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At least 235 records · Page 13

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DOE OSTI2025

The decay of HIV under anti-retroviral therapy is biphasic even in humanized mice with just T cells

HIV-1 plasma viral load decays in a biphasic manner during antiretroviral therapy (ART). It was hypothesized that this is due to infection of different cell types, namely CD4+ T cells and macrophages. We studied this possibility directly by modeling the decay of HIV-1 in humanized mice. We utilized previously published data from humanized T-cell only mice (TOM) and myeloid-only mice (MOM) infected with HIV-1 and treated with a potent ART regimen. Viral load decay dynamics were modeled using either a single or a biexponential decay fitted using nonlinear mixed effects techniques. Fits were compared using the corrected Bayesian information criterion (BICc). In TOM, the biphasic model was significantly better than a single-phase decay model (ΔBICc ≈ 16) despite additional parameters. In MOM, the biphasic decay was statistically better, but there was substantial uncertainty because the virus goes below detection very fast. The first-phase half-life was consistent between groups (1.2 days in MOM and 1.3 days in TOM) and similar to the half-life estimated in human infection. The second-phase decay in these mice was minimal likely due to low initial viral loads. Additional analyses with mice containing both CD4+ T cells and macrophages or X4-tropic virus-infected MOM mice confirmed the biphasic pattern, demonstrating the robustness of this result. The biphasic decline in HIV-1 occurs, even with only CD4+ T cells, refuting the hypothesis that distinct cell populations (CD4+ T cells and macrophages) drive each decay phase. These findings support an alternative model in which the observed dynamics arise from intrinsic properties of the viral infection lifecycle rather than from cellular compartmentalization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Structural basis for varying drug resistance of SARS-CoV-2 M pro E166 variants

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) has an essential role in the virus lifecycle and, accordingly, it is a target for antiviral drugs. Multiple studies have identified an M pro mutation (E166V) that confers strong resistance to clinically relevant inhibitors, including nirmatrelvir, but the underlying mechanism is not fully understood. Here, we report on crystal structures of SARS-CoV-2 M pro E166V in complex with nirmatrelvir, ensitrelvir, and bofutrelvir. The structures suggest that resistance is caused in part by the loss of a direct hydrogen bond and also, especially for nirmatrelvir, by a steric clash with the substituted valine residue. In comparison, the binding of bofutrelvir shows greater flexibility, which may help alleviate this steric effect and allow bofutrelvir to fit the mutant active site despite the loss of a direct polar contact. Thermal stability analyses also corroborate E166V most severely affecting the binding of nirmatrelvir and, to lesser and different extents, ensitrelvir and bofutrelvir. We further show that E166I causes even more severe nirmatrelvir resistance, whereas E166A and E166L have much milder effects. These studies shed light on the molecular mechanisms of a key M pro drug resistance mutation and may help inform the design of next-generation inhibitors. IMPORTANCE Using a combination of high-resolution X-ray crystallographic and biochemical analyses, we reveal the molecular mechanisms by which a mutation in the severe acute respiratory syndrome coronavirus 2 main protease (M pro ) confers strong resistance against clinically relevant antiviral drugs that inhibit M pro activity. The results presented here may help inform the design of next-generation inhibitors to combat the problem of therapy resistance.

Microbiology↗

DOE OSTI2025

Secure API-Driven Research Automation to Accelerate Scientific Discovery

The Secure Scientific Service Mesh (S3M) provides API-driven infrastructure to accelerate scientific discovery through automated research workflows. By integrating near real-time streaming capabilities, intelligent workflow orchestration, and fine-grained authorization within a service mesh architecture, S3M enables secure and flexible programmatic access to high performance computing (HPC) resources. This framework allows intelligent agents and experimental facilities to dynamically provision resources and execute complex workflows, accelerating experimental lifecycles, and enabling AI-augmented autonomous science. S3M establishes a modern foundation for scientific computing infrastructure that significantly reduces traditional barriers between researchers, computational resources, and experimental facilities.

