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At least 379 records · Page 21

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanistic Insights Revealed by YbtPQ in the Occluded State

Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of “alternating access” like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic Escherichia coli in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the “screwdriver” action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.

59 BASIC BIOLOGICAL SCIENCES↗

Latent Catalysis as a Platform for Accessing Diverse Material Properties in Vat Photopolymerization 3D Printing

Vat photopolymerization (VP) 3D printing is an attractive strategy to manufacture customized polymer parts. The properties of printed materials are limited by the need to employ a low viscosity liquid resin and achieve rapid polymerization kinetics. To circumvent this limitation, dual‐cure methods have been developed using reagents embedded in the liquid resin formulation; however, the reagent‐based approach requires the discovery and optimization of new chemistry for each desired material. Here, in this work, we demonstrate a catalytic, dual‐cure platform that enables access to both Nylon‐6 and polyester interpenetrating networks through VP 3D printing under a universal approach. Structure–reactivity relationships of the latent NHC catalysts led to the identification of a magnesium chloride–NHC adduct as a latent catalyst that is orthogonal to radical polymerization and can be unmasked at elevated temperatures post‐printing to initiate ring‐opening polymerization of lactones and lactams. This strategy results in access to semicrystalline materials, which are a challenging morphology to access via VP 3D printing, that have attractive mechanical properties and can be printed at high resolution. This work represents the first photochemical‐based 3D printing of Nylon‐based materials and demonstrates the value of catalytic approaches to access new material properties in VP 3D printing.

Colliver, Cali N. [University of North Carolina, C↗

Effect of microstructure and temperature on nuclear graphite oxidation using the 3D Random Pore Model

This work compared the 3D Random Pore Model (3D-RPM) with experimental and characterization data to systematically study the effect of nuclear graphite microstructure and air oxidation temperature. It is well known that oxidation-induced weight loss at elevated temperatures degrades graphite structure and properties; however, a fundamental understanding of the role of graphite microstructure is still unclear. In this work, three diverse grades of nuclear graphite—IG-110, NBG-18, and PCEA—were examined and tested at air oxidation temperatures of 600, 650, 700, and 750 °C following ASTM D7542. Here, the 3D-RPM reproduced the microstructure and temperature dependence of mass loss curves for these grades. For the first time, measurements and modeling were combined to show how bulk density and the amount and spatial distribution of open and closed porosity affects oxidation. IG-110 was less dense and had an open pore network that is finer and more uniformly spread, and showed fastest oxidation. PCEA porosity was less uniform and showed less oxidation, while NBG-18 was more dense, had the least fine and uniform porosity, and showed the slowest oxidation. In general, oxidation proceeds faster if open porosity is more uniformly distributed and can incrementally access closed pore surface area with more ease.

36 MATERIALS SCIENCE↗

Impact of operating reserve rules on electricity prices with high penetrations of renewable energy

In competitive wholesale electricity markets, significant effort is devoted to designing markets that set efficient prices for maintaining supply-demand balance. One factor that can impact prices is administratively-set scarcity pricing, which sets prices to a preset level when the market is not able to meet operating reserve or energy requirements. When energy and operating reserves are co-optimized, assumptions surrounding operating reserve requirements and scarcity pricing can impact system-wide price outcomes for both operating reserves and energy. This study uses production cost modeling of an ERCOT-like system to evaluate the impact of operating reserve eligibility, scarcity pricing, and quantity rules on electricity prices, and therefore also on generator revenues. Results reveal economic and operational benefits with allowing open participation in reserve markets, as this enables greater access to the full set of capable resources at lowest cost. Furthermore, both energy and reserve prices are strongly impacted by reserve scarcity pricing events, which reveals that reserve scarcity pricing assumptions can impact price outcomes even for units not providing reserves. This study highlights the importance of operating reserve scarcity pricing rules because of the strong coupling between energy and reserve prices and because these rules serve as proxies for true price responsive demand.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Structural Reorganization of Noncellulosic Polymers Observed In Situ during Dilute Acid Pretreatment by Small-Angle Neutron Scattering

