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At least 919 records · Page 51

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DOE OSTI2021

Towards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometry

Top-down mass spectrometry (TD-MS) generates fragment ions that returns information on the polypeptide amino acid sequence. In addition to terminal fragments, internal fragments that result from multiple cleavage events can also be formed. Traditionally, internal fragments are largely ignored due to a lack of available software to reliably assign them, mainly caused by a poor understanding of their formation mechanism. To accurately assign internal fragments, their formation process needs to be better understood. Here we applied a statistical method to compare fragmentation patterns of internal and terminal fragments of peptides and proteins generated by collisionally activated dissociation (CAD). Internal fragments share similar fragmentation propensities with terminal fragments (e.g., enhanced cleavages N-terminal to proline and C-terminal to acidic residues), suggesting that their formation follows conventional CAD pathways. Internal fragments should be generated by subsequent cleavages of terminal fragments and their formation can be explained by the well-known mobile proton model. Additionally, internal fragments can be coupled with terminal fragments to form complementary product ions that span the entire protein sequence. These enhance our understanding of internal fragment formation and can help improve sequencing algorithms to accurately assign internal fragments, which will ultimately lead to more efficient and comprehensive TD-MS analysis of proteins and proteoforms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Validating automated resonance evaluation with synthetic data

The integrity and precision of nuclear data are crucial for a broad spectrum of applications, from national security and nuclear reactor design to medical diagnostics, where the associated uncertainties can significantly impact outcomes. A substantial portion of uncertainty in nuclear data originates from the subjective biases in the evaluation process, a crucial phase in the nuclear data production pipeline. Recent advancements indicate that automation of certain routines can mitigate these biases, thereby standardizing the evaluation process and enhancing reproducibility. This research aims to provide a methodology, framework, and metrics for the validation of automated nuclear data evaluation software leveraging high-quality synthetic data that closely mimic real experimental observables. An introduced error metric provides a scale and intuitive measure of the evaluation quality by quantifying the estimate’s accuracy and performance across the specified energy range. Synthetic data provides access to experimental observables and underlying resonance parameters, enabling comparison of different evaluations. The methodology is demonstrated using Ta-181 isotope data in the resolved resonance region. The Automated Resonance Identification Subroutine (ARIS), which operates without prior resonance information, was used to test and showcase the framework’s capabilities utilizing the proposed error metrics. The results demonstrate the effectiveness of the proposed approach and framework for optimizing software parameters and testing hypotheses through “what-if” controlled experiments, such as modifying assumptions about experimental conditions or average resonance parameters.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Machine learning framework for predicting uranium enrichments from M400 CZT gamma spectra

A machine learning framework was developed for predicting uranium enrichments from M400 CZT gamma spectra. This framework leverages the availability of a large amount of measured M400 gamma spectra and uses a recently updated version of Gamma Detector Response and Analysis Software (GADRAS) for gamma spectrum analysis and generation. It also leverages the existing machine learning modules in Python for gamma spectrum data processing, curation, model training, benchmarking, and optimization of the deep machine learning models. The framework is used to develop a deep learning model to analyze gamma spectra from a set of U 3 O 8 samples with enrichments ranging from 0.31 to 93.17% and UF 6 cylinders with enrichments ranging from 0.2 to 4.95%, and the model performance is tested using a set of measured spectra and the respective declared enrichment values. Results show that the model can correctly classify 99.35% of the U 3 O 8 sample enrichments, and can predict the samples’ enrichments within an average absolute error of 0.099% (in percentage points of enrichment). For the UF 6 cylinders, the average absolute error was approximately 0.03%, with an accuracy of 98% in classifying discrete enrichment values of UF 6 samples. Finally, the results also show that the model has performed significantly better in terms of predicting enrichments in UF 6 cylinders based on measured gamma spectra than the GEM code, with a standard deviation (of the relative errors) of 2.23% (compared with the 11.51% value for the GEM code) based on results from a set of test data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Economic and embodied energy analysis of integrated circuit manufacturing processes