Skluzacek, Tyler [ORNL] (ORCID:0000000322424931)↗

DOE OSTI2025

A Digital Twin of Scalable Quantum Clouds

Quantum computing has emerged as a transformative technology capable of solving complex problems beyond the limit of classical systems. The rapid development of quantum processors has led to the proliferation of cloud-based quantum computing services offered by platforms such as IBM, Google, and Amazon. These platforms introduce unique challenges in resource allocation, job scheduling, and multi-device orchestration as quantum workloads become increasingly complex. In this work, we present a digital twin of quantum cloud infrastructures: a framework designed to model and simulate the behavior of real quantum cloud systems. Developed in Python using the SimPy discrete-event simulation library, the framework replicates key aspects of quantum cloud environments, including detailed quantum device modeling, job lifecycle management, and job fidelity. It incorporates noise-aware fidelity estimation, making it the first of its kind to simulate superconducting gate-based quantum cloud systems at an administrative level with job fidelity. We present use cases as proof of concept, demonstrating that our quantum cloud simulation framework can act as a digital twin of a quantum cloud and support the modeling and implementation of practical systems.

Luo, Waylon [Kent State University]↗

DOE OSTI2021

NRIC Digital Engineering Ecosystem

The NRIC Digital Engineering Ecosystem is a software suite designed to eliminate procedural failures in the engineering lifecycle of complex projects. It focuses on improving the flow of scheduling data, safety information, engineering requirements, and CAD files among stakeholders of complex engineering projects. The project comprises software adapters that move engineering data from disparate software tools in and out of a central database. The ecosystem is designed to efficiently incorporate data sources from many different engineering toolsets, making it software agnostic, and adaptable to many different engineering applications.

Harris, BrennanK↗

DOE OSTI2023

pnnl/datalife

data flow lifecycle analysis

Lee, Hyungro↗

DOE OSTI2024

A Data Processing Pipeline To Extract A Knowledge Graph From Sec Documents For Socio-technical Analysis Of Critical Infrastructure Influence

Weaver, GabrielA.↗

DOE OSTI2024

Hydrogen Hub Systems Analysis and Mapping Tool (ParaCraft) v1

A plug and play techno-economic analysis (TEA) and lifecycle assessment (LCA) tool was built that could incorporate new projects into the California ARCHES LLC Hydrogen hub, and generate results for the project, as well as the overall hub on an annual basis. The model was first constructed in Microsoft Excel and ArcGIS, but required labor intensive updating and manual decision making regarding the matching of hydrogen supplier and offtaker and estimation of transportation distances and utility sources. The project team converted the Excel model used for the ARCHES LLC hub conceptualization into a highly flexible and nearly completely automated R code. The R code runs the TEA and LCA, as well as provides mapping capabilities that automatically link projects by latitude and longitude to nearby utilities.

Breunig, Hanna↗

DOE OSTI2026

IPC-Fusion (Infrastructure Perception and Control (IPC): Multisensor Data Fusion Software) [SWR-25-153]

As part of the National Laboratory of the Rockies' (NLR’s) Infrastructure Perception and Control Laboratory, the IPC-Fusion toolkit provides a probabilistic, scalable, multi-sensor fusion framework that integrates (late-stage fusion) heterogeneous object detection data from traffic sensors to enable robust, real-time tracking of roadway occupants. The algorithmic design of the toolkit is motivated by the need for creating a digital twin of traffic at the edge in a scalable and affordable manner. The software operates by combining object-level measurements (such as position and velocity) from a suite of sensors (such as radar, lidar, camera) using Kalman filtering and probabilistic data association techniques to overcome individual sensor limitations and achieve superior tracking performance in complex traffic zones. The framework addresses key challenges including heterogeneous measurement uncertainties, asynchronous data streams, varying spatiotemporal data resolutions, robust data association, and adaptive object lifecycle management. Validated on real-world traffic intersection data including vehicles and pedestrians, IPC-Fusion demonstrates enhanced tracking reliability across scenarios involving occlusions, sensor failures, and varying traffic densities, supporting the broader IPC initiative's goal of transforming transportation infrastructure through advanced perception capabilities for intelligent transportation systems, traffic safety applications, and autonomous vehicle support.

