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This branch extends the wa-hls4ml (FERMILAB-CODE-2026-09-CSAID) work to ASIC technology nodes (Nangate 45 nm and GlobalFoundries 22FDX FD-SOI) using Siemens Catapult HLS. Code is available at: https://github.com/fastmachinelearning/wa-hls4ml-paper/tree/Catapult-ASIC-dev
This study explores the added value (AV) of a regional Earth system model (ESM) compared to an atmosphere-only regional climate model (RCM) in simulating West African monsoon (WAM) rainfall. The primary goals are to foster discussions on the suitability of coupled RCMs for WAM projections and deepen our understanding of ocean–atmosphere coupling’s influence on the WAM system. The study employs results from dynamical downscaling of the ERA-Interim reanalysis and Max Plank Institute ESM, low resolution (MPI-ESM-LR), by two RCMs, atmosphere only (REMO) and REMO coupled with Max Planck Institute Ocean Model (MPIOM) (ROM), at ~25-km horizontal resolution. Results show that in regions distant from coupling domain boundaries such as West Africa (WA), constraint conditions from ERA-Interim are more beneficial than coupling effects. REMO, reliant on oceanic sea surface temperatures (SSTs) from observations and influenced by ERA-Interim, is biased under coupling conditions, although coupling offers potential advantages in representing heat and mass fluxes. Contrastingly, as intended, coupling improves SSTs and monsoon fluxes’ relationships under ESM-forced conditions. In this latter case, the coupling features a dipole-like spatial structure of AV, improving precipitation over the Guinea Coast but degrading precipitation over half of the Sahel. Our extensive examination of physical processes and mechanisms underpinning the WAM system supports the plausibility of AV. Additionally, we found that the monsoonal dynamics over the ocean respond to convective activity, with the Sahara–Sahel surface temperature gradient serving as the maintenance mechanism. While further efforts are needed to enhance the coupled RCM, we advocate for its use in the context of WAM rainfall forecasts and projections.
Most steelhead trout hatcheries increase growth rate during rearing to produce and release yearling smolts for harvest augmentation, but natural steelhead exhibit variable age of smoltification, so this common rearing practice may not be ideal for programs focused on recovering imperiled wild stocks; therefore, it is important to investigate and compare alternative hatchery rearing methods that promote life history diversity. Over six consecutive years, the Winthrop National Fish Hatchery on the Methow River, WA reared and released paired groups of age-1 (S1) and age-2 (S2) steelhead smolts. To understand how the two rearing methods affected developmental ontogeny and life-history, fish were sampled prior to hatchery release for factors associated with smoltification (size, gill Na+/K+ ATPase activity, and a qualitative smolt phenotype) and sexual maturation (sex, pituitary and testis mRNA transcripts, gonadosomatic index, and plasma 11-ketotestosterone). Our objectives were to quantify levels of smoltification and male maturation during hatchery rearing, combine metrics to estimate residualism (failure to migrate upon release), and compare the treatments by sex. Overall, S2 rearing produced 7.8% more smolts and 44-fold (4.4 vs. 0.1%) more precociously mature males than S1 rearing. Conversely, S1 rearing produced 31.6% more residuals than S2 rearing. While the proportion of total male residuals was comparable between treatments, the S1 treatment produced approximately five-fold more female residuals (20.6 vs. 4.2%). Because residuals contribute minimally to adult returns and the number of returning adult females is critical to the success of salmonid supplementation efforts, developing rearing techniques that maximize migration in females is a management priority. Physiological assessments are useful for characterizing and quantifying the effects and risks of different hatchery rearing regimes on steelhead life-history, in addition to providing sex-specific guidance to inform and optimize conservation management goals in supplementation programs.
This dataset includes processed data from the Lab Homes (LH) Test Facility located on the PNNL campus in Richland, WA. This a set of 2 identical homes that allow for the side-by-side comparison/performance evaluation of different technologies under the same weather at any given time. The dataset spans December 6, 2021 to December 27, 2021 and represents a series of tests performed; calibration, set-point excitation, pre-heating, free-floating and warm up. The measurements correspond to whole building electrical power, HVAC energy use, water heating, appliances and lighting, as well as space temperatures, space humidity, window glass surface temperatures, through glass solar radiation, and meterological data from an onsite meteorological weather station. In addition to the measurements, a metadata .json file, a .ttl file to visualize the data as per BRICK schema, and a detailed .pdf description of the dataset are also provided.