Production of second-generation bioethanol from lignocellulosic biomass requires pretreatment to open the plant cell wall structure and improve enzyme access. Many different thermochemical pretreatments have been extensively developed and employed, but the exact nature of plant cell wall recalcitrance and the most efficient and economical approach to alter plant cell wall structure via pretreatment still remain elusive. In order to understand the role of noncellulosic switchgrass polymers on the overall efficiency of pretreatment, the structural evolution of the noncellulosic polymers of the plant cell wall were investigated during dilute acid pretreatment (DAP) by employing in-situ small-angle neutron scattering (in-situ SANS). In this study, we observed real-time structural changes not possible to observe by any other technique. To deconvolute the structural evolution of lignin and hemicellulose polymers during DAP, native switchgrass (NATV), and isolated holocellulose (HOLO) and cellulose (CELL) fractions from NATV were studied. Our results show that aggregate particles first appear around 80 °C for NATV and HOLO samples. Further, due to the low temperature and pretreatment severity condition, these particles are likely derived from hemicellulose. The formations of much larger aggregate particles, only observed in the NATV sample, were attributed to lignin. For the HOLO sample, as the temperature and pretreatment severity condition increased, hemicellulose-derived aggregate particle sizes increased, suggesting this process was the nucleation and early stage formation of pseudolignin particles. Consistent with our interpretation of structural evolutions in NATV and HOLO samples, no formation of aggregate particles was observed in CELL samples for the entire duration of the pretreatment. These results suggest that not only lignin but also hemicellulose can form aggregate particles within plant cell walls during pretreatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A materials data framework and dataset for elastomeric foam impact mitigating materials

The availability of materials data for impact-mitigating materials has lagged behind applications-based data. For example, data describing on-field helmeted impacts are available, whereas material behaviors for the constituent impact-mitigating materials used in helmet designs lack open datasets. Here, we describe a new FAIR (findable, accessible, interoperable, reusable) data framework with structural and mechanical response data for one example elastic impact protection foam. The continuum-scale behavior of foams emerges from the interplay of polymer properties, internal gas, and geometric structure. This behavior is rate and temperature sensitive, therefore, describing structure-property characteristics requires data collected across several types of instruments. Data included are from structure imaging via micro-computed tomography, finite deformation mechanical measurements from universal test systems with full-field displacement and strain, and visco-thermo-elastic properties from dynamic mechanical analysis. These data facilitate modeling and design efforts in foam mechanics, e.g., homogenization, direct numerical simulation, or phenomenological fitting. The data framework is implemented using data services and software from the Materials Data Facility of the Center for Hierarchical Materials Design.

36 MATERIALS SCIENCE↗

Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes

X-ray absorption spectroscopy (XAS) is a premier technique for materials characterization, providing key information about the local chemical environment of the absorber atom. In this work, we develop a database of sulfur K-edge XAS spectra of crystalline and amorphous lithium thiophosphate materials based on the atomic structures reported in Chem. Mater., 34, 6702 (2022). The XAS database is based on simulations using the excited electron and core-hole pseudopotential approach implemented in the Vienna Ab initio Simulation Package. Our database contains 2681 S K-edge XAS spectra for 66 crystalline and glassy structure models, making it the largest collection of first-principles computational XAS spectra for glass/ceramic lithium thiophosphates to date. This database can be used to correlate S spectral features with distinct S species based on their local coordination and short-range ordering in sulfide-based solid electrolytes. The data is openly distributed via the Materials Cloud, allowing researchers to access it for free and use it for further analysis, such as spectral fingerprinting, matching with experiments, and developing machine learning models.

36 MATERIALS SCIENCE↗

Analysis of two-color photoelectron spectroscopy for attosecond metrology at seeded free-electron lasers

The generation of attosecond pulse trains at free-electron lasers opens new opportunities in ultrafast science, as it gives access, for the first time, to reproducible, programmable, extreme ultraviolet (XUV) waveforms with high intensity. In this work, we present a detailed analysis of the theoretical model underlying the temporal characterization of the attosecond pulse trains recently generated at the free-electron laser FERMI. In particular, the validity of the approximations used for the correlated analysis of the photoelectron spectra generated in the two-color photoionization experiments are thoroughly discussed. The ranges of validity of the assumptions, in connection with the main experimental parameters, are derived.

