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At least 271 records · Page 15

Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS)

Support customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. Evaluate and improve the integration of ion mobility to existing MS analysis methods of the Mass Profiler Professional workflow (Mass Profiler, ID Browser and Mass Profiler Professional).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

3D high-fidelity automated neutronics guided optimization of fusion blanket designs

The compact Fusion Pilot Plant (FPP) is defined in the recent National Academies of Sciences, Engineering, and Medicine report as the next step of fusion energy demonstration with a $50$ MWe peak net electricity production, $Q_e$ greater than $1$, and at least $3$ hours of continuous operation. This fusion pilot plant will be a test bed enabling materials, designs, and fuel management assessment, and it will represent an engineering challenge because of its high-fusion power and compact design targets. Previous reactor data is limited to experiments operating in different design space ranges. Therefore, design iterations and assessments should rely on high-fidelity first-principle theoretical and computational models. The high-fidelity integrated modeling of the plasma is a fundamental part of fusion energy research. However, the whole device modeling is often neglected, utilizing low-fidelity, system-level analysis. Recently, the need for high-fidelity multi-physics modeling was recognized, resulting in a selection of integrated tools. Further, autonomous design optimization requires a streamlined framework that perturbs the design point, reruns the analysis, and examines the outputs. However, high-fidelity analysis requires complex geometry specification that is difficult to perturb. This work presents the parametric CAD generation tool TRACER and a new neutronic workflow. TRACER allows the perturbation of the geometry representation, creating geometry files ready for further analysis. The streamlined neutronic workflow allows efficient and accurate calculations. The two new tools coupled together were used to perform a 3D high-fidelity multi-objective, multi-input optimization of an "ARC Class" compact tokamak design. The workflow was driven by an optimization driver for full automation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Image-based symptom scoring of plant diseases is a powerful tool for associating disease resistance with plant genotypes. Advancements in technology have enabled new imaging and image processing strategies for statistical analysis of time-course experiments. There are several tools available for analyzing symptoms on leaves and fruits of crop plants, but only a few are available for the model plant Arabidopsis thaliana (Arabidopsis). Arabidopsis and the model fungus Botrytis cinerea (Botrytis) comprise a potent model pathosystem for the identification of signaling pathways conferring immunity against this broad host-range necrotrophic fungus. Here, we present two strategies to assess severity and symptom progression of Botrytis infection over time in Arabidopsis leaves. Thus, a pixel classification strategy using color hue values from red-green-blue (RGB) images and a random forest algorithm was used to establish necrotic, chlorotic, and healthy leaf areas. Secondly, using chlorophyll fluorescence (ChlFl) imaging, the maximum quantum yield of photosystem II (Fv/Fm) was determined to define diseased areas and their proportion per total leaf area. Both RGB and ChlFl imaging strategies were employed to track disease progression over time. This has provided a robust and sensitive method for detecting sensitive or resistant genetic backgrounds. A full methodological workflow, from plant culture to data analysis, is described.

59 BASIC BIOLOGICAL SCIENCES↗

Model Diagnostics for Equation Oriented Models: Roadblocks and the Path Forward

This poster was presented at the Foundations of Computer Aided Process Design (FOCAPD) 2024 conference with a paper describing efforts to develop a unified workflow and toolbox for diagnosing issues in equation-oriented models as part of the IDAES modeling framework. The poster presents the work currently underway within the IDAES project to develop and integrate cutting edge model analysis techniques into a common toolbox and workflow for model developers to use.

Lee, Andrew↗

Model Diagnostics for Equation Oriented Models: Roadblocks and the Path Forward

Conference paper for FOCAPD24 describing efforts to develop a unified workflow and toolbox for diagnosing issues in equation-oriented models as part of the IDAES modeling framework. The paper presents the work currently underway within the IDAES project to develop and integrate cutting edge model analysis techniques into a common toolbox and workflow for model developers to use.

