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At least 37 records · Page 2

Establishing Data Analysis Pipeline for Bulk ATAC-Seq Datasets

We developed an analysis pipeline for transposase-accessible chromatin sequencing (ATAC-Seq) data derived from bulk samples, which brings together publicly available R packages in addition to command-line tools designed for analysis of bulk ATAC-Seq data and can be run on any computer running a Linux-like operating system such as Ubuntu or Apple OSX.

97 MATHEMATICS AND COMPUTING

AGC-2 Graphite Preirradiation Data Analysis Report

This report describes the specimen loading order and documents all preirradiation examination material property measurement data for graphite specimens contained within the Second Advanced Graphite Capsule (AGC 2) irradiation capsule. The AGC 2 capsule is the second in six planned irradiation capsules comprising the Advanced Graphite Creep (AGC) test series. The AGC test series is used to irradiate graphite specimens in order to garner quantitative data necessary for predicting the irradiation behavior and operating performance of new nuclear grade graphites. This testing will ascertain the in service behavior of the graphite for pebble bed and prismatic very high temperature reactor designs. Similar to the First Advanced Graphite Capsule (AGC 1) preirradiation examination report, material property tests were conducted on specimens from 18 nuclear grade graphite types. However, AGC 2 tested an increased number of specimens (i.e., 512) prior to loading them into the AGC 2 irradiation assembly. All AGC 2 specimen testing was conducted at Idaho National Laboratory from July 2009 to August 2010. This report also details the specimen loading methodology for graphite specimens inside the AGC 2 irradiation capsule. The AGC 2 capsule design requires “matched pair” creep specimens that have similar dose levels above and below the neutron flux profile mid plane. This provides similar specimens with and without an applied load. Analysis in this document utilizes the neutron flux profile calculated for the AGC 2 capsule design, the capsule dimensions, and the size (i.e., length) of the selected graphite specimens to create a stacking order that produces “matched pairs” of graphite specimens above and below the AGC 2 capsule elevation mid point, thus providing specimens with similar neutron dose levels.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Understanding and Estimating Error Propagation in Neural Networks for Scientific Data Analysis

Neural networks are increasingly integrated into scientific discovery, where input data reduction and model quantization play a key role in accelerating inference. However, understanding and mitigating the impact of these techniques on output error is critical for ensuring reliable results, particularly in tasks demanding high numerical precision. This paper introduces a comprehensive framework for optimizing neural network inference in scientific computing by combining data reduction and weight quantization while maintaining error-controlled outcomes. We develop theoretical analyses to bound error propagation under these reductions and propose a framework that balances computational performance with error constraints. Evaluation on real-world learning-based combustion simulations and satellite image classification demonstrates that our derived error bounds accurately predict observed errors while enabling significant computational speedup under our framework. This work highlights the potential for further leveraging advancements in modern lossy compression algorithms and hardware accelerators that support lower-precision formats.

He, Weiming [New Jersey Institute of Technology]

Operating Experience Data Analysis for Digital Instrumentation and Control System Reliability and Risk Assessment in Nuclear Power Plants

The implementation of advanced digital instrumentation and control (DI&C) systems in U.S. nuclear power plants (NPPs) can bring significant advancements in reliability, monitoring, and control capabilities. However, these systems also introduce new challenges, particularly in assessing risks such as common-cause failures (CCFs) and establishing robust reliability estimates for DI&C components. Addressing these challenges is critical for ensuring the safe and efficient operation of NPPs. Recently, Idaho National Laboratory was tasked by the U.S. Nuclear Regulatory Commission (NRC) to conduct a DI&C reliability study using operating experience data from the nuclear industry. The two operating experience data sources for the study are the Institute of Nuclear Power Operations’ Industry Reporting and Information System (IRIS) and the NRC’s Licensee Event Report database which is hosted at Idaho National Laboratory at https://lersearch.inl.gov/LERSearchCriteria.aspx. This report provides a comprehensive examination of DI&C systems, including their architecture, operational advantages, and associated challenges. It reviews existing industry DI&C studies and failure mode taxonomies, along with reliability data from various industries. Through a detailed analysis of these databases, the study provides insights into DI&C system performance. Considerations should be given to incorporate DI&C failure data into the NRC's Integrated Data Collection and Coding System and updating the Reliability and Availability Data System to support ongoing DI&C reliability studies. Recommendations are also provided for modeling DI&C reliability and CCF in probabilistic risk assessment, thereby supporting risk-informed decision-making and enhancing the reliability and safety of NPPs.