Sandhu, Rimple [National Laboratory of the Rockies↗

DOE OSTI2025

CEC Quest: Long Duration Energy Storage Impact Analysis Tool

SAND2025-14389O CEC Quest is a Python tool with a user interface designed to analyze the greenhouse gas impacts of long-duration energy storage projects in California. The tool automates data collection from public sources and uses an Application Programming Interface (API) to enable users to download photovoltaic resource availability, marginal operating emissions rate, and utility rate data. It guides users in inputting parameters for a battery energy storage model and uploading site electrical load data, while also prompting for relevant analysis parameters like timestep and grid limits. CEC Quest performs monthly optimization of one year of data to assess impacts on the site’s electrical bill and the grid’s greenhouse gas emissions. Finally, it conducts a lifecycle analysis to evaluate changes over a defined quantification period, with results aggregated through automated report generation. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Rosewater, David [Sandia National Lab. (SNL-CA), L↗

DOE OSTI2025

ACTIVE

The Automated Control Testbed for Integration, Verification, and Emulation (ACTIVE) framework is a software platform designed to support the optimized operation and management of a wide range of building types. It enables the development, testing, and validation of diverse control strategies, including AI-based, rule-based, and model-based approaches. The platform facilitates a seamless transition from simulation-based evaluation of control strategies to real-world field validation and deployment. ACTIVE supports the full building management lifecycle, encompassing data acquisition and management, system monitoring, optimized control, adaptive learning services, device dispatch and coordination, as well as advanced analytics and visualization. Together, these capabilities provide an integrated environment for improving building performance, operational efficiency, reducing energy cost, and reliability.

Smith, Robert [Oak Ridge National Laboratory (ORNL↗

DOE OSTI2025

A Data Processing Pipeline To Extract A Knowledge Graph From Heterogeneous Data For Socio-technical Analysis Of Critical Infrastructure Influence

The code is written in Python and consists of the following pipeline that is implemented in Apache Airflow. This pipeline intends to understand the companies that are directly or indirectly involved with a type of critical infrastructure system at some point in that system's lifecycle. The pipeline takes a configuration file that specifies a list of initial companies to consider, a geographic region of interest, and a set of SEC form types as well as other data sources (e.g. CrunchBase) from which to extract entities and relations. There are four main components to this pipeline as currently implemented: Entity Extraction, Network Construction, Analysis, and Visualization. First, Entity Extraction, is implemented as the `topear-extract_organizations` Apache Airflow workflow. Given an initial query that specifies a geographic region of interest and a time interval, the software will extract CI facilities of interest and organizations that have a direct influence relationship to those facilities (e.g. ownership). During the course of the LDRD, we focused on Electric Vehicle charging stations and this information is available via the Department of Energy (DOE) database on fueling stations maintained by NREL. Within the context of the DOE CESER project, we have focused on Battery Energy Storage Systems (BESS). Second, the Network Extraction component will iteratively construct a social network graph given the set of organizations and people extracted in the previous step. Organizations (and eventually People if desired) are then fed as a query to the `topgear-construct_social_network` Apache Airflow workflow which given a set of initial companies and data sets (e.g. SEC EDGAR form types, OpenCorporates, Crunchbase). This Airflow workflow will iteratively query such data sources to discover relationships with new organizations and people. For example, this module can iteratively query SEC EDGAR for metadata that documents the number of each type of form for the given set of companies and their location. This forms metadata represents a catalog of data sources from SEC EDGAR for the extracted social network knowledge graph. The pipeline then downloads these forms from the website and saves them in a build directory for further processing. These documents are then parsed for entities and relations. Again, we note that in additional to SEC data sources, this step can also pull in information on organizations via API services such as CrunchBase and OpenCorporates or bulk data sources. At the end of this step, the resultant social network, the Critical Infrastructure network, and the edges that encode relationships between organizations and CI facilities, form the Adversarial Socio-Technical Network (ASTN) that informs the analysis. Third, the Analysis component processes these generated ASTN. Previously, that has included the ability to compare prevalence of different vendors for a given infrastructure component type across different regions as well as identify common public and private investors across those vendors. This was demonstrated for EV Charging Stations across several different metropolitan areas within an IEEE PES GridEdge publication. More recently, we have looked at ways to identify infrastructure owners and operators of BESS with the most nameplate capacity across different states as well as other indictors of risk resulting from changes in ownership over time. Finally, the Visualization component consists of an HTML/CSS/JS framework by which users can interact geospatial, operational, and organizational relationships across a given portfolio of Critical Infrastructure facilities. The objective is to provide a library of UI/UX modules that can be repurposed for stakeholder-specific dashboards. All of the modules are related via a common event model that enables UI actions in one view to percolate across the other views.

