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At least 145 records · Page 8

Adaptive Site Management Strategies for the Hanford Central Plateau Groundwater

Adaptive site management (ASM) is a systematic and iterative management approach that can be used to expedite the remediation of large and/or complex sites. ASM is defined as a formal and systematic project or site management approach centered on rigorous site planning and a firm understanding of site conditions and uncertainties, using science and technology to routinely re-evaluate and prioritize site remedial actions and characterization activities. The goal of the approach is to create a framework of structured and continuous planning, implementation, and assessment processes that accommodates new information and changing site conditions to develop effective and efficient cleanup approaches that achieves the required outcome(s) while optimizing costs, cleanup timeframe, and performance. Central to ASM is an evolving conceptual site model (CSM). Over time, incremental reductions in uncertainty associated with the CSM will occur, while supporting continued progress toward site cleanup and closure through remedy optimization and evaluation. ASM has the potential to expedite cleanup for the Central Plateau area at Hanford through a planned and systematic approach for reducing uncertainty with targeted characterization activities, while continuing remediation activities that advance cleanup for key risk-driving contaminants. A core component of cleanup within the Central Plateau is the 200 West Pump-and-Treat (P&T) system. Even with an active P&T remedy, uncertainty exists with respect to plume distributions, total mass in the aquifer, and currently known continuing sources. Additional uncertainty is associated with multiple contaminant source locations in the vadose zone, which have the potential to create new groundwater plumes in the absence of any source control measures, although not all contaminant fluxes to groundwater will result in contaminant concentrations above cleanup levels. Collectively, these uncertainties need to be addressed in the CSM to support effective and efficient site progress toward cleanup goal(s). Other nontechnical factors that may warrant an ASM approach at the Hanford Central Plateau are associated with the formation of operable units (OUs) used to manage cleanup. With the exception of the 200-ZP-1 OU, the three remaining groundwater OUs only have interim action records of decision. Nine vadose zone source area OUs are also in the early stages of the remedial investigation and feasibility study process, with pending characterization and technology identification activities. A set of proposed site objectives for the Central Plateau are provided in this document as an initial consideration/example and basis for discussion for ASM implementation. These example site objectives were selected with the goal of maintaining protectiveness at the Columbia River through confinement of contaminant plumes within an administratively controlled area below existing surface waste sites and waste disposal facilities. Although site decision makers and regulators need to provide concurrence, these site objectives are used in this document to describe the elements of an ASM approach, including selection of interim objectives and a long-term adaptive management plan. Interim objectives are also defined to yield measurable incremental progress toward the overall site goals. This document identifies initial technical considerations for developing an ASM framework for the Central Plateau cleanup decisions. These considerations are intended to facilitate more specific decisions, such as objectives, near- and long-term actions, and performance metrics, to develop an overall approach that maintains protectiveness but recognizes the uncertainty, long timeframe, and technical challenges that need to be considered in selecting, implementing, and managing remediation at the Hanford Central Plateau.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Methodology to Generate the Decay Gamma Source for a Second Target Station Target Wedge

This report details the specifics of applying the Position-Averaged Method methodology for the calculation of the rotating lasagna-style target wedge activation and the resulting decay gamma source terms. The methodology uses MCNP® Code Version 6.2.0 with the RNUCS patch coupled with CINDER2008 from the AARE V1.0 package. The process begins with model preparations that include ensuring impurities are included in the materials in the regions of interest along with segmentation of the geometry in order to capture the decay gamma source gradients. This report also details the physics models and other MCNP®, CINDER2008, and ADVANTG 3.2.0 related options used to calculate the decay gamma source terms. ADVANTG 3.2.0 is used to generate a weight window set to aid in convergence of the neutron fluxes in the initial MCNP® protons-on-target particle transport calculation to calculate the neutron fluxes and spallation products in the regions of interest. The neutron fluxes and spallation products are then used in the CINDER2008 transmutation calculation, and the decay gamma sources are generated by the AARE_GAMMA_SOURCE_SCRIPT as a part of the AARE V1.0 package. These decay gamma sources include the energy distributions as well as the necessary distributions to sample the location of the source using the cell rejection method. The gamma sources that are produced using the methodology may be used for a wide variety of analysis involving the target wedge. This report includes the material specifications, physics options, proton source term description, geometrical configuration, and post-processing details.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Radiochemical capabilities for astrophysics experiments at the national ignition facility

