SEARCH · Search NASA

Results for “COVID-19 modeling”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6

All sources NASA NTRS DOE OSTI

DOE OSTI2023

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. In conclusion, solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Microchannel-based Membrane-less Extraction of Li from Unconventional Lithium Sources & the Separation of REE

This final report provides an overview of the Project's entire duration, covering July 1, 2021 to December 31, 2023. It primarily focuses on the achievements, technological developments, and unique challenges the team faced while working on separating and extracting Lithium from produced waters. The project's primary aim was to create an integrated, high-throughput, membrane-less, and modular microfluidic platform that could extract Lithium from unconventional sources. We have successfully met all goals and milestones envisioned in the SOPO document. The most critical primary milestones, including the Go-No-Go milestone (refer to the Gantt chart in the Appendices), were successfully accomplished. We demonstrated phase separation (>90%) and extraction (>85%) performance in the MPSE using synthetic, and representative produced water composition feed at 50 ml/min total flow through MPSE 36. We have also performed a parametric study of the MPSE operations, beyond the scope of SOPO, exploring operating conditions of current and broader interest. The extended investigation of operational parameters is concurrent with our efforts to seek further development of the MPSE technology beyond the scope of the Project. Along these lines of development, we have made efforts to be responsive to DOE calls for technological developments of other types of resources (beyond PW) for the recovery of Critical Materials and higher TRL development (beyond TRL 4). During the work on this Project, we developed and implemented three innovative technical approaches that emerged from our efforts to successfully meet the Project milestones. The innovative & original technical approaches developed and implemented in this Project are now the contributions to process engineering that could be clearly credited to the Project. First, Convergent Design Approach is a comprehensive feedforward & feedback loop of four design phases: i) design for functionality, ii) design for manufacturing, iii) design for sustainability, and iv) design for market. Next was Process Intensification. A major aim of this Project was to create an innovative phase separation & extraction microscale-based technology for Li separation – thus the words microchannel-based in the Project title. A microscale-based technology is intrinsically in the center of the Process Intensification domain as defined by its unique principles. Therefore, Process Intensification was implicitly envisioned in the Project’s SOPO. Lastly, Time Scale Analysis is a novel tool for discovering the needs and directions of Process Intensification implementations in any process technology. This Project is fully credited for developing and implementing the three novel technical approaches mentioned above. These are general contributions to process engineering that emerged from this Project. Beyond the original SOPO scope, the OSU-U.Pitt research group utilized a Convergent Design methodology, integrating first-principles mathematical modeling with experimental validation on the Minimum Development Vehicle. By creating these Digital Twins, the team rapidly assessed manufacturing iterations to support TEA analysis. This framework further enabled the development of advanced Surface Modification Techniques, where hydrophobic and oleophobic coating strategies were optimized via Digital Twin tools and validated through rigorous 100-hour longevity testing. TEA Analysis: The closing efforts of this Project were focused on the TEA analysis. TEA analysis had two primary functions: i) enabling critical assessments of design variations withing 10 the Concurrent Design Approach, thus enabling evolution of the MPSE design to reach faster- better-cheaper alternatives; and ii) to create a bridge between the accomplishments of this Project and future projects of higher TRL, beyond TRL 6 level. It is important to note that the TEA model created in the Project stirred the technological solutions for the recovery of critical materials toward a vision of a very profitable modular plant that has unique zero-waste water discharge signature. More importantly, thanks to our experimental performance data and conservative assumptions, the TEA model predicts minimal technological and investment risks. Low cost of a modular unit of a nominal capacity of [1000 tons of Li 2 CO 3 /year] positions the MPSE based technology within the reach of community investors, thus offering a paradigm shift in the development of critical technologies. The project successfully navigated two primary challenges: solvent selection and manufacturing adaptation. Restricted by the SOPO to existing literature for lithium recovery, the team identified a critical need for a "material excellence program" to develop next-generation solvents, eventually concluding with a preliminary investigation into promising Ionic Liquids (ILs). Simultaneously, COVID-19 supply chain disruptions forced a pivot from traditional manufacturing to advanced additive methods at ATAMI-OSU. By transitioning from stainless steel to 3D-printed polymer substrates, the team achieved a transformative three-order-of- magnitude reduction in manufacturing costs and compressed prototyping timelines from several months to just two days. The MPSE technology offers significant energy, environmental, and economic advantages by overcoming the traditional bottlenecks of phase-separation hardware and contactor size. Unlike conventional mixer-settlers or membrane-based systems, MPSE operates without moving parts or fouling-prone membranes, achieving robust performance even with challenging, viscous, or particulate-heavy feeds. Key performance metrics include an energy intensity reduction of 5–50x (3–40 kJ/m 3 ) compared to incumbent technologies and a dramatic reduction of processing time to under 60 seconds, which drastically reduces the physical plant footprint. These technical efficiencies translate into superior economic outcomes; for a 100 t/year Li 2 CO 3 facility, implementing MPSE is projected to nearly halve contactor CAPEX (from $\$$6.08M to $\$$3.01M) and significantly increase the project's Net Present Value (NPV), derisking new investment and enabling distributed critical-mineral processing configurations. The commercialization of MPSE technology is being spearheaded by Vigsur Dynamics Inc., which has adopted a structured, parallel approach to technical and business development since its formation in January 2026. Following extensive customer discovery and engagement with the Oregon State University accelerator, Vigsur Dynamics is working to establish a business model that transitions from pilot demonstrations to modular hardware sales, ultimately aiming for a "build-own-operate" service strategy. Current technical milestones—including 100 hours of continuous operation, superior energy efficiency, and successful 6-unit modular scale-up— provide a foundation for this transition. Backed by ongoing IP licensing and a growing network of industrial and venture advisors, the company is actively de-risking the platform to replace conventional mixer-settler systems in the critical minerals market.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Mortality of older construction and craft workers employed at Department of Energy (DOE) nuclear sites: Follow‐up through 2021

