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At least 217 records · Page 12

Report on the "Symposium on Advancements in Simulating Neutron Scattering Instruments and Experiments"

An international group of researchers gathered for the “Symposium on Advancements in Simulating Neutron Scattering Instruments and Experiments” at Oak Ridge National Laboratory (ORNL) on October 29- 30, 2024. The symposium highlighted state-of-the-art advancements in neutron scattering instrument simulations and the development of digital twins for scattering instruments. This document summarizes the recurring themes from the 19 talks and discussions. A key focus was on the role of neutronics simulations in the design, analysis, and performance optimization of neutron instruments. Presentations featured the most widely used software packages, such as McStas, McVine, Vitess, and MCNP. Another major theme addressed the analysis and interpretation of experimental neutron data, where materials models and simulations play a critical role. Talks on relevant software tools, including NCrystal, OCLimax, and Paradyse, were delivered by their respective developers. During the symposium, both talks and breakout sessions explored strategies to enhance the interplay between neutronics simulations and materials models. A key question emerged: How can we develop a RealTime Explainable Digital Twin of a neutron scattering experiment? Discussions include the idea that the Digital Twin concept has implications for instrument control and testing. Through this symposium, we gained valuable insights into the challenges and requirements for developing a Real-Time Explainable Digital Twin of a neutron scattering experiment. The discussions and presentations paved the way for future innovations in this rapidly advancing field.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Understanding Biases in Sample Preparation Techniques for Coupled Scanning Electron Microscopy and MAMA PuO 2 Morphological Analysis

In this project, the scanning electron microscopy (SEM) sampling method used during the statistical design study (SDS) was investigated to determine if any sampling biases were present in the analyzed data. Using standard particle size distribution powders from the National Institute of Standards and Technology (NIST 1984 standard reference material) with the origin wet dispersion method, it was determined that a bias to smaller particles was present. This was supported by theoretical calculations using Stokes’ law to determine the settling rate of spherical particles of roughly the same size and mass as those found in the SDS. Based on the theoretical calculations, it was determined that the settling rate for each of the 76 powder sets in the SDS could be unique based on specific particle shape and mass distributions, making a universal correction factor/formula not applicable. Therefore, priority shifted to developing an improved wet dispersion method that significantly reduced the particle settling rate for all particle size and shapes. This was achieved by replacing the original solvent (isopropyl alcohol) with a heavy liquid (lithium heteropolytungstates), which dramatically slowed the settling rate and allowed for the capture of a suitable homogeneous aliquot. SEM imaging and Morphological Analysis for Material Attribution (MAMA) software analysis were conducted on the NIST standard, and the SEM/MAMA data were compared to data captured by a dynamic image analysis particle size analyzer. The resulting data confirmed that the new wet dispersion method does indeed deliver an improved representative aliquot to the SEM stub. For instance, in the NIST certificate, the average particle size is ~17.1 µm ± 2.2 µm with a normal distribution. The initial wet dispersion method resulted in a drastically reduced average particle size of 6.1 µm in addition to a non-representative heavy bi-modal distribution whereas the improved LST wet dispersion method resulting in an average particle size that was much closer to the NIST certificate (12.7 µm) with a similar normal distribution. Although the improved method was still short of the NIST certificate average, atomic force microscopy analysis determined that the resulting ~20-25% reduction in size was due to particles sinking into the carbon sticky tape used for SEM imaging. It is believed that that this bias can be calibrated in a much more predicable manner than the original settling rate bias. In addition, the matching normal distribution curves between the NIST certificate and the heavy liquid method indicate a much-improved representative aliquot has been sampled and imaged. A surrogate CeO 2 powder was used to reflect PuO 2 more accurately and to aid in implementing radiological controls and shielding. The resulting data sets from the SEM/MAMA method and the particle size analyzer give almost identical average particle sizes and particle distribution statistics. Future work will re-analyze several select runs from the SDS to determine if morphological signatures can be found with the improved sampling method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A cloud platform for atomic pair distribution function analysis: PDFitc

A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data ( PDFitc ) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping , are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc . In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.

97 MATHEMATICS AND COMPUTING↗

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMLinear

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs.

97 MATHEMATICS AND COMPUTING↗

Preliminary Feasibility of Printing, Microstructure Analysis and Mechanical Performance of a Down Selected Ni Alloy

This report is submitted as completion of a Milestone 3 deliverable under work package ORNL CT-23OR1304051 in support of the Advanced Materials and Manufacturing Technologies (AMMT) program. The AMMT program is aiming at the faster incorporation of new materials and manufacturing technologies into complex nuclear-related systems. An integrated approach, combining advanced characterization, high-throughput and accelerated testing, modeling and simulation including machine learning and artificial intelligence will be employed. While 316H (Fe-16-18Cr-10-14Ni-2-3Mo-0.04-0.1C) has been identified as a key alloy to be integrated into the AMMT accelerated alloy qualification approach due its relevance for many current and future nuclear energy reactors, many other alloys could be considered for the advanced fabrication of innovate high-performance nuclear components. ANL, INL, ORNL and PNNL are collaborating on identifying the most promising alloy candidates relevant for the AMMT program. A selection criteria matrix was established to evaluate the alloys considering their relative importance and technological readiness levels for nuclear energy applications, with a focus on laser powder bed fusion (LPBF). Due to the broad range of potential candidate alloys, ORNL and INL focused on Ni-based alloys, while ANL and PNNL mainly evaluated Fe-based alloys. PNNL previously published materials scorecards reports on several key alloys and this report is providing a broader overview of Ni-based candidate alloys, expending beyond alloys well-known to the nuclear community. Of particular interest are alloys that are currently commercially available in powder form due to the growing demand from other industries that have invested heavily in additive manufacturing. Among these alloys, Haynes 282 (Fe-20Cr-20Co-8Mo) was selected due to its superior strength at high temperature compared to the code-qualified alloy 617 (Ni-20-24Cr-10-15Co-8-10Mo). To assess the integration of this new alloy into the AMMT digital manufacturing framework, we performed the rapid optimization of alloy 282 printing parameters on a Renishaw 250 machine, the fabrication of sufficient materials for extensive characterization and mechanical testing both at ORNL and INL, and added the printing data into the digital platform via the Peregrine software. A detailed analysis of the LPBF 718 alloy was also conducted, with creep specimens being tested at 600-650°C and characterized by advanced electron microscopy. The alloy superior mechanical strength and great printability associated with the extensive database that has already been generated highlight the promising potential of LPBF 718 as a candidate alloy for the AMMT program. INL, ANL and PNNL have generated similar reports and all the information will be compiled into a final M2 milestone report to provide the AMMT leadership team with clear recommendations on the down selection of reactor materials, as well as establish a roadmap for the qualification of these selected alloys.

