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At least 415 records · Page 23

Streaming Data in HPC Workflows Using ADIOS

The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

Study on Intelligent Compaction-Equipment Logistics Scheduling and Propagation Characteristics of Vibration Wave in Nonlinear Systems with Multistability Based on Field Test

The equipment scheduling and propagation characteristics of vibration wave from vibratory roller ⟶ filling material nonlinear systems with multistability are the core problems of subgrade intelligent construction technology, and the logistics scheduling of the equipment is directly related to the construction efficiency. Aiming at the shortages, one typical subgrade located at the Gu’an station of Beijing-Xiong’an city railway is selected to research and finish the field tests; some findings are shown as follows: first, some valuable suggestions about the logistics scheduling of intelligent equipment are proposed, which can break the barriers between the organizations and improve construction efficiency; second, when the vibration wave propagates from the vibratory roller ⟶ surface of filling material ⟶ different buried depths of filling material, the peak acceleration of vibration wave gradually decreases and is hyperbolic distribution approximately. At the same time, the sensitive of attenuation is shown as follows: Z R 2 >0.9), and the concrete functional relationship among different amplitudes of harmonics can be summarized as y = Ae −BX ; fourth, the vibration energy is mainly concentrated near 10–30 Hz in the vibratory roller, but when the vibration wave propagates from vibratory roller⟶filling material, the vibration energy gradually decreases with the increase in depth, and the marginal spectrum gradually changes from one peak to two peaks, that is, 30–50 Hz and 50–100 Hz; fifth, the vibration energy in the vibrational wheel is distributed averagely in the compaction process, and the effective compaction time is two seconds, which will be helpful for revealing the propagation characteristics of vibration wave, optimizing the compaction quality control models and providing some support for the development of intelligent compaction theory of railway subgrade.

Han, Yixuan↗

TR-XPS Realtime Analysis Tool (ArroyoXPS) v0.1

The ALS has developed a Time-Resolved X-ray Photoelectron Spectroscopy (TR-XPS) technique, which involves applying a specific pattern of voltage curves to a sample while measuring XPS peaks. This pattern is repeated over multiple cycles, and changes in the material's response provide valuable scientific insights. Traditionally, file-based analysis workflows have been used: scans are run for a predetermined time, and after one or more scans are complete, calculations are made. ArroyoXPS changes this by offering in-experiment scan and analysis, allowing researchers to gain insights before a scan is finished. This enables them to adjust experimental parameters quickly, potentially saving valuable beamtime. ArroyoXPS includes tools for integrating with beamline control systems, performing analysis, and visualizing scan data in a web browser.

McReynolds, Dylan [Lawrence Berkeley National Labo↗

DIVA/DeviceEditor v6.1.2

DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.

Plahar, Hector [Lawrence Berkeley National Laborat↗

GRinding Automated Classification Engine

This work is an ML-driven framework for automated surface analysis of microscopy images. We create a training dataset by imaging stainless steel samples to benchmark four developed deep neural network architectures. These models, based on a YOLOv8n-cls backend, integrate image features and process metadata using various fusion methods to distinguish between acceptable and unacceptable surface finishes. This code is associated with publication "Classifying Alloy Surface Preparation Quality with Metadata-Infused Machine Learning for Rapid Alloy Discovery" for project APEX LDRD-ER (25-ERD-039)