74 ATOMIC AND MOLECULAR PHYSICS↗

NeuroCoreX: An Open-Source FPGA-Based Spiking Neural Network Emulator with On-Chip Learning

Spiking Neural Networks (SNNs) are computational models inspired by the event-driven communication and connectivity patterns of biological neural circuits. They enable high energy efficiency and natural support for diverse architectures ranging from layered networks to small-world and graphstructured topologies. In this work, we introduce NeuroCoreX, an open-source, FPGA-based spiking neural network emulator that provides real-time, on-chip learning and flexible network organization. NeuroCoreX supports both feedforward sensory inputs streamed directly from sensors or PCs via UART and recurrent on-chip connectivity, enabling simultaneous processing and learning from external stimuli and internal network dynamics-capabilities rarely available in existing FPGA SNN platforms. The system implements a Leaky Integrate-and-Fire (LIF) neuron model with current-based synapses and supports pair-based STDP learning on both feedforward and recurrent synapses. A lightweight Python interface enables interactive configuration, live monitoring, weight read-back, and experiment control. Importantly, NeuroCoreX is tightly integrated with the SuperNeuroMAT simulator, allowing SNN models to be transferred seamlessly from software to hardware for hardware-in-the-loop development. By combining real-time plasticity, flexible connectivity, and an open-source VHDL implementation, NeuroCoreX provides an extensible and accessible platform for neuromorphic research, algorithm-hardware co-design, and energy-efficient edge intelligence.

Gautam, Ashish [ORNL]↗

Event generators for high-energy physics experiments

We provide an overview of the status of Monte-Carlo event generators for high-energy particle physics. Guided by the experimental needs and requirements, we highlight areas of active development, and opportunities for future improvements. Particular emphasis is given to physics models and algorithms that are employed across a variety of experiments. These common themes in event generator development lead to a more comprehensive understanding of physics at the highest energies and intensities, and allow models to be tested against a wealth of data that have been accumulated over the past decades. A cohesive approach to event generator development will allow these models to be further improved and systematic uncertainties to be reduced, directly contributing to future experimental success. Event generators are part of a much larger ecosystem of computational tools. They typically involve a number of unknown model parameters that must be tuned to experimental data, while maintaining the integrity of the underlying physics models. Making both these data, and the analyses with which they have been obtained accessible to future users is an essential aspect of open science and data preservation. It ensures the consistency of physics models across a variety of experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

OPEXatLANL Survey Results [Slides]

The survey was open online July 19-August 4, 2021. It was open to all employees with LANL email addresses, Google access. It was used to measure OPEXatLANL awareness, usage. It consisted of 7 multiple-choice questions, 3 short-answer questions. A total of 383 responses were collected (55 managers, 328 non-managers).

99 GENERAL AND MISCELLANEOUS↗

Open data sets for assessing photovoltaic system reliability

Photovoltaic (PV) systems have become a cornerstone of renewable energy strategies, particularly due to the significant reduction in solar power costs over the past decade. However, the long-term reliability of PV installations presents a persistent challenge, requiring the development of advanced monitoring and predictive maintenance strategies. A wide range of data types is used to evaluate the health of PV systems, including environmental conditions, electrical performance, and inspection imagery. These data enable methodologies such as machine learning (ML) models for lifetime prediction and computer vision techniques for defect detection. However, the acquisition of high-quality and comprehensive data is difficult, particularly in terms of long-term consistency and data variety. Publicly available data sets serve as valuable resources for addressing these challenges, but they often suffer from fragmentation and are difficult to access. This paper presents a comprehensive review of existing open-source data sets related to PV degradation, analyzing their features, functionalities, and potential applications. We categorize these data sets based on the specific aspects of PV system information they cover, such as environmental conditions, operational monitoring, image inspection and module materials, and propose relevant tools and ML models for processing them. In addition, we propose practices for future data collection and usage, while also discussing potential directions in data-driven research. Our aim is to enhance data utilization and publication among researchers and industry professionals, promoting a deeper understanding of the role of data in enhancing the performance and durability of PV systems.