Weaver, Gabriel [Idaho National Laboratory (INL), ↗

DOE OSTI2026

JGI Archive and Metadata Organizer (JAMO) v2.0.0

JAMO (JGI Archive and Metadata Organizer) helps researchers keep large collections of scientific files organized, findable, and safe. It lets you submit files with consistent, template-driven metadata, bundle related files into sets, and track them as a group instead of one by one. As data ages, JAMO automatically moves it from fast disk to cost-saving tape and can bring it back when needed, keeping storage lean without losing access. A simple web/CLI workflow supports submitting, checking status, retrying, and updating metadata. Compared with generic storage, JAMO's strengths are: clear, searchable metadata tuned for science; set-level organization that mirrors real projects; and built-in lifecycle care (archive, purge, restore) so you don't have to manage those steps yourself.

Cassol, Daniela [Lawrence Berkeley National Labora↗

DOE OSTI2026

A Reverse Logistics Tool For Ev Battery Recycling And Repurposing,

The demand for electric vehicles (EVs) in the United States is projected to rise significantly, with sales expected to reach approximately 4.1 million units by 2030. However, the U.S. remains heavily reliant on imports for the batteries and critical raw materials—such as lithium, cobalt, and nickel—that power these vehicles. As of 2024, around 70% of these imports originate from China. This dependency has become even more precarious following China’s imposition of export restrictions in April 2025, a retaliatory move against U.S. tariffs. These developments highlight the strategic vulnerabilities posed by China’s dominant position in the critical materials market. Compounding the issue, decades of intensive extraction have severely depleted global reserves of critical materials, widening the gap between supply and growing demand. This situation underscores the urgent need for the U.S. and other nations to diversify their sources of critical materials and enhance domestic capabilities to secure these resources—an essential step toward ensuring long-term energy security. At the end of their lifecycle—whether due to the battery’s degradation or the retirement of the vehicle—EV batteries are often improperly disposed of or sent to landfills. However, many of these batteries still retain usable capacity and can follow one of three alternative pathways: (a) Re-used: deployed in another vehicle with a shorter driving range, (b) Re-purposed: utilized act as a backup storage/power for data centers, solar panels, and e-scotters or (c) Recycled: broken down to recover the critical materials. To that end, the proposed tool (REBORN) is designed to optimize the reverse logistics network for battery repurposing and recycling. Its goal is to minimize associated costs while identifying optimal locations for battery collection and processing. Ultimately, REBORN ensures that each battery is used to its fullest potential.

Srinivas, SrikarV. [Idaho National Laboratory (INL↗

DOE OSTI2026

BLEECAM™ (Benchmarking Life Cycle Environmental, Economic, and Social Metrics for Critical and Advanced Minerals and Materials) [SWR-25-125]

The National Laboratory of the Rockies' (NLR) Benchmarking Life Cycle Environmental, Economic, and Social Metrics for Critical and Advanced Minerals and Materials (BLEECAM™) is an open-source, integrated decision-support tool for evaluating the impacts, risks, and trade-offs across U.S. and global materials supply chains. Funded by the U.S. Department of Energy, BLEECAM supports supply chain and market analysis. The tool integrates multi-objective supply chain optimization, system dynamics, network design, lifecycle assessment, techno-economic modeling, and social impact assessment methods to evaluate how supply chains evolve over time, geography, and deployment scenarios. BLEECAM also supports analysis related to energy infrastructure, data centers and digital infrastructure, advanced manufacturing, and other sectors that depend on critical materials.