Background To determine if construction and trades workers formerly employed at US Department of Energy (DOE) nuclear weapons sites are at significant risk for occupational diseases, we studied the mortality experience of participants in the Building Trades National Medical Screening Program (BTMed). Methods The cohort included 26,922 participants enrolled between 1998 and 2021 and 8367 deaths. Standardized mortality ratios were calculated based on US death rates. Cox models compared construction workers (n = 22,747; 7487 deaths) to two nonconstruction subpopulations: administrative, scientific and security workers (n = 1894; 330 deaths), and all other nonconstruction workers (n = 2218; 550 deaths). Results Mortality was elevated for all causes, all cancers, cancers of the trachea, bronchus, lung, kidneys, and lymphatic and hematopoietic system, mesothelioma, chronic obstructive pulmonary disease (COPD), asbestosis, transportation injuries, and other injuries, particularly accidental poisonings. There were 167 deaths from coronavirus disease 2019 (COVID-19), which was lower than expected using US death rates. Overall cause-specific mortality was significantly higher among construction workers than for internal comparison groups. Conclusions Construction workers employed at DOE sites have a significantly increased risk for occupational illnesses. Apart from COVID-19 deaths, this update: (1) found that mortality among construction workers is significantly elevated compared to the US population and significantly higher than in the internal comparison populations, and (2) confirmed excess risk for these workers for first employment after 1990. Cancer mortality risks are similar to the cancers identified for DOE compensation from radiation exposures. In conclusion, the high lung cancer risk supports the value of early lung cancer detection. Continued medical surveillance is important.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2023

29 th International Training Course on the Physical Protection of Nuclear Materials and Nuclear Facilities (Project Summary)

Sandia National Laboratories (Sandia) has hosted the International Training Course on the Physical Protection of Nuclear Materials and Nuclear Facilities since 1978. This course is the flagship training course of the International Atomic Energy Agency (IAEA). On behalf of the National Nuclear Security Administration (NNSA), Sandia manages, develops, and coordinates all course materials, and works closely with the IAEA to arrange all logistical details for the course ITC-29 incorporated some updates to the facility models, based on feedback received in ITC-28 and the ITC-29 dry run. In addition, all the graphics were refreshed after ITC-28 and implemented in the posters, data handbooks, etc. As in ITC-28, the ITC-29 staff worked closely with the IAEA on course materials, including a peer review process to ensure all course materials were aligned with Nuclear Security Series No. 13 and other relevant international guidance documentation from the IAEA. Due to the COVID-19 pandemic, ITC-29 was postponed twice and eventually took place in the late summer/early fall of 2022. Due to ongoing COVID-19 restrictions and safety requirements, the number of participants was reduced by about 31 percent from 59 participants in ITC-28 to 41 in ITC-29. As a result, the number of subgroups also decreased from eight in ITC-28 to six for ITC-29. This enabled the Sandia team to implement more opportunities for social distancing, particularly in the large classrooms. Despite the challenges, ITC-29 still passed a significant milestone, with the one-thousandth participant of the international training course attending during this event. Finally, the ITC staff continued the use of its improved method of evaluation to capture participants’ satisfaction with the updated course and to gather feedback concerning future improvements. This document provides a brief description of ITC-29, including a summary of lessons learned and key recommendations for future development efforts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2024

Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values

Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R 2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control.