14 SOLAR ENERGY↗

Open Architecture for Cost Savings in Advanced Nuclear Reactors

Recently, nuclear power plant build projects in the West have run over budget due to high capital costs and schedule overruns. Compared to other sources of energy, nuclear power plants have higher capital costs. Reactors are often different at every site, resulting in a lack of standardization. Nuclear is expected to compete with other low carbon sources of energy which have lower capital costs making it essential for nuclear to develop ways of reducing costs. Strategies such as standardization, learning rates, modularization, and schedule reduction in advanced reactors can reduce nuclear costs by about 40%. Standardization as a way of cutting capital costs has been explored even in large nuclear power plants. Standardization of certain plant components can result in lower component and installation costs and higher learning from experience. Standardization can be achieved by adopting a criterion of key performance indicators and general design principles for a specific system or component such as the balance of plant. Modularization allows the construction of certain components of SMRs in a factory, which saves time, increases productivity, and encourages higher learning rates. Production learning decreases the time and the cost related to an activity. The potential for modularized components of advanced reactors to be manufactured in factories makes it conducive to achieving higher learning rates. Developing large-capacity nuclear programs through sequential builds cultivates a higher learning rate, which in effect may reduce schedule overruns. Open architecture has been identified as a way to drive standardization among advanced reactor designs and result in cost savings. Open architecture (OA) is defined as a design enabling a diverse supply chain by defining and publishing requirements of systems or equipment in functional and/or interface terms, utilizing technical standards in widespread use. Currently, the nuclear industry’s approach is to use closed architecture, making most designs proprietary. However, collaboration between various advanced reactor vendors and suppliers utilizing the concept of open architecture can result in modular and standardized architecture of subsystems or subcomponents of a nuclear power plant. Completely standardizing nuclear power plants may be impossible, however, certain common subsystems amongst the various reactor designs could be standardized and/or access a wider supply chain and leverage existing learning from other sectors. Open architecture will save time and allocate resources to the parts of the plants that have the most unique features. A key advantage of open architecture is its ability to improve production learning across advanced reactors (AR) types in the industry, by providing and utilizing the same kind of component. Sodium fast reactor (SFR), High Temperature Gas Reactor (HTGR) and Molten Salt Reactor (MSR) are the advanced reactors considered for this project. This paper aims to determine the cost savings in advanced reactor programs due to open architecture learning rate. This work is an extension of work done on light water reactor small modular reactors; the cost methodology was utilized to investigate the impact of open architecture on advanced reactors with a particular focus on sodium fast reactors. The cost data on sodium fast reactors used in the model presented the most adequate information required for the analysis.

Advanced Nuclear Reactors↗

Toward a Seamless Integration of Computing, Experimental, and Observational Science Facilities: A Blueprint to Accelerate Discovery

The Department of Energy, Office of Science operates world-leading facilities for experimental, observational, and computational science. DOE supercomputing facilities will reach performance at the scale of ExaFLOPs in the coming years, enabling new vistas of scale and precision for large scale simulations and data analysis. Experimental scientific facilities are undergoing similar upgrades that will lead to higher data rates and correspondingly larger computational demands, and will increase the need for near-real-time processing and resilient support for more complex workflows. A transformation of science is underway, with workloads at supercomputing facilities increasingly driven by this explosion of data from instruments and experimental facilities, as well as the accelerating use of Artificial Intelligence (AI) as a tool for scientific discovery. A seamless integration of computing, networking, instruments, and experimental facilities is required to support these emerging workloads and open up a new frontier of U.S. leadership in scientific discovery. We propose to accomplish this by providing frictionless access to the ASCR supercomputing facilities. We describe our vision of combining the power of ASCR supercomputers and networking infrastructure into an integrated scalable fabric, available to end user scientists via interfaces that aim to automate and simplify access to high performance computing systems. This will enable unprecedented computational science capabilities for experimental and observational facilities, and will create new opportunities to combine large simulations and modeling with experimental facility data analysis. This blueprint for creating an integrated network of computational and experimental facilities will provide an enriched discovery environment and open doors for new scientific communities to access the DOE’s world-leading computing and networking capabilities.