The Nuclear and Radiochemistry Group at Lawrence Livermore National Laboratory (LLNL) has developed a suite of diagnostics and techniques that can be used for astrophysics experiments at the National Ignition Facility (NIF). Capabilities have been developed to add material to the outside of NIF hohlraum assemblies as well as to the interior of NIF target capsules or the fill gas. The ability to place very small amounts of material close to the NIF target enables activation with very large, short-pulse neutron fluxes. The Solid Radiochemistry Diagnostic can be used to collect solid debris from a NIF shot within 2 h of the execution of a shot, and this can be analyzed for radioactive signatures with or without post-shot chemical processing. The Radiochemical Analysis of Gaseous Samples diagnostic system can be used to collect gaseous products produced during a NIF shot. Capsule doping and radiochemical analysis capabilities at NIF will be discussed. The application of these techniques to astrophysical measurements will be discussed as well as some preliminary results.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

The cytochrome bc 1 complex as an antipathogenic target

The cytochrome bc 1 complex is a key component of the mitochondrial respiratory chains of many eukaryotic microorganisms that are pathogenic for plants or humans, such as fungi responsible for crop diseases and Plasmodium falciparum, which causes human malaria. Cytochrome bc 1 is an enzyme that contains two (ubi)quinone/quinol-binding sites, which can be exploited for the development of fungicidal and chemotherapeutic agents. In this article, we review recent progress in determination of the structure and mechanism of action of cytochrome bc 1 , and the associated development of antimicrobial agents (and associated resistance mechanisms) targeting its activity.

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases

Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequenc- and structure-based annotation approaches are often accurate for predicting broad categories of substrate specificity, they generally cannot predict which specific molecules will be accepted as substrates for a given enzyme, particularly within a class of closely related molecules. Combining targeted experimental activity data with structural modeling, ligand docking, and physicochemical properties of proteins and ligands with various machine learning models provides complementary information that can lead to accurate predictions of substrate scope for related enzymes. Here we describe such an approach that can predict the substrate scope of bacterial nitrilases, which catalyze the hydrolysis of nitrile compounds to the corresponding carboxylic acids and ammonia. Each of the four machine learning models (logistic regression, random forest, gradient-boosted decision trees, and support vector machines) performed similarly (average ROC = 0.9, average accuracy = ~82%) for predicting substrate scope for this dataset, although random forest offers some advantages. Finally, this approach is intended to be highly modular with respect to physicochemical property calculations and software used for structural modeling and docking.

59 BASIC BIOLOGICAL SCIENCES↗

Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD

Pseudomonas aeruginosa is an increasingly antibiotic-resistant pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. P. aeruginosaproduces the siderophore pyochelin through the use of a non-ribosomal peptide synthetase (NRPS) biosynthetic pathway. Targeting members of siderophore NRPS proteins is one avenue currently under investigation for the development of new antibiotics against antibiotic-resistant organisms. Here, the crystal structure of the pyochelin adenylation domain PchD is reported. The structure was solved to 2.11 Å when co-crystallized with the adenylation inhibitor 5'-O-(N-salicylsulfamoyl)adenosine (salicyl-AMS) and to 1.69 Å with a modified version of salicyl-AMS designed to target an active site cysteine (4-cyano-salicyl-AMS). In the structures, PchD adopts the adenylation conformation, similar to that reported for AB3403 from Acinetobacter baumannii.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimizing mixed cool thermal storage systems across a connected community