COVID19↗

DOE OSTI2025

Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series

The COVID-19 pandemic has underscored the need for accurate epidemic forecasting to predict pathogen spread, evolution, and evaluate intervention strategies. Forecast reliability hinges on detailed knowledge of disease transmission across population segments, which may be inferred from contact surveys or mobility data. However, these indirect approaches make it difficult to estimate rare transmissions between socially or geographically distant communities. We show that the steep ramp-up of genome sequencing surveillance during the pandemic can be leveraged to directly identify transmission patterns between geographically defined communities. Our approach uses a hidden Markov model to infer the fraction of infections a community imports from others based on how rapidly allele frequencies in the focal community converge to those in the donor communities. Applying this method to SARS-CoV-2 sequencing data from England and the United States, we uncover networks of intercommunity transmission that reflect geographical relationships while exposing significant long-range interactions. The scaling of importation rate with distance is consistent across both countries, yet weaker than expected based on mobility data, highlighting limitations of indirect inference. We show that transmission patterns can change between waves of variants of concern and analyze how the inferred heterogeneity in intercommunity transmission impacts evolutionary forecasts. While applied here to geographically defined communities, our approach could be applied to those defined by other traits (e.g., age, socioeconomic status), provided time-series data can be stratified accordingly. Overall, our study highlights population genomic time series data as a crucial record of epidemiological interactions, which can be deciphered using tree-free inference methods.

Okada, Takashi [Department of Physics; University ↗

DOE OSTI2024

PRIME - A Software Toolkit for the Characterization of Partially Observed Epidemics in a Bayesian Framework

PRIME is a modeling framework designed for the “real-time’” characterization and forecasting of partially observed epidemics. Characterization is the estimation of infection spread parameters using daily counts of symptomatic patients. The method is designed to help guide medical resource allocation in the early epoch of the outbreak. The estimation problem is posed as one of Bayesian inference and solved using a Markov Chain Monte Carlo technique. The framework can accommodate multiple epidemic waves and can help identify different disease dynamics at the regional, state, and country levels. We include examples using publicly available COVID-19 data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Threat Agnostic Virulence Assessment of Pathogens

Virulence assessment of new, emerging, and engineered pathogens is critical to mounting an appropriate response to a biothreat agent. The capacity of the pathogen to colonize human and harm tissues must be characterized to understand pathogenicity pathways and optimize diagnosis and treatment of resulting disease. Respiratory pathogens are of interest because they can have high transmissibility rates, as observed with the SARS-CoV-2 virus, the causative agent of Covid-19. Current technologies are insufficient to assess threats due to their reliance on systems with only one cell type and on sequencing the pathogen. However, it is known that sequence is not an accurate predictor of function, and sequencing can be unreliable for newly emerged or engineered pathogens. An ideal system would consist of relevant epithelial cell types and an assay sensitive enough to detect changes in host responses that do not rely on DNA sequencing. We chose a system consisting of host lung epithelial cells that can be used to assess the virulence of unknown respiratory pathogens. We interrogated pathogens using this model and assess features of pathogenicity. Our objective is to leverage PNNLs strengths in tissue engineering and proteomics capabilities to build a multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) liquid chromatography-tandem mass spectrometry assay for human host cell proteins whose abundance is influenced by infection. These responses can were then assessed for relative virulence using pathogen agnostic signatures. When confronted with a pathogen, cells activate dedicated signaling pathways, typically through phosphorylation of regulatory proteins and downstream activation of host cell networks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

TDCOSMO - XVII. New time delays in 22 lensed quasars from optical monitoring with the ESO-VST 2.6m and MPG 2.2m telescopes