Lee, Andrew↗

Data Federation Challenges in Remote Near-Real-Time Fusion Experiment Data Processing

Fusion energy experiments and simulations provide critical information needed to plan future fusion reactors. As next-generation devices like ITER move toward long-pulse experiments, analyses, including AI and ML, should be performed in a wide range of time and computing constraints, from near-real-time constraints, between-shot analysis, and to campaign-wide long-term analysis. However, the data volume, velocity, and variety make it extremely challenging for analyses using only local computational resources. Researchers need the ability to compose and execute workflows spanning edge resources to large-scale high-performance computing facilities.We present Delta, a system to address data analysis challenges, including AI/ML, in fusion science, by leveraging the ADIOS I/O library and middleware, to support executing science workflows over the wide area network for near-real-time streaming. We discuss the data federation challenges in performing remote workflows, focusing on on-going research work in (1) managing, reducing, and streaming data to minimize I/O and data movement overheads, (2) decompressing and reorganizing data for analysis, and (3) executing workflows for automated data analysis. We introduce examples for deep-learning based data analysis for the fusion domain and demonstrate how we use Delta to construct end-to-end workflows for a fusion device in Korea, connecting a remote DOE facility in the USA. The capability demonstrated by this project is the basis for improving the state of the art for near-real-time data federation amongst remote facilities.

Choi, Jong Youl↗

Catching the Killer: Dynamic Disorder Design Rules for Small–Molecule Organic Semiconductors

Small-molecule organic semiconductors are promising materials for applications ranging from solar cells to medical sensors. Their nearly infinite design space means that, in theory, it is possible to tailor the material to the exact specifications of a particular application. In reality; however, design rules to improve mobility (μ) remain elusive because of the complex calculations required to understand its limiters. Transient localization theory posits that charge carriers are slowed down by the collective phonon motions, called dynamic disorder, which localize charge carriers temporarily. Traditionally, a mode-by-mode analysis is performed to try and identify “killer” modes. Herein, the flaws are demonstrated with this analysis and present a streamlined simulation workflow that simplifies simulation of dynamic disorder and enables engineering of new molecular structures based on phonon dynamics. This workflow is combined with a novel visualization technique that enables per-atom insights into how μ is limited. Furthermore, this workflow is applied and analyzed to a series of -acenes and a series of BTBT-based molecules. Then design rules are identified in each series that identify possible ways to improve the μ beyond current experimental limits using phonon engineering.

36 MATERIALS SCIENCE↗

A coupled fluid-mechanical workflow to simulate the directed energy deposition additive manufacturing process

Simulation of additive manufacturing processes can provide essential insight into material behavior, residual stress, and ultimately, the performance of additively manufactured parts. In this work, we describe a new simulation based workflow utilizing both solid mechanics and fluid mechanics based formulations within the finite element software package SIERRA (Sierra Solid Mechanics Team in Sierra/Solid Mechanics 4.52 User’s Guide SAND2019-2715. Technical report, Sandia National Laboratories, 2011) to enable integrated simulations of directed energy deposition (DED) additive manufacturing processes. In this methodology, a high-fidelity fluid mechanics based model of additive manufacturing is employed as the first step in a simulation workflow. This fluid model uses a level set field to track the location of the boundary between the solid material and background gas and precisely predicts temperatures and material deposition shapes from additive manufacturing process parameters. Next, the resulting deposition shape and temperature field from the fluid model are then mapped into a solid mechanics formulation to provide a more accurate surface topology for radiation and convection boundary conditions and a prescribed temperature field. Solid mechanics simulations are then conducted to predict the evolution of material stresses and microstructure within a part. By combining thermal history and deposition shape from fluid mechanics with residual stress and material property evolutions from solid mechanics, additional fidelity and precision are incorporated into additive manufacturing process simulations providing new insight into complex DED builds.

36 MATERIALS SCIENCE↗

Morphologically-Directed Raman Spectroscopy as an Analytical Method for Subvisible Particle Characterization in Therapeutic Protein Product Quality

Abstract Subvisible particles (SVPs) are a critical quality attribute of injectable therapeutic proteins (TPs) that needs to be controlled due to potential risks associated with drug product quality. The current compendial methods routinely used to analyze SVPs for lot release provide information on particle size and count. However, chemical identification of individual particles is also important to address root-cause analysis. Herein, we introduce Morphologically-Directed Raman Spectroscopy (MDRS) for SVP characterization of TPs. The following particles were used for method development: (1) polystyrene microspheres, a traditional standard used in industry; (2) photolithographic (SU-8); and (3) ethylene tetrafluoroethylene (ETFE) particles, candidate reference materials developed by NIST. In our study, MDRS rendered high-resolution images for the ETFE particles (> 90%) ranging from 19 to 100 μm in size, covering most of SVP range, and generated comparable morphology data to flow imaging microscopy. Our method was applied to characterize particles formed in stressed TPs and was able to chemically identify individual particles using Raman spectroscopy. MDRS was able to compare morphology and transparency properties of proteinaceous particles with reference materials. The data suggests MDRS may complement the current TPs SVP analysis system and product quality characterization workflow throughout development and commercial lifecycle.