This technical assistance is part of the Communities Local Energy Action Program (CLEAP) for the community of Beacon Hill, Seattle, WA. This analysis focuses on opportunities to reduce energy burden, energy consumption, and energy bills for both single family homes and large multifamily buildings. It uses state-level data from the ResStock modelling tool that was filtered to be relevant to Beacon Hill. Hence, this content includes single family detached homes and large multifamily buildings in the income group of 0-80% AMI, and climate zone 4c (mixed temperatures, relatively cooler summers) within Washington State.
The “Development of the Hanford Grout Modeling Framework” project as part of the Network of National Laboratories for Environmental Management and Stewardship (NNLEMS) funding program is underway. An initial project team workshop was held in Richland, WA on June 4 and 5, 2024 with participants from PNNL, SRNL, SNL, WRPS and CRESP (VU and UCF). The workshop covered an overview of the current state of the art in grout modeling tools provided by the team. Based on a focus on liquid waste immobilization grout and encapsulation grout for solid wastes and tank closure grout at Hanford, the team identified preliminary conceptual models for these three applications which will be used to form the basis of the Hanford Grout Modeling Framework. The key processes that can drive mechanisms impacting the grout performance were identified for each test case. The programmatic plan was also identified with five core Themes being selected that will form the focus of the project. Within each theme, individual tasks for Year 1 were planned in support of the development of an updated Hanford Grout Modeling Framework. This report presents a summary of the information presented during the workshop.
Wildfires significantly impact human health, air quality, visibility, weather, and climate change and cause substantial economic losses. While state and county-operated air quality monitors provide critical insights during wildfires, they are not available in all regions. This highlights the need for affordable, accessible tools that allow the general public to assess air quality impacts. In this study, we apply machine learning with deep neural networks to diagnose air quality rapidly from sky images taken at the Pacific Northwest National Laboratory in Richland, WA, USA. Using a convolutional neural network (CNN) framework, we trained a deep learning model to classify air quality indices based on sky images. By leveraging transfer learning, our approach fine-tunes a pre-trained model on a small dataset of sky images, significantly reducing training time while maintaining high accuracy. Our results demonstrate the potential of deep learning to provide rapid air quality diagnostics during wildfire episodes, offering early warnings to the public and enabling timely mitigation strategies, particularly for vulnerable populations. Additionally, we show that lower respiratory infections pose the highest health risk during acute smoke exposures. Reactive oxygen species (ROS) from wildfire particles further exacerbate health risks by triggering inflammation and other adverse effects.
Type Ia supernovae (SNe Ia) were instrumental in establishing the acceleration of the Universe’s expansion. By virtue of their combination of distance reach, precision, and prevalence, they continue to provide key cosmological constraints, complementing other cosmological probes. Individual SN surveys cover only over about a factor of 2 in redshift, so compilations of multiple SN data sets are strongly beneficial. We assemble an up-to-date “Union” compilation of 2087 cosmologically useful SNe Ia from 24 data sets (“Union3”). We take care to put all SNe on the same distance scale and update the light-curve fitting with SALT3 to use the full rest-frame optical. Over the next few years, the number of cosmologically useful SNe Ia will increase by more than a factor of 10, and keeping systematic uncertainties subdominant will be more challenging than ever. We discuss the importance of treating outliers, selection effects, light-curve shape/color populations/standardization relations, unexplained dispersion, and heterogeneous observations simultaneously. We present an updated Bayesian framework, called UNITY1.5 (Unified Nonlinear Inference for Type-Ia cosmologY), that incorporates significant improvements in our ability to model selection effects, standardization, and systematic uncertainties compared to earlier analyses. As an analysis byproduct, we also recover the posterior of the SN-only peculiar-velocity field, although we do not interpret it in this work. We compute updated cosmological constraints with Union3 and UNITY1.5, finding weak 1.7σ–2.6σ tension with flat cold dark matter and possible evidence for thawing dark energy (w0 > − 1, wa < 0). We release our SN distances, light-curve fits, and UNITY1.5 framework to the community.