Integrated circuits (ICs) are the fundamental microelectronic building blocks of typical information and communication technology (ICT) devices such as laptops and smartphone. With the emergence of faster and cheaper low-power ICs for the growing ICT market, there is a limited information on their manufacturing energy and economic impacts owing to the lack of recurrent upgradation of proprietary IC manufacturing process data. In this work, economic and life cycle energy assessments (LCAs) of IC manufacturing and assembly processes were conducted using the latest bill of materials (BOM) manufacturing data in a state-of-the-art IC manufacturing cost software tool developed by IC Knowledge, LLC. IC manufacturing cost was estimated to be $\$$1.00-$\$$5.00/cm 2 ; the high-end cost represents the most advanced 3D NAND IC technology with the Wafer Level Chip Scale Package cost of $4/cm 2 . Total cumulative energy demand (CED) estimates of IC manufacturing using the OpenLCA software ranged from 9 to 38 MJ/cm 2 or 56–235 BJ/month with the largest share (~ 75%) from on-site energy. The IC manufacturing CED is projected to increase with the progress in IC technology node, which has increased by more than two times for technology node evolution from 110 to 14 nm. Furthermore, the representative detailed BOM data were considered to reduce the CED uncertainties of the estimated standard deviation of 35%- 42%.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

VDiSC: An Open Source Framework for Distributed Smart City Vision and Biometric Surveillance Networks

Recent global growth in the interest of smart cities has led to trillions of dollars of investment toward research and development. These connected cities have the potential to create a symbiosis of technology and society and revolutionize the cost of living, safety, ecological sustainability, and quality of life of societies on a world-wide scale. Some key components of the smart city construct are connected smart grids, self-driving cars, federated learning systems, smart utilities, large-scale public transit, and proactive surveillance systems. While exciting in prospect, these technologies and their subsequent integration cannot be attempted without addressing the potential societal impacts of such a high degree of automation and data sharing. Additionally, the feasibility of coordinating so many disparate tasks will require a fast, extensible, unifying framework. To that end, we propose the Distributed Smart City framework for Vision, or VDiSC. VDiSC serves as a unified biometric API harness that allows for seamless evaluation, deployment, and simple pipeline creation for heterogeneous biometric software. VDiSC additionally provides a fully declarative capability for defining and coordinating custom machine learning and sensor pipelines, allowing the distribution of processes across otherwise incompatible hardware and networks. VDiSC ultimately provides a way to quickly configure, hot-swap, and expand large coordinated or federated systems online without interruptions for maintenance. Because much of the data collected in a smart city contains Personally Identifying Information (PII), VDiSC also provides built-in tools and layers to ensure secure and encrypted streaming, storage, and access of PII data across distributed systems.

Brogan, Joel↗

DOE OSTI2023

Implementation and Demonstration of P4 Software for Improving ICS Protocol Visibility and Control [Slides]

No prior enabling funded work applicable to this proposal. Programming Protocol-independent Packet Processors (P4) is an open source, domain-specific programming language for network switching devices. P4 complements traditional Software Defined Networking (SDN) which is primarily concerned with the management of packets (e.g. routing/dropping decisions) rather than how each packet is processed. The introduction of P4 provided new capabilities (e.g. firewall, load balancing, enhanced security) but has primarily been deployed in data centers. This effort investigates ways to expand P4 into other niches such as ICS networks.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

GADRAS-DRF Enhancements for Safeguards – Custom Peak Fitting to Enhance Model Fitting and Isotopics

One major software update was accomplished within the Gamma Detector Response and Analysis Software-Detector Response Function (GADRAS-DRF) package. This update allows users to adjust individual peak fits for use in subsequent analysis processes within GADRAS-DRF. A graphical user interface (GUI) was implemented so users can see the effect of their fit adjustments on the spectrum. This new feature will enhance the capability of the previously funded auto-enrichment and peak-based 1D model fit feature that was implemented in FY23 (Fiscal Year). Isotopic analysis was performed using M400 data obtained from uranium standards and the isotopic assessment is given with and without manual peak adjustments.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2025

EJFAT Scientific Perspective

Presented new computing model to the test by deploying the EJFAT system alongside a data-stream processing framework running the production-level CLAS12 event reconstruction application. In this experiment, a continuous stream of CLAS12 Level-1 identified events was processed in real-time using the EJFAT load balancer, distributing the workload across 90 computing nodes located across the U.S. This marks the first-ever large-scale, real-time distributed data stream processing experiment, demonstrating that scientific data-streaming pipelines can efficiently scale across four dimensions, thanks to EJFAT’s advanced hardware and software capabilities.