Gongora, AldairE [Lawrence Livermore National Labo↗

IRMA

IRMA (In)elastic Representation of Materials As S(α,β) evaluations IRMA turns one phonon model into three outputs that usually require three separate tool chains: an evaluated nuclear-data file, predicted neutron-scattering spectra, and scattering kernels for Monte Carlo transport. The three outputs draw on a single, consistent description of the material, so the evaluation, the spectroscopy that can validate it, and the transport that uses it always agree about the physics. Nuclear data. IRMA writes ENDF-6 File 7 thermal scattering evaluations on automatically constructed (α, β) grids. This part reimplements and generalizes NJOY's LEAPR: the classic kernels reproduce freshly generated NJOY2016 tapes digit for digit and published reference tapes to about 1e-4, and the generalized paths add the exact coherent one-phonon term, anisotropic Debye-Waller tensors, coherent elastic for arbitrary crystals, and a per-species partition for polyatomic materials. The tapes feed NJOY, AMPX, FUDGE, and every transport code downstream of them. Neutron spectroscopy. The irma.spectra forward model projects the same physics onto an instrument's kinematics and resolution: INS spectra for VISION and generic indirect geometries, and 2-D S(Q,E) powder maps for direct-geometry spectrometers, from a phonopy model or straight from a phonon DOS. It can be used to predict a proposed measurement before beam time; in analysis, it supplies the calculated single-scattering counterpart of a measured spectrum, from the same material description the evaluation was built from. Monte Carlo transport. The irma.ncrystal exporter writes per-temperature scattering kernels for the companion NCrystal plugin, so McStas, OpenMC, and other NCrystal-aware codes sample the same physics. The exported kernels carry the per-site anisotropic Debye-Waller tensors, keeping directional coherent-elastic physics that NCrystal's standard scalar treatment does not represent. With the same physics inside a transport code, an entire beamline becomes a virtual experiment: IRMA's end-to-end validation ran a custom McStas implementation of the ARCS spectrometer, assembled from the existing McVine and McStas models, against measured data. From a bare crystal structure. The irma mlip front end builds the phonon model itself: a structure file and a choice of potential are enough. Nine pretrained machine-learned interatomic potentials are supported, on a laptop CPU, with no first-principles calculation; an approximate phonon model for a new material costs minutes, not a DFT campaign, and the build emits prefilled inputs for all three outputs. The result is a good starting point rather than a finished evaluation: survey-quality physics with every parameter exposed for review. A converged atomistic calculation enters the same way, as a phonopy model, when higher fidelity is needed.

Ramic, Kemal [Oak Ridge National Laboratory (ORNL)↗

Advancing continuous enzymatic hydrolysis for improved biomass saccharification

Background: A deployable, continuous enzymatic hydrolysis (CEH) process can address cost and commercialization risks associated with second-generation (Gen2) biorefinery sugar/lignin/ethanol production while contributing to energy supply and security. Developments in commercial enzymatic hydrolysis formulations targeting Gen2 pretreated biomass such as deacetylated mechanically refined (DMR) biomass necessitate a reassessment of the existing hybrid simultaneous saccharification and fermentation (SSF) approach. Notably, the practice of "finishing hydrolysis" in SSF has become problematic with the introduction of oxidative enzymes, such as lytic polysaccharide monooxygenases (LPMOs), into commercial cellulase formulations as these require specific redox conditions and cofactor. Moreover, continuous SSF has not been demonstrated at commercial scale, limiting deployment and the associated economic benefits to farmers, producers, and support industries. Results: Continuous enzymatic hydrolysis (CEH) was demonstrated at bench scale to enable optimal saccharification performance of deacetylated mechanically refined (DMR) pretreated biomass. Diafiltration was demonstrated to retain pretreated biomass solids and enzymes for continuous reaction while removing solubilized product sugars in situ. A significant breakthrough afforded by the CEH process is its ability to achieve equivalent endpoint conversions with approximately 50% lower enzyme loading. Yields of glucose and xylose were increased ~ 15% and ~ 4%, respectively, over batch hydrolysis. Unlike SSF using yeast or Zymomonas, CEH allows precise optimization of pH, temperature, oxygen tension, LPMO mediator concentration, and removal of end-product inhibitors. Conclusions: Advanced CEH holds promise as a transformational, process-intensified, and cost-effective method for producing soluble clarified biomass sugars and insoluble lignin-rich streams. Enhancing saccharification performance, optimizing operating parameters, and employing membrane filtration will help overcome existing challenges and enable the efficient production of valuable biomaterials from lignocellulosic biomass.

