or abdominal hemorrhage at multiple locations in the torso. Multiple ultrasound imaging systems were used to acquire ultrasound scans with or without injury present and were used to train deep learning image classification predictive models. Performance of the artificial intelligent (AI) models trained in this study achieved over 97% accuracy for each eFAST scan site. We used a previously trained AI model for pneumothorax which achieved 74% accuracy in blind predictions for images collected with the novel eFAST tissue phantom. Grad-CAM heat map overlays for the predictions identified that the AI models were tracking the area of interest for each scan point in the tissue phantom. Overall, the eFAST tissue phantom ultrasound scans resembled human images and were successful in training AI models. Tissue phantoms are critical first steps in troubleshooting and developing medical imaging automation technologies for this application that can accelerate the widespread use of ultrasound imaging for emergency triage.

60 APPLIED LIFE SCIENCES↗