Gyurjyan, Vardan [Thomas Jefferson National Accele↗

DOE OSTI2026

Persistent DynAMICS

Persistent DynAMICS is a lightweight software platform that enables distributed sensing systems to operate as a unified, responsive network. It integrates with existing sensors, data systems, and processing tools as an overlay, without requiring hardware replacement or increasing user burden. As data is collected, the system identifies situations that require additional attention and directs selected sensors to gather more information. For example, if a sensor detects an unusual condition along a pipeline, the system can task nearby sensors or different sensing modalities to confirm the event and focus data collection where it is needed. To support this, the platform forms temporary groups of sensors that work together to address specific objectives. Once complete, these groups are dissolved and resources are reassigned as needed. Communication is handled through an integrated messaging framework with client and server components, enabling reliable operation and data continuity even in low-bandwidth or intermittent connectivity environments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗

DOE OSTI2021

Moab Desert Crust - Sample 4E

Chivian, Dylan↗

DOE OSTI2025

Machine Learning-Driven Conservative-to-Primitive Conversion in Hybrid Piecewise Polytropic and Tabulated Equations of State

We present a novel machine learning (ML)-based method to accelerate conservative-to-primitive inversion, focusing on hybrid piecewise polytropic and tabulated equations of state. Traditional root-finding techniques are computationally expensive, particularly for large-scale relativistic hydrodynamics simulations. To address this, we employ feedforward neural networks (NNC2PS and NNC2PL), trained in PyTorch (2.0+) and optimized for GPU inference using NVIDIA TensorRT (8.4.1), achieving significant speedups with minimal accuracy loss. The NNC2PS model achieves 𝐿 1 and 𝐿 ∞ errors of 4.54 × 10 −7 and 3.44 × 10−6, respectively, while the NNC2PL model exhibits even lower error values. TensorRT optimization with mixed-precision deployment substantially accelerates performance compared to traditional root-finding methods. Specifically, the mixed-precision TensorRT engine for NNC2PS achieves inference speeds approximately 400 times faster than a traditional single-threaded CPU implementation for a dataset size of 1,000,000 points. Ideal parallelization across an entire compute node in the Delta supercomputer (dual AMD 64-core 2.45 GHz Milan processors and 8 NVIDIA A100 GPUs with 40 GB HBM2 RAM and NVLink) predicts a 25-fold speedup for TensorRT over an optimally parallelized numerical method when processing 8 million data points. Moreover, the ML method exhibits sub-linear scaling with increasing dataset sizes. We release the scientific software developed, enabling further validation and extension of our findings. By exploiting the underlying symmetries within the equation of state, these findings highlight the potential of ML, combined with GPU optimization and model quantization, to accelerate conservative-to-primitive inversion in relativistic hydrodynamics simulations.

conservative-to-primitive conversion↗

DOE OSTI2022

Tsdat: An Open-Source Data Standardization Framework for Marine Energy and Beyond: Preprint

Many organizations are tasked with the collection and processing of large quantities of data from various measurement devices. Data reported from these sources are often not interoperable with datasets and software used by analysts and other organizations in the same field, introducing barriers for collaboration on large-scale projects. This poses a particular problem for cross-device comparisons and machine learning applications. To address these challenges, the open source Time-Series Data Pipelines (Tsdat) software was developed by a joint collaboration between Pacific Northwest National Laboratory, the National Renewable Energy Laboratory, and Sandia National Laboratories to facilitate collaboration and accelerate advancements in the Marine Energy domain through the development of an open-source ecosystem of tools. This paper will describe the Tsdat software and the data standards within which the framework operates. A beta version of the framework has been released and is currently being used by several projects in marine energy, wind energy, and building energy systems.

big data↗

DOE OSTI2021

Deep Learning Systems for Increased Safeguards Surveillance Review Productivity

Nuclear safeguards inspectors expend significant time and maintain intense focus in reviewing video surveillance for safeguards relevant events. To increase efficiency and reduce the time burden of safeguards inspectors performing surveillance data review, this paper presents a novel deep learning (DL) systems concept to integrate generalized DL models into the safeguards surveillance review workflow. The Agency is investigating several DL algorithms for object recognition, localization, tracking, and flagging relevant activities. The project team is working closely with nuclear safeguards inspectors to identify review use cases (based on specific safeguards objectives) and collect their associated requirements. We focused on CANDU and LWR Nuclear Power Plants (NPPs) and their associated dry storage areas as these present a particularly heavy burden on the inspector surveillance review process due to the number of these facilities under safeguards worldwide. Initial DL algorithm results on safeguards data are promising. Using a convolutional neural network, the team attained a mean average precision (mAP) of 92.9% identifying and localizing spent fuel (SF) casks from a 475 surveillance image dataset. Further, the team had initial success in training a recurrent neural network to identify reactor area activities in video clips, successfully indicating when SF casks enter or exit a pool. We discuss how such DL algorithms would be integrated into the Next Generation Surveillance Review (NGSR) software application. Another issue impacting review productivity is the long time inspectors may have to wait when running these algorithms in NGSR. We present a concept to pre-process remotely collected surveillance data with DL models as the data arrives to IAEA headquarters so that results are already available when starting a new review in NGSR. The proposed DL system concept shows a pathway and workflow for increasing an inspector’s surveillance review productivity by quickly and accurately identifying declared and undeclared safeguards relevant objects and activities in large quantities of surveillance imagery data.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2026