We present new time delays, the main ingredient of time delay cosmography, for 22 lensed quasars resulting from high-cadence r-band monitoring on the 2.6 m ESO VLT Survey Telescope and Max-Planck-Gesellschaft 2.2 m telescope. Each lensed quasar was typically monitored for one to four seasons, often shared between the two telescopes to mitigate the interruptions forced by the COVID-19 pandemic. The sample of targets consists of 19 quadruply and 3 doubly imaged quasars, which received a total of 1918 hours of on-sky time split into 21 581 wide-field frames, each 320 seconds long. In a given field, the 5-σ depth of the combined exposures typically reaches the 27th magnitude, while that of single visits is 24.5 mag – similar to the expected depth of the upcoming Vera-Rubin LSST. The fluxes of the different lensed images of the targets were reliably de-blended, providing not only light curves with photometric precision down to the photon noise limit, but also high-resolution models of the targets whose features and astrometry were systematically confirmed in Hubble Space Telescope imaging. This was made possible thanks to a new photometric pipeline, lightcurver, and the forward modelling method STARRED. Finally, the time delays between pairs of curves and their uncertainties were estimated, taking into account the degeneracy due to microlensing, and for the first time the full covariance matrices of the delay pairs are provided. Of note, this survey, with 13 square degrees, has applications beyond that of time delays, such as the study of the structure function of the multiple high-redshift quasars present in the footprint at a new high in terms of both depth and frequency. The reduced images will be available through the European Southern Observatory Science Portal.Key words: methods: data analysis / surveys / distance scale

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

A Data-Driven Approach to Real-World Degradation of Backsheets

The objectives of this project are as follows: • The population behavior of fielded modules in various conditions of use • Predictions of materials in specific climatic zones • Understanding of a module’s local environment in the field on its degradation It aims to understand how and what backsheet materials of photovoltaic modules degrade in the real world field. • Field Survey Protocol This project is started from the protocol, because all the data, information, domain knowledge are from experience of the real world field surveys, which is based on the protocol. The Protocol is explored from the experience of the field survey observations. With the increasing of the field surveys, it is refined for three versions, which are Task 1.0 (Section 3.1), Task 6.0 (Section 3.6), Task 10.0 (Section 3.10) respectively. It includes a document and a training video, which is able to direct other teams to follow the same procedure with the sites surveyed during this project. The documents include the detailed information but is not limited to the terminology definition, instruments SOP, preparation items for the surveys, form for the data collections, the order of the information collection. The final version of the protocol can be found at Appendix A, see Section 5. Additional, It can also be found at Open Science Framework (OSF), see Section 3.18 for detail. • Written Waiver Request Before staring the field surveys, the request of the waiver for international surveys is completed, because the limitation of climate zone in the United States, see Appendix B in Section 6 for the request documents. Unfortunately, only 1 international site from Taiwan, China can be finished, due to the COVID-19. • Field Survey According to the protocol we built in Section 3.1, 3.6 and 3.10, 41 sites have been surveyed across seven different climate zones (Cfa, Csa, Csb, BSk, Dfa, Dfb, Am). A variety of materials, including Polyethylene Naphthalate (PEN), Polyethylene Terephthalate (PET), Polyvinyl Fluoride (PVF), Polyvinylidene Fluoride (PVDF), Acrylic PVDF, Fluoroethylene Vinyl Ether (FEVE), and Glass, were identified. These sites are located in various states including California, South Carolina, New Mexico, Maryland, Ohio, Tennessee, Florida, Massachusetts, Illinois, Minnesota, Oregon, Colorado, and Taiwan, Republic of China. The ages of the sites ranged from 2 - 38 years in service and the field size varied from 1 MW - 25 MW. All requirements for the modeling have been satisfied. Some observations like ’Edge Effect’ for the rows and Junction box heating will also be a useful knowledge to build the model. Section 3.7 provides detailed information on the sites visited during this reporting period.