A high level of electric demand flexibility must be integrated into our building infrastructure to enable greater renewable energy penetration in the grid. In the U.S., 9% of electricity generated is used to cool buildings in a periodic manner, making this end-use an ideal target for active management through cool thermal energy storage (CTES) technologies. Historic uses for CTES are designed around central chilled water plants, but these systems cool less than 25% of U.S. commercial floorspace. Emerging technologies are under development to serve the many smaller distributed cooling systems, such as rooftop units (RTUs), and have the potential to add CTES to an additional 66% of cooled commercial floorspace. However, these unitary thermal storage systems (UTSS) lack the modeling and analysis tools to evaluate them in the future interactive grid context. Here, this study develops the modeling and optimization tools necessary to simultaneously examine central and distributed ice storage systems within the multi-building, connected community context. An integrated simulation-optimization workflow is created to allow for rapid customized analysis. Results demonstrate the energy and flexibility tradeoffs of various implementations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Evolution of storage monitoring – update in response to commercial and regulatory drivers

Carbon Capture and Storage (CCS) is in transition from first-of-a kind projects and research-orientated pilots to commercially-motivated applications. Monitoring results from many newly developed and planned large scale commercial projects are limited; however, it is worthwhile to assess their evolution and consider new strategies as part of an effort to assess and document best practices. Commercial monitoring is targeted to activities that comply with regulatory drivers and de-risk investments. Commercial monitoring also supports accounting that storage has occurred and is tied to project financing. It deals with long time frames and large volumes injected into multiple wells and multiple projects in favorable areas. We see developing trends toward reproducible workflows that systematically reduce risks and clarify expectations for oversight and long-term surveillance. Monitoring techniques showing increasing trends include injection zone pressure as a history-matching and compliance tool. To reduce cost and environmental impact of time-lapse seismic data collection, deploying new approaches and tools, such as use of fibre and installed sources are increasingly applied. Concern over the risk of induced seismicity by regulatory bodies and the general public has increased, which has also resulted in increased monitoring. Some techniques used in the early research phases have been sidelined or used only in restricted applications. For example, geochemical analyses in the injection zone as well as the environment are now being deployed less than it was in research-oriented programs, except in the US where it is required by the permitting process. Expectations of frequent area-wide near surface monitoring have also decreased.

25 ENERGY STORAGE↗

MuSIC@Indiana: An effective tool for accurate measurement of fusion with low-intensity radioactive beams

The design, construction, and characterization of the Multi-Sampling Ionization Chamber, MuSIC@Indiana, are described. This detector provides efficient and accurate measurement of the fusion cross-section at near-barrier energies. The response of the detector to low-intensity beams of 17,18 O, 19 F, 23 Na, 24,26 Mg, 27 Al, and 28 Si at E lab 50–60MeV was examined. MuSIC@Indiana was commissioned by measuring the 18 O+ 12 C fusion excitation function for 11 < E cm < 20 MeV using CH 4 gas. Here, a simple, effective analysis cleanly distinguishes proton capture and two-body scattering events from fusion on carbon. With MuSIC@Indiana, measurement of 15 points on the excitation function for a single incident beam energy is achieved. The resulting excitation function is shown to be in good agreement with literature data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Classification of events from α -induced reactions in the MUSIC detector via statistical and ML methods

The Multi-Sampling Ionization Chamber (MUSIC) detector is typically used to measure nuclear reaction cross sections relevant for nuclear astrophysics, fusion studies, and other applications. From the MUSIC data produced in one experiment scientists carefully extract an order of 10 3 events of interest from about 10 9 total events, where each event can be represented by an 18-dimensional vector. However, the standard data classification process is based on expert driven, manually intensive data analysis techniques that require several months to identify patterns and classify the relevant events from the collected data. Here, to address this issue, we present a method for the classification of events originating from specific α-induced reactions by combining statistical and machine learning methods that require significantly less input from the domain scientist, relative to the standard technique. Here, we applied the new method to two experimental data sets and compared our results with those obtained using traditional methods. With few exceptions, the number of events classified by our method agrees within ±20% with the results obtained using traditional methods. With the present method, which is the first of its kind for the MUSIC data, we have established the foundation for the automated extraction of physical events of interest from experiments using the MUSIC detector.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ad-apoptin inhibits glycolysis, migration and invasion in lung cancer cells targeting AMPK/mTOR signaling pathway