Science & Technology - Other Topics↗

Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins

Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS), where only terminal fragments are assigned for disulfide-intact proteins, can access disulfide information, but suffers from low fragmentation efficiency, thereby limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide-intact proteins by 20–60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. Further, the inclusion of internal fragments can extend the sequence information of disulfide-intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into the TD-MS workflow for analyzing disulfide-intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody–drug conjugates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimization of distributed compute resources utilization in the CMS Global Pool

The CMS Submission Infrastructure is the primary system for managing computing resources for CMS workflows, including data processing, simulation, and analysis. It integrates geographically distributed resources from Grid, HPC, and cloud providers into federated pools managed by HTCondor and Glidein- WMS, for a total of around 500k CPU cores. This system dynamically manages workloads based on priorities defined by the collaboration. Additionally, CMS scheduling strategies must be flexible to handle multiple concurrent workloads while considering changing processing demands and resource availability from various providers.Efficient utilization of vast amounts of distributed compute resources is a key element for the success of the scientific programs of the LHC experiments. Optimizing the system is essential to maximize resource efficiency and fully utilize the distributed computing power. The CMS Submission Infrastructure team thus systematically investigates sources of inefficiency in workload scheduling to reduce their impact. In addition, a strategy of pilot overloading has been introduced to compensate for other inefficiency sources, thereby optimizing resource utilization and enhancing computational throughput.

Mascheroni, Marco [UC, San Diego (main)]↗

Assessing correlated truncation errors in modern nucleon-nucleon potentials

We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semilocal momentum-space implementation of the chiral EFT (𝜒⁢EFT ) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a 𝜒⁢EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are that, first, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter 𝑄 must be well chosen for the coefficients to exhibit a regular convergence pattern—a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for 𝑄, the EFT breakdown scale Λ 𝑏 , the scale associated with soft physics in the 𝜒⁢EFT potential 𝑚 eff , and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other 𝜒⁢EFT NN potentials.

Bayesian methods↗

Addressing qubits with a software-defined radio FPGA (Full Technical Final Report)

Superconducting transmons can be configured as qubits and can also be used for weak signal axion searches. During a prior LDRD (17-ERD-006), a robust capability for system simulation and analysis, algorithm development, algorithm to FPGA workflow and experimental measurements was developed. During that project it was determined that a new software-defined radio FPGA would be a significant improvement in cost, simplicity, and software maintainability over the X6-1000M FPGA plus RF front-end system that had been used. In this Feasibility Study, we successfully developed the interface to the new NI USRP-2954R SDR platform, generated and optimized the VHDL of the existing algorithms, and experimentally tested the new FPGA system on real qubit in the laboratory. These tests showed it had the same SNR on weak measurements as the prior FPGA.

42 ENGINEERING↗

A Technical and Economic Assessment of LWR Flexible Operation for Generation and Demand Balancing to Optimize Plant Revenue