09 BIOMASS FUELS↗

Cylinders’ percolation: Decoupling and applications

In this paper we establish a strong decoupling inequality for the cylinder’s percolation process introduced by Tykesson and Windisch (Probab. Theory Related Fields 154 (2012) 165–191). This model features a very strong dependency structure, making it difficult to study, and this is why such decoupling inequalities are desirable. It is important to notice that the type of dependencies featured by cylinder’s percolation is particularly intricate, given that the cylinders have infinite range (unlike some models like Boolean percolation) while at the same time being rigid bodies (unlike processes such as random interlacements). Here our work introduces a new notion of fast decoupling, proves that it holds for the model in question and finishes with an application. More precisely, we prove that for a small enough density of cylinders, a random walk on a connected component of the vacant set is transient for all dimensions d≥3.

97 MATHEMATICS AND COMPUTING↗

Efforts to enhance reproducibility in a human performance research project

Background: Ensuring the validity of results from funded programs is a critical concern for agencies that sponsor biological research. In recent years, the open science movement has sought to promote reproducibility by encouraging sharing not only of finished manuscripts but also of data and code supporting their findings. While these innovations have lent support to third-party efforts to replicate calculations underlying key results in the scientific literature, fields of inquiry where privacy considerations or other sensitivities preclude the broad distribution of raw data or analysis may require a more targeted approach to promote the quality of research output. Methods: We describe efforts oriented toward this goal that were implemented in one human performance research program, Measuring Biological Aptitude, organized by the Defense Advanced Research Project Agency's Biological Technologies Office. Our team implemented a four-pronged independent verification and validation (IV&V) strategy including 1) a centralized data storage and exchange platform, 2) quality assurance and quality control (QA/QC) of data collection, 3) test and evaluation of performer models, and 4) an archival software and data repository. Results: Our IV&V plan was carried out with assistance from both the funding agency and participating teams of researchers. QA/QC of data acquisition aided in process improvement and the flagging of experimental errors. Holdout validation set tests provided an independent gauge of model performance. Conclusions: In circumstances that do not support a fully open approach to scientific criticism, standing up independent teams to cross-check and validate the results generated by primary investigators can be an important tool to promote reproducibility of results.

59 BASIC BIOLOGICAL SCIENCES↗

Temporal contrast degradation from mid-spatial-frequency surface error on stretcher mirrors

Temporal contrast degradation due to mid-spatial-frequency error in chirped-pulse amplification stretcher optics is studied. Third-order cross-correlation measurements reveal a temporal peak that appears when using two different mirrors processed by magnetorheological finishing, despite an improvement in rms roughness compared to a third unprocessed mirror. Simulations based on measured power spectral density show how the actual impact on contrast is different from measurements using a typical bandwidth-limited third-order cross correlator. Furthermore, strategies are proposed to avoid this type of contrast degradation while exploiting computer numerically controlled polishing techniques for enhancement of surface figure and roughness.

47 OTHER INSTRUMENTATION↗

Bacteria isolated from the grape phyllosphere capable of degrading guaiacol, a main volatile phenol associated with smoke taint in wine

Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.

Castro, Claudia [United States Department of Agric↗

Data and scripts associated with: “Burn severity and vegetation type control phosphorus concentration, molecular composition, and mobilization”