97 MATHEMATICS AND COMPUTING↗

Polysilaketals: High‐Performance Polyether‐Based Electrolytes with Tunable Disubstituted Silane Linkers

Abstract Polymer electrolytes exhibit higher energy density and improved safety in lithium‐ion batteries relative to traditionally used liquid electrolytes but are currently limited by their lower electrochemical performance. Aiming to access polymer electrolytes with competitive electrochemical properties, we developed the anionic ring‐opening polymerization (AROP) of cyclic silaketals to synthesize amorphous silicon‐containing polyether‐based electrolytes with varying substituent bulk of the general formula [OSi(R) 2 (CH 2 CH 2 O) 2 ] n (R=alkyl, phenyl). As opposed to previously reported uncontrolled polycondensation routes toward low molecular weight polysilaketals, AROP allows access to targeted molecular weights above the entanglement threshold of the polymers. The polysilaketal with the lowest steric bulk (P(OSi Me,Me ‐2EO)) exceeds the conductivity of poly(ethylene oxide) (PEO), a leading polymer electrolyte. To the best of our knowledge, this is the first solid polymer electrolyte to achieve this benchmark. Steric bulk in polysilaketals was found to impart stability and two bulkier polysilaketals, P(OSi Et,Et ‐2EO) and P(OSi Me,Ph ‐2EO), exhibited higher current fractions than PEO over a wide range of salt loadings. Moreover, the efficacy of P(OSi Et,Et ‐2EO) was competitive with that of PEO. Taken together, the tunable and competitive electrochemical properties of polysilaketals validate the systematic incorporation of silyl groups as a strategy to access high performance polymer electrolytes.

Rugh, Haley J.↗

Salt Sampling FY21 Technical Report

The goal of the salt sampling program at Argonne is to develop and deploy automated molten salt sampling approaches to enable high-precision in-process salt sample analysis to improve the timeliness of sampling-based accountancy measurements. Tools currently under development in support of this goal include (1) a modular vacuum sampler with an accompanying sample handling method for coupling vacuum sampling with high-precision at-line sample analysis, (2) a pneumatic sample generator that enables high-throughput sample analysis to improve the precision of existing analytical techniques, and (3) a windowless flow cell to enable on-line optical analysis of molten salt in a sampling loop. Compared to point sampling approaches (i.e., dip probes), vacuum sampling systems and on-line sampling loops facilitate access to a larger cross-section of a process fluid. This is known to improve the characterization of the process fluid by producing more representative samples and by enabling the analysis of a larger cross section of the fluid. A vacuum sampling approach for molten salts eliminates the risk of dross contamination of samples and avoids the use of moving parts in the salt. In FY21, two methods for integrating a vacuum sampler with a pneumatic sample generator were tested. These included direct fluidic coupling and coupling using a solid salt transfer mechanism. Solid salt transfer was ultimately selected over fluidic coupling, primarily to enable the transport of samples over longer distances to support automated at-line integration with high-precision techniques (such as microcalorimetry) that cannot withstand the extreme conditions near an electrorefining process. To facilitate rapid solid salt coupling, new mechanisms were developed for rapidly charging and discharging salt sample tubes at the vacuum sampler and pneumatic sample generator, respectively. While the charging mechanism will be deployed in FY22, the tube transfer method and discharge mechanism were tested in FY21. These were deployed at one of Argonne’s engineering-scale electrorefiners to implement at-line high-throughput pneumatic micro-sample generation capabilities. The method was used to generate precise uranium- and lanthanide-bearing electrorefiner micro-samples with the specific dimensions requested by researchers at Los Alamos National Laboratory for use in testing their novel microcalorimeter x-ray techniques. The solid salt transfer mechanism proved not only to be an effective means of integrating the precision sample generator with vacuum sampling, but also improved the performance of the sampler generator. Because the modular sampling approach described here eliminates the need for new high-radiation sample handling capabilities, salt-wetted seals, salt-wetted moving parts, and heated transfer lines outside the electrorefiner, it will address most of the remaining technical challenges for the at-line deployment of high-precision analytical techniques. This will enable significant reductions in the time delay for sampling-based accountancy measurements by eliminating the need for manual off-line sample processing and analysis. On-line optical analysis of molten salt in a sampling loop would provide complementary information to at-line and in-situ techniques. In FY21, an open-aperture molten salt gravity flow cell with windowless optical access to flowing salt was successfully demonstrated. Future work should include the refinement and performance testing of the on-line and at-line sampling tools, integration of additional analysis techniques, stakeholder outreach and collaboration, evaluation of the integrated methods, and analyses to determine how the various tools might fit into an integrated safeguards monitoring system of unattended near real time monitoring tools.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