With increased penetration of subsidized variable renewable energy (VRE) resources and competition from low natural gas prices, existing light water reactor (LWR) nuclear power plants (NPPs) are struggling to remain economically competitive. This work examines the potential economic competitiveness of various thermal energy storage (TES) technologies when coupled directly or indirectly with a NPP. To highlight their relative economic competitiveness, we contrast several energy storage solutions in stochastic dispatch optimization. We leverage data from recent work analyzing a range of TES technologies with varying capital costs, performance, and technology readiness level (TRL) to establish our case. We explore inserting these technologies into an electricity market with existing nuclear generation and large projected variable renewable energy (VRE) penetration. Although these technologies' projected capital costs may make them unlikely candidates in their current state, this analysis demonstrates a high-fidelity techno-economic analysis of energy storage. Furthermore, as the projected cost of energy storage technologies evolves, this analysis sets a precedent for similar future investigations. One region with projected trends that may be unfavorable for existing nuclear capacity is the New York Independent System Operator (NYISO) market. New York state’s baseload generation has been historically provided by fossil-fired and nuclear assets. However, amid economic pressures from subsidized VREs and low natural gas prices, the state has recently deactivated Indian Point nuclear power plant units 2 and 3. Furthermore, the state plans to meet its zero-emission generation target by 2040 by replacing fossil-fired capacity with significant investments in VRE resources like wind and solar photovoltaic (PV) and battery storage. Increased intermittent resource penetration lowers the baseload power requirement, adding further economic pressure to the state’s three remaining NPPs still in operation. With three NPPs still in operation in New York, this work analyzes potential economic benefits to NPPs on the New York grid when directly or indirectly coupled with various TES technologies. This work requires two modeling steps to analyze the potential economic benefits of various system configurations of the TES directly or indirectly coupled with nuclear. First, this analysis leverages capacity expansion modeling by experts at the Electric Power Research Institute (EPRI). Using their deterministic capacity expansion model, U.S. Regional Economy, Greenhouse Gas, and Energy (US-REGEN), EPRI analysts evaluated the capacity and generation evolution of the New York state energy market under four projection scenarios. These four projection scenarios were developed to represent the potential evolution of the capacity and generation in NYISO from 2015 to 2050 under various economic, technology, and policy constraints. The results from these capacity expansion models are then used as boundary conditions in the second modeling step. The second modeling step uses the Holistic Energy Resource Optimization Network (HERON) for a set of stochastic techno-economic analyses (STEAs) to investigate the potential increase in the economic viability of various configurations of the TES. With no current capacity expansion capabilities, HERON takes the data generated from US-REGEN for 2050 to generate synthetic load, solar, and wind data. Then HERON economically optimizes the capacity and dispatch of the various TES configurations. The potential economic benefit is the differential net present value (NPV) of the TES configurations from the no-TES baseline. As a stochastic techno-economic analysis package, HERON introduces uncertainty into the economic metrics, while US-REGEN trades resolution for reduced computational complexity. Using HERON also allows the modeling of direct thermal coupling, a feature not common in capacity and dispatch models. As expected, with high capital costs, the costs of introducing energy storage for all the technologies considered outweighed the potential economic benefit of this strategy for flexible plant operation. The benefit of this analysis is primarily in demonstrating a workflow that examines innovative solutions to increase NPP revenue via TES coupling. HERON’s stochastic capacity and dispatch optimization process used in this work has proven an effective tool in observing and evaluating the impact of introducing storage technologies in a grid energy system.

25 ENERGY STORAGE↗

pvplr-python: Python package implementation of PVplr for Performance Loss Rate (PLR) analysis

Due to software fragmentation, PV system modeling teams can be limited to language specific packages, preventing cross-sectional analysis of different modeling techniques and workflows. To this end, PVplr, a popular PV performance modeling R software package, has been ported to the Python programming language. To verify and test the robustness of the port, NSRDB data has been used to simulated PV installations at native resolution (~2 million Sites), with a variety of degradation rates, degradation patterns, and modules. Performance Ratios were calculated using the ported functions from pvplr-python and compared against Rdtools YoY values. Due to the complicated nature of degradation, a new metric has been proposed to quantify the performance loss of a system. The cumulative production loss, is the total amount of energy lost due to the degrading performance of the system. Cumulative production loss alleviates the problems with fitting linear functions to non-linear degradation. Cumulative Production loss was shown to better estimate the total lost revenue for non-linear degradation patterns. $XbX + UTC$ was found to most accurately predict the total lost revenue in simulated systems.

Kumar, Suraj↗

M3SF-24LL010302052-Comprehensive Analysis of Radionuclide Interaction with Hydrothermally Altered Repository Materials

This progress report (Level 3 Milestone Number M3SF-24LL010302052) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline Work Package Number SF-24LL01030205. The research is focused on actinide and radionuclide sequestration in hydrothermally altered repository materials. In FY24, we completed a rigorous analysis of Se sorption to iron oxide phases using our L-SCIE sorption database. This effort explicitly accounts for surface titration behavior of oxide surfaces that was the subject of a recently published manuscript (Han et al., 2023). With this in mind, our Se sorption analysis now yields a more robust workflow for developing self-consistent surface complexation modeling approaches that can be adapted to specific SCM conceptual and numerical approaches (i.e. non-electrostatic, diffuse layer, triple layer models). In late FY24, we plan to publish the results of our comprehensive surface complexation modeling of Se(IV) and Se(VI) sorption to iron oxide mineral phases and provide a path forward to developing robust radionuclide sorption models for use in performance assessment. In FY24, we also submitted a manuscript summarizing our approach to integrating radionuclide sorption and coprecipitation phenomena and evaluation of radionuclide partitioning values across a range of radionuclides relevant to performance assessment. We demonstrated our approach in detail using Se sorption and coprecipitation with iron oxide minerals as a test case. This manuscript was recently accepted for publication in Applied Geochemistry (Balboni et al., Accepted). We also continued experiments to identify radionuclide interaction with hydrothermally altered crystalline repository and backfill materials. Recent research performed at Los Alamos National Laboratory (LANL) and Sandia National Laboratory (SNL) has provided key insights regarding the hydrothermal alteration behavior of bentonite backfill in the presence of repository materials (steel, concrete, etc.). We are now examining how mineral alteration affects retardation behavior of a suite of radionuclides of interest to repository performance assessment. These experiments also allow us to test the predictive ability of our component additivity approach to surface complexation and ion exchange. Our guiding hypothesis is that a robust surface complexation/ion exchange model and associated database, developed using our L-SCIE approach, can effectively predict changes in radionuclide sorption behavior resulting from the hydrothermal alteration of mineralogy in a repository near field. A short update of results to date is presented below.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Analyzing the Impact of Future Weather Data on Energy Consumption in Weatherization Assistant