22 GENERAL STUDIES OF NUCLEAR REACTORS

In Situ Data Analysis Through Physics-informed Tensor Decompositions (LDRD Final Report)

We introduce a new low-dimensional model of high-dimensional numerical simulation data based on low-rank tensor decompositions. Our new model aims to minimize differences between the model data and simulation data as well as functions of the model data and functions of the simulation data. This novel approach to dimensionality reduction of simulation data provides a means of directly incorporating quantities of interests and invariants associated with conservation principles associated with the simulation data into the low-dimensional model, thus enabling more accurate analysis of the simulation without requiring access to the full set of high-dimensional data. Computational results of applying this approach to two standard low-rank tensor decompositions of data arising from simulation of combustion and plasma physics are presented.

97 MATHEMATICS AND COMPUTING

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES

Filling data analysis gaps in time-resolved crystallography by machine learning

There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.

Trujillo, Justin (ORCID:0000000285505360)

Calibration and Data Analysis of a Frequency Selectable Laser Source for CMB Detector Characterization

Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.

Pumarino, Rafael [Unlisted]

Calibration and Data Analysis of a Frequency Selectable Laser Source for CMB Detector Characterization

Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.

Pumarino Meza, Rafael [Unlisted, US; Fermilab]

Calibration and Data Analysis of a Frequency Selectable Laser Source for CMB Detector Characterization

Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.

Pumarino Meza, Rafael [Unlisted, US; Fermilab]

Imaging and analysis data of short-term co-culture in soilchip

Fluorescently tagged bacterial soil isolates were cultured with N-acetylglucosamine, chitopentose, or chitin in porous SoilChip devices designed to mimic the structural habitats found in soil. Imaging analysis was used to examine how microbial traits, nutrient substrate solubility and degree of polymerization, and time affected microbial growth and species’ spatial assembly.

Feng, Song [Pacific Northwest National Laboratory

Block Island Acoustic Data Analysis and Peak Detection Tools

This dataset contains acoustic signal analysis tools and processed datasets for pile driving noise characterization during Block Island Wind Farm construction (October 25, 2015), including peak detection algorithms, signal extraction methods, and visualization products for multi-channel hydrophone array data.

17 WIND ENERGY

Visualization for Insight and Data Analysis in Energy Research

This talk explores how advanced visualization technologies are transforming analytical reasoning and knowledge discovery in energy research, drawing on recent work at the National Laboratory of the Rockies' Computational Science Center. Through a series of scientific case studies, we demonstrate how immersive and high-resolution visualization environments enable scientists and engineers to identify previously unseen patterns and features - insights that often remain hidden in traditional desktop-based analysis. By embedding richer information into interactive analytics tools, these approaches support the exploration of complex, multivariate parameter spaces, where interaction itself catalyzes understanding. Beyond capability, we emphasize the critical role of visualization design grounded in perception and cognition, showing how visual encodings directly influence analytical outcomes. Spanning applications from materials science to integrated energy systems, these visualization approaches accelerate innovation and improve decision-making by enabling deeper, more reliable insight into increasingly complex energy data.

97 MATHEMATICS AND COMPUTING

Immersive Visualization for Scientific Data Analysis

We will present the use of immersive visualization at the National Renewable Energy Laboratory (NREL), showcasing how immersive visualization is advancing scientific research and engineering practices and transforming our day-to-day operations. We are leveraging immersive visualization to support scientific discovery and engineering in various domains, including material design, computational fluid dynamics, immersive analytics, grid modernization, digital twins, and situated visualization. We have observed several benefits across four key areas: enhanced spatial judgments, improved understanding through interaction, increased capacity to embed high-dimensional data, and improved collaboration.

immersive analytics

Simulations, Modeling and Data Analysis of Parity Violating Electron Scattering Experiments