This data package is associated with the publication “Burn severity and vegetation type control phosphorus concentration, molecular composition, and mobilization” published in European Geophysical Union - Biogeosciences (Barnes et al. 2025). This study investigates how phosphorus (P) biogeochemistry is altered by burn severity in contrasting types of vegetation chars. This data package documents the workflow used to process and generate the main figures and statistics in the manuscript. The R scripts reference minimally processed P nuclear magnetic resonance (P-NMR) and X-ray absorption near edge structure (P-XANES) data, as well as fully processed data including total elemental composition of the solid chars, total elemental composition of the char leachates (particulate and aqueous phases), and leachate aqueous phase molybdate reactive P concentration. These source data and associated metadata can be found on ESS-DIVE at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1894135 (Grieger et al. 2022; v3). Files and scripts included in this data package finish the processing workflow for P-NMR and P-XANES data. These data can be used to gain a better understanding of bulk chemical changes in chars and their leachates, as well as detailed molecular changes to P. This data package is associated with the GitHub repository found at https://github.com/river-corridors-sfa/rcsfa-RC3-BSLE_P. This data package is comprised of a “data” folder and a series of data processing and analysis scripts. Details on how to recreate the workflow can be found in the Critical Details section of the readme and the “workflow_readme.md” file. The file-level metadata file (file ending in “flmd.csv”) lists all files contained in this data package and descriptions for each. The data dictionary (file ending in “dd.csv”) describes all tabular data columns and their respective definitions and units.

54 ENVIRONMENTAL SCIENCES↗

Spectroscopy of Palladium Nanoparticle Synthesis: Tailoring Nanoparticle Growth Parameters for Hydrogen Storage

Using palladium for hydrogen storage requires palladium (Pd) particles exhibiting specific parameters, including surface area, particle size, and particle shape, with increased interest in palladium nanoparticles (Pd NPs). In order to routinely monitor the synthesis of these particles a spectroscopic method is being developed using infrared (IR), Raman, and UV-Vis spectroscopy. By monitoring the production of Pd NPs, the growth of the NPs can be controlled to ensure quality of the product to match the desired finished particle specifications. For the reaction presented, the conversion of the intermediate tetraamminepalladium(II) chloride (PTC) to diamminepalladium(II) chloride (PDC) can influence the Pd NPs properties. This study is first being developed in lab bench scale quantities to allow ultimate control of the Pd NPs.

08 HYDROGEN↗

New Improved Horizontal Electropolishing System for SRF Cavities

The best performance of niobium SRF accelerating cavities is obtained with surfaces smoothed with electropolishing chemical finishing. Jefferson Lab has recently specified, procured, installed, and commissioned a new versatile production electropolishing (EP) tool. Experience with EP research and operations at JLab as well as vendor interactions and experience guided development of the system specification. Detailed design and fabrication was awarded by contract to Semiconductor Process Equipment Corporation (SPEC). The delivered system was integrated into the JLab chemroom infrastructure and commissioned in 2020. The new EP tool provides much improved heat exchange from the circulating H₂SO₄/HF electrolyte and also the cavity via variable temperature external cooling water flow, resulting in quite uniform cavity wall temperature control and thus improved removal uniformity. With the JLab infrastructure, stabilized process temperature as low as 5 C is available. We describe the system and illustrate operational modes in this contribution.

Reece, C. E.↗

Comprehensive Data Analysis and Analytic Method Development for PBX9501 Material (FY2019 Annual Report of Aging and Lifetimes Program)