Ad-apoptin is a recombinant oncolytic adenovirus constructed by our laboratory that can express apoptin. It can selectively kill tumor cells without damaging normal cells. This study investigated the effects of Ad-apoptin on glycolysis, migration and invasion of non-small cell lung cancer. Cell viability and apoptosis were detected by CCK-8 and flow cytometry, respectively. Glycolysis was investigated by glucose consumption, lactic acid production and glycolytic key enzyme protein levels. Migration and invasion were evaluated via wound healing, transwell assays and epithelial-mesenchymal transition (EMT) protein levels. The interaction between apoptin and AMPK was detected by Co-IP. A nude mice tumor model was established to investigate the anti-cancer role of Ad-apoptin in vivo. The results showed that Ad-apoptin inhibits cell viability and induces apoptosis of A549 and NCI–H23 cells. Ad-apoptin can reduce the glucose uptake and lactic production in lung cancer cells, and reduce the expression of related glycolysis-limiting enzymes. At the same time, Ad-apoptin inhibited the migration and invasion of lung cancer. Immunoprecipitation showed that apoptin and AMPK could interact directly. Moreover, knockdown of AMPK significantly attenuated the inhibitory effect of Ad-apoptin on glycolysis, migration and invasion of A549 and NCI–H23 cells. Ad-apoptin can inhibit the growth of tumors in nude mice. Compared with the control group, Ad-apoptin had a significant inhibitory effect on AMPK knockdown tumors. The immunohistochemical results of tumor tissues were consistent with those in vitro. Collectively, Ad-apoptin targets AMPK and inhibits glycolysis, migration and invasion of lung cancer cells through the AMPK/mTOR signaling pathway. This suggests that Ad-apoptin may have therapeutic potential for lung cancer by targeting AMPK activation.

60 APPLIED LIFE SCIENCES↗

Pt Atomic Single-Layer Catalyst Embedded in Defect-Enriched Ceria for Efficient CO Oxidation

The local coordination structure of metal sites essentially determines the performance of supported metal catalysts. Here, using a surface defect enrichment strategy, we successfully fabricated Pt atomic single-layer (Pt ASL ) structures with 100% metal dispersion and precisely controlled local coordination environment (embedded vs adsorbed) derived from Pt single-atoms (Pt 1 ) on ceria-alumina supports. The local coordination environment of Pt 1 not only governs its catalytic activity but also determines the Pt 1 structure evolution upon reduction activation. For CO oxidation, the highest turnover frequency can be achieved on the embedded Pt ASL in the CeO 2 lattice, which is 3.5 times of that on the adsorbed Pt ASL on the CeO 2 surface and 10–70 times of that on Pt1. The favorable CO adsorption on embedded Pt ASL and improved activation/reactivity of lattice oxygen within CeO 2 effectively facilitate the CO oxidation. This work provides new insights for the precise control of the local coordination structure of active metal sites for achieving 100% atomic utilization efficiency and optimal intrinsic catalytic activity for targeted reactions simultaneously.