Khalifa, SherifA. [National Laboratory of the Rock↗

DOE OSTI2022

A Succession of Cloud, Precipitation, Aerosol and Air Quality Field Experiments in the Coastal Urban Environment

The interactions and feedbacks among clouds, aerosols, pollutants, and the thermodynamic and kinematic environment remains an area of active research with important implications for our understanding of climate, weather and air quality. These linkages are further complicated in coastal and urban environments where local circulations and anthropogenic influences impact each of these components and their interactions. Within this context, fundamental questions regarding the lifecycle of convective clouds, aerosols and pollutants have brought together a diverse, integrated, and interagency collaboration of scientists to collect and analyze measurements, in the Houston, Texas, area, from the summer of 2021 through the summer of 2022, with subsequent modeling studies to address these important research objectives. Herein, the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Facility and Atmospheric System Research (ASR) Program, the National Science Foundation’s (NSF) Physical and Dynamic Meteorology Program, the National Aeronautic and Space Administration’s (NASA’s) Tropospheric Composition Research and Health and Air Quality Applied Sciences Programs and the Texas Commission on Environmental Quality (TCEQ) are collaborating on a joint set of field campaigns to study the interactions of cloud, aerosol, and pollutants within the coastal, urban environment. In the Houston area, onshore flow from the Gulf of Mexico and the associated sea breeze circulation generates numerous isolated convective cells, particularly in the summer months, that interact with a variety of urban and industrial emissions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Studying Aerosol, Clouds, and Air Quality in the Coastal Urban Environment of Southeastern Texas

A multi-agency succession of field campaigns was conducted in southeastern Texas during July 2021 through October 2022 to study the complex interactions of aerosols, clouds and air pollution in the coastal urban environment. As part of the Tracking Aerosol Convection interactions Experiment (TRACER), the TRACER- Air Quality (TAQ) campaign the Experiment of Sea Breeze Convection, Aerosols, Precipitation and Environment (ESCAPE) and the Convective Cloud Urban Boundary Layer Experiment (CUBE), a combination of ground-based supersites and mobile laboratories, shipborne measurements and aircraft-based instrumentation were deployed. These diverse platforms collected high-resolution data to characterize the aerosol microphysics and chemistry, cloud and precipitation micro- and macro-physical properties, environmental thermodynamics and air quality-relevant constituents that are being used in follow-on analysis and modeling activities. We present the overall deployment setups, a summary of the campaign conditions and a sampling of early research results related to: (a) aerosol precursors in the urban environment, (b) influences of local meteorology on air pollution, (c) detailed observations of the sea breeze circulation, (d) retrieved supersaturation in convective updrafts, (e) characterizing the convective updraft lifecycle, (f) variability in lightning characteristics of convective storms and (g) urban influences on surface energy fluxes. The work concludes with discussion of future research activities highlighted by the TRACER model-intercomparison project to explore the representation of aerosol-convective interactions in high-resolution simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Clarifying remotely-retrieved precipitation of shallow marine clouds from the NSF/NCAR Gulfstream V

Precipitation is a key process within the shallow cloud lifecycle. The Cloud System Evolution in the Trades (CSET) campaign included the first deployment of a 94 GHz Doppler radar and 532 nm lidar. Despite a larger sampling volume, initial mean radar/lidar retrieved rain rates (Schwartz et al. 2019) based on the upward-pointing remote sensor datasets are systematically less than those measured by in-situ precipitation probes in the cumulus regime. Subsequent retrieval improvements produce rainrates that compare better to in-situ values, but still underestimate. Retrieved shallow cumulus drop sizes can remain too small and too few, with an overestimated shape parameter narrowing the raindrop size distribution too much. Three potential causes for the discrepancy are explored: the gamma functional fit to the dropsize distribution, attenuation by rain and cloud water, and an underaccounting of Mie dampening of the reflectivity. A truncated exponential fit may represent the dropsizes below a showering cumulus cloud more realistically, although further work would be needed to fully evaluate the impact of a different dropsize representation upon the retrieval. The rain attenuation is within the measurement uncertainty of the radar. Mie dampening of the reflectivity is shown to be significant, in contrast to previous stratocumulus campaigns with lighter rain rates, and may be difficult to constrain well with the remote measurements. An alternative approach combines an a priori determination of the dropsize distribution width based on the in-situ data with the mean radar Doppler velocity and reflectivity. This can produce realistic retrievals, although a more comprehensive assessment is needed to better characterize the retrieval errors.

54 ENVIRONMENTAL SCIENCES↗