In the polymer bonded explosive (PBX) 9501, a binder consisting of 2.5 wt% nitroplasticizer (NP) and 2.5 wt% Estane R 5703 (Estane) is combined with 94.9 wt% of the high-explosive HMX and 0.1 wt% stabilizer. Because of its flexibility and tensile strength, this binder lowers the sensitivity and improves the manufacturability of PBX 9501. However, like many plasticizers comprised of low molecular weight components, NP has a tendency to diffuse out of the PBX 9501 matrix and can decompose at moderate temperatures into reactive byproducts, such as NO, NO 2 , H 2 O, and HNO x . Through oxidation and hydrolysis, these molecules can further degrade NP and Estane, ultimately degrading the properties of PBX 9501. While gaseous molecules can readily diffuse out of the PBX 9501 charges, the intermediates with lower volatility are more likely trapped in the condensed phase inside the charges and, in a closed system, will co-exist with Estane for an extended period of time creating an ongoing reactive environment. Understanding the rates of formation for these volatiles and intermediates during the NP degradation is therefore a critical prerequisite for understanding the long-term stability of polymeric binders used in munition systems. To work toward this ultimate goal, in the past year, we have conducted comprehensive studies on the physical properties of NP and finished three-year long aging experiment to understand the aging behavior of NP under thermal treatment. Important results are summarized in this annual report. Although NP is widely used in the DOE complex, their physical properties are rather scattered and inconsistent in the open literature. For example, there are at least two widely different values, 14.5°C and -15°C, for the melting point of NP. Although it is known that NP is a eutectic 50:50 mixture of BDNPA and BDNPF, their eutectic phase diagram is not well documented. Furthermore, the effect of temperature on the miscibility between water and eutectic BDNPA/F mixture is rarely reported. To fill these knowledge gaps, a large set of BDNPA/F mixtures with BDNPA concentration ranging from 0 to 100 wt% was analyzed using DSC techniques. In addition to determining the eutectic melt point as -25°C, a phase diagram of the BDNPA/F system was constructed from -30°C to 45°C. With this phase diagram, the phase transition temperatures and composition can be readily found for the BDNPA/F mixtures with various mass ratios.

36 MATERIALS SCIENCE↗

Quantum Theory of Semiconductor Photo-Catalysis and Solar Water Splitting / Theory and Computation for Semiconductor Catalysis of Solar Water Splitting / Static and Dynamic Thermal Effects in Solids. Final Report

This is the final report. The finished research was published in 27 journal papers listed below. The topics fall roughly into seven categories: Photochemistry of water at the GaN ($10\bar{1}0$) surface; Quasiparticles: Band electrons and Anharmonic phonons; Quasiharmonic theory; Anharmonic lattice thermal conductivity; Water and Ice; Electron-phonon effects; and, Alloy theory.

36 MATERIALS SCIENCE↗

Binder Jet Tooling for Automotive Lighting Industry. CRADA Final Report

The goal of this collaborative project between Oak Ridge National Laboratory’s (ORNL) Manufacturing Demonstration Facility (MDF) and Grote Industries, LLC was to develop additively manufactured tooling to produce lighting products in a production environment. The project explored the use of metal powder bed systems to rapidly manufacture moderately sized injection molding tools (less than 8” x 8” x 2”) for automotive lamps. The team designed the mold (male and female), manufactured the mold using the binder jet process, experimented with finishing processes, manufactured parts using the molds, and monitored the wear on the mold to predict life.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Evaluation of Radiolysis Data for Hydrogen Gas Generation During Gamma Irradiation of Pre-Corroded and Pristine Aluminum Samples - An Aluminum SNF Dry Storage Study Interim Report

Information and data from radiolysis testing to measure hydrogen (H₂) generated from hydrated oxides on aluminum exposed to ⁶⁰Co radiation were reviewed to evaluate hydrogen generation with radiation dose. Hydrogen generation rate is a primary input to the coupled thermal-chemical system model of the performance of aluminum-clad spent nuclear fuel in a dry storage canister (ASNF-in-canister) over its storage life. Hydrogen generation data and hydrogen generation rate (hydrogen generated per absorbed radiation dose, $\Delta$(H₂)/$\Delta$(dose)) were reported in two reports for radiolysis testing [1, 2]. The testing involved first-time data¹ for radiolytic yield of hydrogen from hydrated-oxides-on-aluminum substrates, and from pristine (non-corroded) aluminum substrates. The laboratory-grown hydrated-oxides-on-aluminum substrates contained a ~ 5 μm film consisting of the trihydroxide bayerite (Al(OH)₃) with amounts of the oxyhydroxide boehmite (AlOOH). These specimens were assumed to also contain physisorbed water (unquantified). The pristine substrates were flat coupons of aluminum that were ground to a 600-grit finish but were not immersed in water to grow a hydrated oxide. The pristine substrates were tested as companion specimens to provide information on hydrogen generation from material without chemisorbed water and were assumed to contain physisorbed water (unquantified).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