This study supports the mission of the U.S. Department of Energy’s Weatherization Assistance Program (WAP), which aims to increase the energy efficiency of dwellings and reduce their total residential expenditures. Specifically, we examine how projected future climate conditions may affect residential building energy performance by integrating future weather data into the National Energy Audit Tool (NEAT). Since WAP evaluates the cost-effectiveness of retrofit measures over lifespans of up to 30 years, accounting for evolving climate conditions is increasingly important. To reflect future household energy demands, this study replaces historically based Typical Meteorological Year (TMY3) weather inputs with Future Typical Meteorological Year (fTMY) datasets derived from global climate model (GCM) projections. A simulation-based framework was established to enable NEAT analysis under future weather conditions. This workflow involves converting EPW-format weather files into JSON inputs compatible with NEAT and generating degree-hour metrics needed for load calculations. The fTMY dataset used in this study was developed by Oak Ridge National Laboratory through downscaling of six GCMs under different emission scenarios and covers the period from 2020 to 2100. In contrast, the TMY3 dataset is based on historical weather data from 1961 to 1990. Simulations were conducted for benchmark single-family prototype buildings across ASHRAE climate zones 1–7, which cover all regions of the U.S. except the subarctic Zone 8 in northern Alaska, evaluating both heating and cooling loads under TMY3 and fTMY conditions. Four foundation types were tested, while heating systems were standardized, as NEAT does not differentiate thermal energy load by HVAC system type in its load calculations. Results show that fTMY weather input consistently yield lower heating loads and higher cooling loads across most locations, aligning with expected climate warming trends. Notably, colder regions such as zones 6A, 6B, and 7 experience marked reductions in heating load, while warmer and transitional zones, such as 2A (Lufkin, TX) and 3C (San Francisco, CA), have substantial increases in cooling loads. Although this study does not directly assess the performance of retrofit measures under future climate conditions, it provides a critical foundation for doing so. By quantifying shifts in baseline (i.e., pre-retrofit case) energy loads between historical and future weather files, the study highlights the importance of integrating climate-responsive data into audit tools. These findings will inform future efforts to evaluate the long-term effectiveness and cost-effectiveness of weatherization measures under changing climate conditions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Toward a persistent event-streaming system for high-performance computing applications

High-performance computing (HPC) applications have traditionally relied on parallel file systems and file transfer services to manage data movement and storage. Alternative approaches have been proposed that use direct communications between application components, trading persistence and fault tolerance for speed. Event-driven architectures, as popularized in enterprise contexts, present a compelling middle ground, avoiding the performance cost and API constraints of parallel file systems while retaining persistence and offering impedance matching between application components. However, adapting streaming frameworks to HPC workloads requires addressing challenges unique to HPC systems. This paper investigates the potential for a streaming framework designed for HPC infrastructures and use cases. We introduce Mofka, a persistent event-streaming framework designed specifically for HPC environments. Mofka combines the capabilities of a traditional streaming service with optimizations tailored to the HPC context, such as support for massively multicore nodes, efficient scaling for large producer-consumer workflows, RDMA-enabled high-performance network communications, specialized network fabrics with multiple links per node, and efficient handling of large scientific data payloads. Built using the Mochi suite of HPC data service components, Mofka provides a lightweight, modular, and high-performance solution for persistent streaming in HPC systems. We present the architecture of Mofka and evaluate its performance against Kafka and Redpanda using benchmarks on diverse platforms, including Argonne's Polaris and Oak Ridge's Frontier supercomputers, showing up to 8× improvement in throughput in some scenarios. We then demonstrate its utility in several real-world applications: a tomographic reconstruction pipeline, a workflow for the discovery of metal-organic frameworks for carbon capture, and the instrumentation of Dask workflows for provenance tracking and performance analysis.

HPC↗