14 SOLAR ENERGY↗

DOE OSTI2023

Computational and Experimental Investigation of Thermal-Mechanical- Chemical Mechanisms of High-burnup Spent Nuclear Fuel (SNF) Processes at Elevated Temperatures and Degradation Behavior in Geologic Repositories

The overarching goal of the combined computational and experimental R&D activities proposed in this project is to enhance understanding of the mechanisms and thermal-mechanical-chemical (TMC) parameters controlling the instant release fraction (IRF) and matrix dissolution of high-burnup (HB; burnup) spent nuclear fuels (SNFs) and the subsequent formation, stability, and phase transformations of SNF alteration products under long-term storage and geological disposal conditions. Uranium dioxide may undergo oxidative corrosion/alteration, and the IRF may be increased for HB SNF, both of which may affect environmental systems associated with SNF long-term storage and disposal. The oxidative matrix dissolution may form various complex uranyl-based phases, including a rich variety of oxides, silicates, carbonates and other secondary minerals in varied geological environments (e.g., studtite, metastudtite, amorphous uranyl peroxide, uranium trioxide, triuranium octoxide, schoepite, dehydrated schoepite, metaschoepite, becquerelite, soddyite, rutherfordine,...). These uranyl phases generally have higher mobility UO 2 +2 species than less soluble U 4+ phases. However, limited information on the thermodynamic properties and formation kinetics of these uranyl-bearing phases is available to predict explicitly paragenesis under the conditions relevant to long-term storage or disposal. The proposed project draws on complementary expertise and research backgrounds from the team members: (i) to apply a combined ab initio modeling (UNLV/UTEP and SNL) and experimental (UNLV) strategy investigating the high-temperature TMC mechanisms of alteration of SNF under α-radiolysis conditions; (ii) to investigate the mechanistic of phase transformations in UNF degradation products under various conditions expected in long-term storage systems (e.g. (UO 2 )O 2 (H 2 O) 4 → (UO 2 )O 2 (H 2 O) 2 → U 2 O 7 → UO 3 → U 3 O 8 ); (iii) to determine high-accuracy TMC parameters for complex uranyl-based phases formed in storage or geological disposal environments (e.g. UO 3 (H 2 O) 2 , Ca[(UO 2 ) 6 O 4 (OH) 8 ] 8 H 2 O, (UO 2 ) 2 (SiO 4 ) 3 2H 2 O,…). The unforeseen COVID-19 pandemic led to the laboratory/campus closure since March 2020, that resulted in a significant delay in reaching milestones in a satisfactory manner, due to (i) the statewide recommendation from stop-working to later limited work in the lab and work-from-home (WFH), (ii) no in-person interactions, and (iii) a hiring freeze at UNLV. Therefore, a no cost extension (10/01/2021- 9/30/2022) was requested to help make up the time we lost during the global pandemic in 2020-2021, leading to paradigm shifts in the focus of the project in the following three main tasks: Task 1 (Computational), Task 2 (Experimental), and Task 3 (Final report, due on 12/29/2022).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Akiachak Energy Efficiency Retrofit Project

The goal of the project is to reduce the overall energy use of the Akiachak Native Community (ANC) by implementing energy efficiency measures in five high-use Tribal buildings. This project will have the following outcomes: Projected annual energy savings of $17,369; projected annual reduction in fuel oil #1 of 1,200 gallons and electricity of 17,751 kWh; annual reduction in carbon dioxide emissions of approximately 60,340 pounds/year. ANC will install energy efficiency measures in the Laundry, Tribal Indian Reorganization Act (IRA) Office, Clinic, Daycare, and Police Station. ANC obtained energy audits on these buildings in 2018, and this project will implement high-payback recommendations such as replacing lighting with LEDs, installing setback thermostats and occupancy sensors, replacing furnaces with more efficient models, replacing the circulation pumps with variable speed ones, air tightening, and adding insulation. Buildings will see energy cost reductions from 15% to 40%. These retrofits will help build ANC’s long-term vision for sustainable energy usage and address the first goal of the Tribal IRA Council’s Energy Efficiency and Conservation Strategy, to “create and maintain functionally appropriate, sustainable, accessible, high quality tribal infrastructure and facilities.” ANC intends to replicate this project by using the resulting energy savings to address audit recommendations in other buildings as well as to demonstrate the value of energy efficiency to community members. Other outcomes will include an increase in community resiliency, reduced dependence on outside shipments of fuel oil, training for maintenance staff, and no-touch control of building appliances to reduce transmission of diseases such as COVID-19.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Conference Report on the 7th International Symposium on Liquid metals Applications for fusion (ISLA-7)