In the Standard Model (SM) of nuclear and particle physics, parity violation is incorporated through the representation of the weak interaction as a chiral gauge interaction. Only the left-handed components of particles and right-handed components of antiparticles participate in weak interactions in the Standard Model. This implies that parity is asymmetric for the weak interaction. Parity violating electron scattering (PVES) experiments are designed to probe the physics parameters related to the SM, with the possibility to discover physics beyond the SM (BSM) by measuring the parity violating asymmetry ¿¿¿ of longitudinally polarized electrons scattered off unpolarized targets with high precision. This dissertation will be focused on two PVES experiments, the next 208Pb Lead Radius Experiment (PREX-II), and the Measurement of a Lepton-Lepton Electroweak Reaction (MOLLER) experiment, as well as in some small sections, the Calcium Radius Experiment (CREX) and P2 experiment which are also PVES experiments). PREX-II and CREX experiments, performed in Hall A at the Thomas Jefferson National Accelerator Facility (Jefferson Lab), measured ¿¿¿ in the elastic scattering of longitudinally polarized electrons from 208Pb and 48Ca targets to provide a precise model independent determination of the neutron skin thickness of 208Pb and 48Ca nuclei, respectively. The MOLLER experiment, proposed to start in 2027 and also to be performed in Hall A at Jefferson Lab, is to measure ¿¿¿ of longitudinally polarized electrons scattered off unpolarized electrons (Møller scattering) to determine the weak charge of electrons ¿¿¿ and the weak mixing angle ¿¿ with high precision. As for the P2 experiment, which will be performed at the upcoming MESA accelerator in Mainz Germany, it is to measure the weak charge of proton ¿¿¿ using ¿¿¿ in the elastic electron-proton scattering of polarized electrons off unpolarized protons. The final results from the PREX-II experiment are presented as ¿¿¿=550±16 (¿¿¿¿)±8 (¿¿¿¿) parts-per-billion (ppb). Combining the PREX-I and PREX-II results, the neutron skin thickness from PREX experiments is determined as ¿¿-¿¿=0.283±0.071 ¿¿ in 208Pb. This thesis lists the software and computational contribution of the author to these PVES experiments, including writing scripts and software to help with the PREX-II/CREX experiments, analyzing data to provide useful information and systematic uncertainty for the PREX-II experiment, modeling and simulations for the MOLLER, and providing an alternative design of an electronic equipment for the P2 experiment.

Chen, Yufan

Simulations, Modeling and Data Analysis of Parity Violating Electron Scattering Experiments

In the Standard Model (SM) of nuclear and particle physics, parity violation is incorporated through the representation of the weak interaction as a chiral gauge interaction. Only the left-handed components of particles and right-handed components of antiparticles participate in weak interactions in the Standard Model. This implies that parity is asymmetric for the weak interaction. Parity violating electron scattering (PVES) experiments are designed to probe the physics parameters related to the SM, with the possibility to discover physics beyond the SM (BSM) by measuring the parity violating asymmetry ¿¿¿ of longitudinally polarized electrons scattered off unpolarized targets with high precision. This dissertation will be focused on two PVES experiments, the next 208Pb Lead Radius Experiment (PREX-II), and the Measurement of a Lepton-Lepton Electroweak Reaction (MOLLER) experiment, as well as in some small sections, the Calcium Radius Experiment (CREX) and P2 experiment which are also PVES experiments). PREX-II and CREX experiments, performed in Hall A at the Thomas Jefferson National Accelerator Facility (Jefferson Lab), measured ¿¿¿ in the elastic scattering of longitudinally polarized electrons from 208Pb and 48Ca targets to provide a precise model independent determination of the neutron skin thickness of 208Pb and 48Ca nuclei, respectively. The MOLLER experiment, proposed to start in 2027 and also to be performed in Hall A at Jefferson Lab, is to measure ¿¿¿ of longitudinally polarized electrons scattered off unpolarized electrons (Møller scattering) to determine the weak charge of electrons ¿¿¿ and the weak mixing angle ¿¿ with high precision. As for the P2 experiment, which will be performed at the upcoming MESA accelerator in Mainz Germany, it is to measure the weak charge of proton ¿¿¿ using ¿¿¿ in the elastic electron-proton scattering of polarized electrons off unpolarized protons. The final results from the PREX-II experiment are presented as ¿¿¿=550±16 (¿¿¿¿)±8 (¿¿¿¿) parts-per-billion (ppb). Combining the PREX-I and PREX-II results, the neutron skin thickness from PREX experiments is determined as ¿¿-¿¿=0.283±0.071 ¿¿ in 208Pb. This thesis lists the software and computational contribution of the author to these PVES experiments, including writing scripts and software to help with the PREX-II/CREX experiments, analyzing data to provide useful information and systematic uncertainty for the PREX-II experiment, modeling and simulations for the MOLLER, and providing an alternative design of an electronic equipment for the P2 experiment.

Chen, Yufan

Nucleus++ : a new tool bridging AME and NUBASE for advancing nuclear data analysis

The newly developed software, Nucleus++ , is an advanced tool for displaying basic nuclear physics properties from NUBASE and integrating comprehensive mass information for each nuclide from Atomic Mass Evaluation. Additionally, it allows users to compare experimental nuclear masses with predictions from different mass models. Building on the success and learning experiences of its predecessor, Nucleus , this enhanced tool introduces improved functionality and compatibility. With its user-friendly interface, Nucleus++ was designed as a valuable tool for scholars and practitioners in the field of nuclear science. Finally, this article offers an in-depth description of Nucleus++ , highlighting its main features and anticipated impacts on nuclear science research.

AME