36 MATERIALS SCIENCE↗

Phosphatidic acid: an emerging versatile class of cellular mediators

Abstract Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Biochemistry & Molecular Biology↗

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4

The plant pathogen Pseudomonas syringae encodes a type III secretion system avirulence effector protein, AvrB, that induces a form of programmed cell death called the hypersensitive response in plants as a defense mechanism against systemic infection. Despite the well-documented catalytic activities observed in other Fido (Fic, Doc, and AvrB) proteins, the enzymatic activity and target substrates of AvrB have remained elusive. Here, we show that AvrB is an unprecedented glycosyltransferase that transfers rhamnose from UDP-rhamnose to a threonine residue of the Arabidopsis guardee protein RIN4. We report structures of various enzymatic states of the AvrB-catalyzed rhamnosylation reaction of RIN4, which reveal the structural and mechanistic basis for rhamnosylation by a Fido protein. Collectively, our results uncover an unexpected reaction performed by a prototypical member of the Fido superfamily while providing important insights into the plant hypersensitive response pathway and foreshadowing more diverse chemistry used by Fido proteins and their substrates.

59 BASIC BIOLOGICAL SCIENCES↗

Real-Time Multi-Vehicle Multi-Camera Tracking with Graph-Based Tracklet Features

An essential application in intelligent transportation systems is multi-target multi-camera tracking (MTMCT), where the target’s activity is tracked from different cameras. Although the tracking-by-detection scheme is the primary paradigm in MTMCT, the object association information from the video frames is lost. This is mainly because the multi-camera multi-object matching uses the information from the video frames separately. To solve this problem and leverage this association information, we propose an MTMCT framework, where features are built in the form of a graph and a graph similarity algorithm is used to match multi-camera objects. In this paper, we focus on the real-time scenario, where only the past images are used to match an object. Our method achieves an IDF1 score (the ratio of the number of correctly identified objects to the number of ground truth and average objects) of 0.75 with a rate of 14 frames per second (fps).

Engineering↗

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity

To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements (MGEs) encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic acid–binding proteins. Based on mutational analyses and functional assays, we deduced that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and MGEs.

59 BASIC BIOLOGICAL SCIENCES↗

Towards provision of regularly updated climate data from the Coupled Model Intercomparison Project

The Coupled Model Intercomparison Project (CMIP) is a flagship of the World Climate Research Programme (WCRP). CMIP has become a recognised ‘brand’ in climate circles evolving over the last thirty years from a targeted research activity by a small number of climate modelling centres intercomparing their Earth System Model (ESM) simulations to a broad international coordinated research effort (Durack et al, 2025). CMIP is organized as a research activity leveraging funded and in-kind contributions from experts within modelling centres and the broader scientific community supported more recently by a fully-funded International Project Office. Within CMIP, Model Intercomparison Projects (MIPs) are community-designed to understand past, present and future climate. CMIP data provides a valuable resource for climate research and is routinely used to assess model representation of climate processes and test scientific hypotheses in the context of model uncertainty and (forced and internal) variability as evident from its prolific use in scientific publications1 . The impact relies on enabling infrastructure (most prominently via the Earth System Grid Federation (ESGF)), which allows sharing of simulation output, provision of the boundary conditions used in each simulation, and definition of the data standards that are essential to facilitating wide use of the data. The impact is supplemented by the wide-ranging scrutiny to which model simulations are subjected. Beyond its use in research, CMIP data is a key resource for communities producing derived climate information from downscaling and impact studies, such as the Coordinated Regional Downscaling Experiment (CORDEX; Gutowski et al., 2016) and the Intersectoral Impacts MIP (ISIMIP; Frieler et al., 2024). Government, academic and commercial entities also increasingly rely on CMIP and its downstream data for climate risk assessments and climate services (for example, Copernicus Climate Change Service and World Bank portal). This means that, although CMIP is a research activity, it increasingly serves a secondary and very relevant role as a provider of climate data – a long-recognised dichotomy (Stevens, 2024). Research and applications have distinct needs, with the former requiring flexibility and generality and the latter consistency. Here we explain how the design of the research activity has been adapted to reduce the burdens imposed by applications and how the research infrastructure might evolve to further enable scientific inquiry. We propose one possible approach to consistently providing model information and projections for applications in the future.

Environmental sciences↗