Supported by the world magnetic fusion research community, a series of International Symposia on Liquid metals Applications for fusion (ISLA) have been held biannually since 2010. The 7th edition (ISLA-7) was held for the period from 12 December through 16 December 2022, at Chubu University located in Kasugai, Aichi, Japan. For the first time in the history of this series of symposia, ISLA-7 was held in a hybrid fashion, due to the COVID-19 situation. The total number of the participants was 60, 34 out of whom attended the symposium in person, and the rest participated online. As to the presentation statistics, 29 papers were presented in person, whereas 21 presentations were delivered online but real-time by the presenters in China, Spain, the UK, and the USA. Both of the presentations delivered in person and online were recorded, and the video has been shared by all participants. These participants represent 11 countries: China, Czech, Italy, Japan, Latvia, Netherlands, Russia, Thailand, the UK, and the USA. All these numbers are among the largest in this series of symposia. Covered by these presentations are; in session-2, program overviews and liquid metal research review; in session-3, liquid metal flows, and MHD issues; in session-4, liquid metal facilities; in sessions-5 and 6, liquid metal experiments and modeling; in session-7, divertor physics and heat flux mitigation; in session-8, plasma and liquid metals interactions; in session-9 liquid metal plasma-facing components, erosion, and wettability. In addition, there were an opening session whereby several opening addresses were delivered and also a closing session where all technical session summaries were presented by the respective session chairs.

divertor↗

DOE OSTI2023

Predicting SARS-CoV-2 Variant Using Non-Invasive Hand Odor Analysis: A Pilot Study

The adaptable nature of the SARS-CoV-2 virus has led to the emergence of multiple viral variants of concern. This research builds upon a previous demonstration of sampling human hand odor to distinguish SARS-CoV-2 infection status in order to incorporate considerations of the disease variants. This study demonstrates the ability of human odor expression to be implemented as a non-invasive medium for the differentiation of SARS-CoV-2 variants. Volatile organic compounds (VOCs) were extracted from SARS-CoV-2-positive samples using solid phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC–MS). Sparse partial least squares discriminant analysis (sPLS-DA) modeling revealed that supervised machine learning could be used to predict the variant identity of a sample using VOC expression alone. The class discrimination of Delta and Omicron BA.5 variant samples was performed with 95.2% (±0.4) accuracy. Omicron BA.2 and Omicron BA.5 variants were correctly classified with 78.5% (±0.8) accuracy. Lastly, Delta and Omicron BA.2 samples were assigned with 71.2% (±1.0) accuracy. This work builds upon the framework of non-invasive techniques producing diagnostics through the analysis of human odor expression, all in support of public health monitoring.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Real time monitoring of COVID-19 intervention effectiveness through contact tracing data

Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while infected. The first benefit–reducing susceptibility–has been established across multiple studies, while the second–reducing infectivity–is less well understood. Using a new statistical method, we estimate the efficacy of vaccines and facemasks at reducing both types of risks from contact tracing data collected in an urban setting. We find that vaccination reduced the risk of onward transmission by 40.7% [95% CI 25.8–53.2%] during the Delta wave and 31.0% [95% CI 19.4–40.9%] during the Omicron wave and that mask wearing reduced the risk of infection by 64.2% [95% CI 5.8–77.3%] during the Omicron wave. By harnessing commonly-collected contact tracing data, the approach can broadly provide timely and actionable estimates of intervention efficacy against a rapidly evolving pathogen.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

PRIMED for the Future: Purposing Raw Intake for Machine Learning-Enabled Detection

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

PRIMED for the Future: Purposing Raw Intake for Machine Learning-Enabled Detection (Final Report)