Recent advancements in use of machine learning (ML) techniques on field-programmable gate arrays (FPGAs) have allowed for the implementation of embedded neural networks with extremely low latency. This is invaluable for particle detectors at the Large Hadron Collider, where latency and used area are strictly bounded. The hls4ml framework is a procedure that converts trained ML model software to a synthesis result to can be used on an FPGA. However, running the pipeline is a time-consuming procedure, and there is a strong risk of failure. In particular, it may not be possible to successfully convert a model into a synthesis result, or the resource consumption of the model may exceed the resources of the target FPGA. To aid with this development, we introduce wa-hls4ml, a surrogate model using a graph neural network to emulate the structure of the source models. The goal is to estimate the chance of success and resource consumption of a given model when passed through the hls4ml pipeline, without needing to run the pipeline.
The Mu2e experiment requires a production target that is capable of operating under extreme thermal conditions caused by an 8 GeV proton beam. This project’s objective supports the development of the Mu2e Pro- duction Target by testing the Stickman model’s thermal behavior. Angel Flores Luviano has assisted Jonathan Williams in progressing this project by contributing to the development of a Radiative Cooling Test Fixture (RCTF) that will be used to evaluate the thermal behavior of the new production target model. Engineering calculations were performed to an- alyze thermal performance and pressure drop within the cold well and wa- ter cooling circuit. These calculations also determined the optimal sizing for key components of the water system. An engineering note was made to document these calculations. CAD models of the water circuit piping, thermocouple mounting bars, and radiator chimney were developed, and prototype test rig components were fabricated using 3D printing. Future work will focus on continued RCTF development which includes control system integration, heater hardware design, and interfaces that can be scaled up to increase thermal capacity.
Zap Energy is developing the sheared-flow-stabilized (SFS) Z-pinch concept for commercial applications. The SFS Z pinch relies on plasma self-organization, in the sense that plasma dynamics play a critical role in confinement. Using plasma axial current for confinement and compression eliminates the need for external confinement or heating technologies. This compact magnetic confinement technology could, in turn, provide the basis for a cost-effective deuterium-tritium fusion power plant. In addition to a robust experimental program pushing plasma performance towards breakeven conditions, Zap Energy has parallel programs developing power handling systems suitable for future power plants. Technologies under development include high average-power repetitive pulsed power, high duty-cycle cathodes, and liquid metal wall systems. Century is the name of Zap Energy’s first effort to integrate these three components into an operational system capable of firing non-reacting hydrogen SFS Z-pinch plasmas into a liquid-metal-lined container at sustained repetition rates on the order of 0.1 Hz. Here, the pulsed power driver and liquid metal heat exchanger are both designed to sustain input powers of 100 kW. Construction and initial operations with an interim ~10 kW liquid metal heat exchanger are described.
The Hanford Site in Washington state previously generated plutonium for nuclear weapons. During operations, radionuclide byproducts and chemical process fluids were intentionally and/or unintentionally released to the subsurface, resulting in more than 800 contaminated waste sites across the Central Plateau, where historical chemical separations and waste management activities took place. As the Hanford Site mission transitioned from operations to site cleanup, remediation of the vadose zone and groundwater became a priority. However, given the depth of the unsaturated zone contamination above the groundwater, the unique nature of the waste, and the continuing impacts on groundwater quality, technologies needed to be identified and evaluated for in situ remediation in the deep vadose zone (DVZ). A laboratory treatability study has been completed to evaluate site-relevant effectiveness for nine in situ technologies that may be used to treat continuing sources of contaminants in specific areas of the Central Plateau waste sites that are grouped into the 200-DV-1 Operable Unit (OU). The 200-DV-1 OU was established in 2010 to address 43 Central Plateau waste sites with complex DVZ remediation challenges. Eight of these technologies were identified through a prescreening effort that evaluated remedial technologies potentially applicable to DVZ contamination in the Central Plateau . These eight technologies were selected for further study based on site specific knowledge gaps about their effectiveness. A ninth technology was added to the treatability study based on new information from separate laboratory investigations (conducted following the prescreening effort) demonstrating the technology’s potential effectiveness (see Section 1.2 for more information) and value for inclusion in the treatability study.
Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.
Abstract Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a broad-host-range platform that enables predictable, iterative genomic integration in transformation-resistant bacteria. cSAGE combines conjugative DNA delivery, standardized low-copy vectors, orthogonal recombinases, and modular genetic parts to support rapid pathway assembly and cross-host benchmarking. Using purple nonsulfur bacteria as a testbed, we integrate promoter engineering, multi-payload genome modification, and genome-scale metabolic modeling to empirically evaluate host-dependent pathway performance. Applying this workflow, we identify strain-specific differences in photosynthetic conversion of lignin-derived p -coumarate to the thermoplastic precursor p -vinylphenol. By enabling genome engineering and functional comparison across diverse bacteria using a single plasmid system, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.
In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.
The National Environmental Policy Act of 1969, as amended (NEPA), mandates that federal agencies assess and document potential environmental impacts before deciding on proposed actions. While significant progress has been made in cataloging and standardizing NEPA documents themselves, the legal challenges that frequently arise from these decisions remain poorly cataloged and largely inaccessible for systematic analysis. Litigation challenging NEPA compliance can substantially delay project timelines, reshape agency decision-making, and establish precedents that influence future environmental reviews — yet no standardized, machine-readable corpus exists that links litigation records to the NEPA projects they contest.
Wet air oxidation (WAO) offers an effective method for treating waste streams, converting pollutants into benign substances, and holds significant potential for processing the aqueous product from the hydrothermal liquefaction (HTL-AP) of wet wastes, a promising renewable fuel technology. Here, we conducted a comprehensive study of the WAO of HTL-AP from four different wet wastes. Through continuous testing under various conditions, we produced samples with different chemical oxygen demand (COD) levels, enhancing understanding of reaction parameters necessary for substantial COD reduction (>95%). Chemical analysis revealed that alcohols and ketones in the HTL-AP rapidly oxidized to acetic acid through aldehyde intermediates, while acetic acid, other carboxylic acids, and phenols oxidized relatively slowly. The light N-containing compounds were found to exhibit a change in concentration only after the whole sample reaches an 80% COD reduction, indicating their refractory nature under applied conditions. Energy released in the WAO reaction was calculated, and anaerobic toxicity assay demonstrated that WAO treatment enhanced methane production kinetics due to reduced inhibitory effects, suggesting partial oxidative transformation of inhibitory compounds into less toxic derivatives. These findings provide insights into designing effective WAO processes for valorizing HTL aqueous products, addressing key barriers to HTL process commercialization.
Accurate timing estimates of when participants acquire HIV in HIV prevention trials are necessary for determining antibody levels at acquisition. The Antibody-Mediated Prevention (AMP) Studies showed that a passively administered broadly neutralizing antibody can prevent the acquisition of HIV from a neutralization-sensitive virus. We developed a pipeline for estimating the date of detectable HIV acquisition (DDA) in AMP Study participants using diagnostic and viral sequence data. Using a Bayesian strategy that combines three streams of data (REN [rev/vpu/env/Δnef] sequence, GP [gag/Δpol] sequence, and diagnostic) where their 95% credible intervals overlap based on pre-specified criteria and decision rules. We evaluated the performance of our AMP pipeline using PacBio viral sequence data from 41 participants across two prospective acute HIV acquisition cohort studies, FRESH and RV217, with twice-weekly sampling. These cohort studies enrolled young women in South Africa and men and women in Kenya and Thailand, respectively, with a high likelihood of HIV acquisition. In evaluating performance, “true DDA” was the center of bounds between last-negative and first-positive RNA diagnostic tests (median time 4 days, range 2–7 days); bias was the mean difference between estimated and true DDA. Using diagnostic data alone yielded timing estimates with a bias of 2.4 days and root mean square error (RMSE) of 7.9 days. These results were improved using sequence + diagnostic data (bias 1.5 days, RMSE 6.9 days), as well as by restricting sequence-based estimation to samples from ≤5 weeks post-DDA (bias 0.2 days, RMSE 7.8 days).