Hardware Aware Mitigation of Timing Side-Channel Vulnerabilities in Critical Infrastructure Software

Program runtime/timing attacks exploit variations in a program’s execution times to extract sensitive information from the program (e.g. encryption keys, sensitive variable data, intellectual property). State-of-the-art solutions to runtime sidechannel attacks attempt to balance the execution time of the sensitive code for different control flow paths to eliminate the timing leakage. However, during the mitigation process, most techniques do not consider the underlying hardware/device on which the target program is supposed to run on. This can lead to over-fixing (unnecessary extra operations), under-fixing (not solving the imbalance properly), and even failures. We propose DISARM, a joint hardware-software methodology (unlike any existing solution) for mitigating runtime side-channel vulnerabilities that utilizes timing values from real embedded devices to generate targeted software fixes. We implement DISARM to support C/C++/Java source codes and validate it across 22 standard benchmarks. DISARM outperforms state-of-the-art solutions such as PENDULUM and DifFuzzAR in terms of execution time overhead (up to −46%), code size overhead (up to −10%), and correctness (no failures) on five different embedded/edge devices.

Suha, Tasneem [University of Maine]↗

DOE OSTI2024

Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units

Atomic structure prediction and associated property calculations are the bedrock of chemical physics. Since high-fidelity ab initio modeling techniques for computing the structure and properties can be prohibitively expensive, this motivates the development of machine-learning (ML) models that make these predictions more efficiently. Training graph neural networks over large atomistic databases introduces unique computational challenges such as the need to process millions of small graphs with variable size and support communication patterns that are distinct from learning over large graphs such as social networks. We demonstrate a novel hardware-software co-design approach to scale up the training of atomistic graph neural networks (GNN) for structure and property prediction. First, to eliminate redundant computation and memory associated with alternative padding techniques and to improve throughput via minimizing communication, we formulate the effective coalescing of the batches of variable-size atomistic graphs as the bin packing problem and introduce a hardware-agnostic algorithm to pack these batches. In addition, we propose hardware-specific optimizations including a planner and vectorization for the gather-scatter operations targeted for Graphcore’s Intelligence Processing Unit (IPU), as well as model-specific optimizations such as merged communication collectives and optimized softplus. Putting these all together, we demonstrate the effectiveness of the proposed co-design approach by providing an implementation of a well-established atomistic GNN on the Graphcore IPUs. We evaluate the training performance on multiple atomistic graph databases with varying degrees of graph counts, sizes and sparsity. Here, we demonstrate that such a co-design approach can reduce the training time of atomistic GNNs and can improve the performance by up to 1.5× compared to the baseline implementation of the model on the IPUs. Additionally, we compare our IPU implementation with a Nvidia GPU-based implementation and show that our atomistic GNN implementation on the IPUs can run 1.8× faster on average compared to the execution time on the GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Distributing User Code with the CernVM FileSystem

The CernVM FileSystem (CVMFS) is widely used in High Throughput Computing to efficiently distributed experiment code. However, the standard CVMFS publishing tools are designed for a small group of people from each experiment to maintain common software, and the tools are not a good fit for publishing software from numerous users in each experiment. As a result, most user code, such as code to do specific physics analyses, is still sent with every job to the place the job is run. That process is relatively inefficient, especially when the user code is large. To overcome these limitations, we have built a CVMFS user code publication system. This publication system enables users to still submit their code with their jobs but the code is distributed and accessed through the standard CVMFS infrastructure. The user code is automatically deleted from CVMFS after a period of no use. Most of the software for the system is available as a single self-contained open source rpm called cvmfs-user-pub and is available for other deployments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY↗