The COVID-19 pandemic demonstrated how a novel, elusive, and diffuse biological threat can engender uncertainty and misinformation, and it underscored the need for flexible analytical modalities agnostic to the identity of biological material. Yet even before the pandemic, recognition of the limitations of the current, list-based approach, which focuses on known pathogens and biotoxins, and of the importance of agent-agnostic biodetection was growing within the biosecurity community. In a 2018 report on “Biodefense in the Age of Synthetic Biology,” for example, the National Academy of Sciences stated that “an overreliance on the Select Agent List is a systematic weakness affecting many aspects of the United States’ current biodefense mitigation capability”. More recently, a group of biodefense researchers proposed the identification and adoption of “bioagent-agnostic signatures (BASs)” as a way of detecting and characterizing not only existing agents but also novel ones, an approach they believe will “enable a more flexible and resilient biodefense posture”. Indeed, the future of biodetection requires us to begin developing novel analytics that can identify anomalies and/or characteristics that indicate a potential threat, whether known or unknown, without looking for a specific signature that has been identified previously. To assess potential threats more rapidly, it is critical to develop agnostic artificial intelligence (AI)/machine learning (ML) systems that can be employed for real-time assessment of the nature and source of a perturbation. Such systems should be multi scale and multi-dimensional, integrating sensor data from a range of biological, chemical, and physical application spaces. Emerging deep learning (DL) models demonstrate exceptional promise for identification of discriminatory features within multi-dimensional datasets. DL models have the capacity to recognize and encode highly complex patterns in a wide range of input data modalities, including images, text, and biological/chemical/physical spectra. As such, they can execute a wide range of assessments and determinations that have traditionally required a human operator. The promise of advances in DL is apparent in the realm of human health and medicine. DL models have been validated for evaluating a variety of clinical threats to human health in a range of contexts, including infection and cancer, and they demonstrated improved performance in predicting stroke relative to human neurologists in some categories of data. Continuously evolving advances in AI/ML are expected to support more efficient evaluation of raw sequence, spectroscopy, and spectrometry data. For instance, recent advances and deployment of large language models (LLM) such as Generative Pre training Transformer (GPT) and Bidirectional Encoder Representations from Transformers (BERT) have already motivated application of these models for biological function prediction. As frameworks such as LLMs become larger and more complex in their representations, their capacity to serve as pre-trained models that can be fine-tuned for biological/biodetection purposes will similarly be amplified. While existing and emerging AI/ML have found broad applicability and use cases in the clinical sciences, development for environmental evaluation and biodetection has been limited. Functionalizing such capabilities for this purpose requires an understanding of the existing technical landscape and how the respective tools and algorithms are currently being employed. This landscape awareness then allows an assessment of the current practical capabilities of existing models and the anticipated requirements and development efforts that will be needed to adapt available algorithms for biodetection applications relevant to DHS. Leveraging expertise in biodetection, ML, and operational biodetection, the effort described in this report is comprised of a systematic landscape assessment (Subtask 2.1), comparative evaluation (Subtask 2.2), and formulation of a value proposition (Subtask 2.3) for the prospect of ML-enabled, agnostic biodetection from raw, or minimally-processed, datasets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The new ITER baseline, research plan and open R&D issues

A new baseline (NB) has been proposed by the ITER Project to ensure a robust achievement of the Projects’ goals, in view of past challenges including delays incurred due to the Covid-19 pandemic, technical challenges in completing first-of-a-kind components and in nuclear licensing. The NB includes modifications to the configuration of the ITER device and its ancillaries (e.g. change from beryllium to tungsten as first wall material, modification of the heating and current drive mix, etc.) as well as additional testing of components (e.g. toroidal field coils) or phased installation (start with inertially cooled first wall before later installation of the final actively water-cooled components) to minimise operational risks. In the NB, the ITER research plan (IRP) will be divided into three main phases: (a) start of research operation, with 40 MW of ECH and 10 MW of ICH, which will focus on the demonstration of 15 MA operation in L-mode, commissioning of all required systems, including disruption mitigation, and the demonstration of H-mode plasma operation in deuterium; (b) DT-1, with 60–67 MW of ECH, 33 MW of neutral beam injection (NBI) and 10–20 MW of ICH, which will demonstrate robust operation in high confinement H-mode plasmas in DT up to Q ⩾ 10 and for burn durations of 300–500 s within an accumulated neutron fluence of ∼1% of the ITER machine’s lifetime total, and; (c) DT-2, with up to 67 MW of ECH, up to 49.5 MW of NBI and up to 20 MW of ICH, with the ITER tokamak and ancillaries in their final configuration to demonstrate routine operation in DT plasmas at high Q and the Q ⩾ 5 long-pulse and steady-state scenarios to the final neutron fluence and to perform R&D on nuclear fusion reactor issues. The logic, physics basis, modelling and experimental evaluations carried out to support the NB and the associated IRP are described. These include the impact of the tungsten wall on plasma scenarios and associated risk mitigation measures, as well as the optimisation of the tokamak components and ancillaries to minimise Project risks. Open R&D issues related to these evaluations and mitigation measures are also described together with experimental, modelling and validation activities required to address them.

ITER↗