36 MATERIALS SCIENCE↗

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMGeometric

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs.

97 MATHEMATICS AND COMPUTING↗

Information Leakage Analysis using a Co-design-Based Fault Injection Technique on a RISC-V Microprocessor

The RISC-V instruction set architecture open licensing policy has spawned a hive of development activity, making a range of implementations publicly available. The environments in which RISC-V operates have expanded correspondingly, driving the need for a generalized approach to evaluating the reliability of RISC-V implementations under adverse operating conditions or after normal wear-out periods. Fault injection (FI) refers to the process of changing the state of registers or wires, either permanently or momentarily, and then observing execution behavior. The analysis provides insight into the development of countermeasures that protect against the leakage or corruption of sensitive information which might occur because of unexpected execution behavior. In this paper, we develop a hardware-software co-design architecture that enables fast, configurable fault emulation and utilize it for information leakage and data corruption analysis. Modern System-on-chip FPGAs enable building an evaluation platform where control elements run on a processor(s) (PS) simultaneously with the target design running in the programmable logic (PL). Software components of the FI system introduce faults and report execution behavior. A pair of RISC-V FI-instrumented implementations are created and configured to execute the Advanced Encryption Standard and Twister algorithms. Key and plaintext information leakage and degraded pseudo-random sequences are both observed in the output for a subset of the emulated faults.

42 ENGINEERING↗

AmpSuite

Seismic amplitudes offer vital information about explosion source characteristics, including discrimination and yield estimation. To take advantage of this, we developed an interactive Python package to measure, control data quality, generate broad area propagation models and perform discrimination and estimate yield. Propagation models are essential in support of transportable yield and broad area discrimination. The key benefit of this package will be its ability to continuously integrate data and new techniques. The AmpSuite framework will provide standardized, repeatable, and accurate model generation and characterization routines. The capability is crucial for monitoring agencies tasked with rapid and high-quality seismic event characterization. The AmpSuite software includes a series of independent modules to perform: • Direct Phase Amplitude Measurement and Storage • Coda Envelope Measurement and Storage • Data Quality Control • New Propagation Model Developments • Seismic Discrimination and Analysis • Yield Estimation and supporting utility software. The AmpSuite software provides comprehensive solutions for monitoring agencies seeking to optimize model generation and event analysis within a contemporary Python framework. Stakeholders (AFTAC) have begun to move towards the Python language for scientific analysis as a new workforce emerges.

Alfaro, Richard↗

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamFVT

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs. The testing of the adjoint code is performed in a separate document.

97 MATHEMATICS AND COMPUTING↗

evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library

Widespread availability of protein sequence-fitness data would revolutionize both our biochemical understanding of proteins and our ability to engineer them. Unfortunately, even though thousands of protein variants are generated and evaluated for fitness during a typical protein engineering campaign, most are never sequenced, leaving a wealth of potential sequence-fitness information untapped. Primarily, this is because sequencing is unnecessary for many protein engineering strategies; the added cost and effort of sequencing is thus unjustified. It also results from the fact that, even though many lower cost sequencing strategies have been developed, they often require at least some sequencing or computational resources, both of which can be barriers to access. In this work, we present every variant sequencing (evSeq), a method and collection of tools/standardized components for sequencing a variable region within every variant gene produced during a protein engineering campaign at a cost of cents per variant. evSeq was designed to democratize low-cost sequencing for protein engineers and, indeed, anyone interested in engineering biological systems. Execution of its wet-lab component is simple, requires no sequencing experience to perform, relies only on resources and services typically available to biology labs, and slots neatly into existing protein engineering workflows. Analysis of evSeq data is likewise made simple by its accompanying software (found at github.com/fhalab/evSeq, documentation at fhalab.github.io/evSeq), which can be run on a personal laptop and was designed to be accessible to users with no computational experience. Here, low-cost and easy to use, evSeq makes collection of extensive protein variant sequence-fitness data practical.

59 BASIC BIOLOGICAL SCIENCES↗

Reimagining Disassembly Interfaces With Visualization: Combining Instruction Tracing and Control Flow With DisViz

In applications where efficiency is critical, developers may examine their compiled binaries, seeking to understand how the compiler transformed their source code and what performance implications that transformation may have. This analysis is challenging due to the vast number of disassembled binary instructions and the many-to-many mappings between them and the source code. These problems are exacerbated as source code size increases, giving the compiler more freedom to map and disperse binary instructions across the disassembly space. Interfaces for disassembly typically display instructions as an unstructured listing or sacrifice the order of execution. Here, we design a new visual interface for disassembly code that combines execution order with control flow structure, enabling analysts to both trace through code and identify familiar aspects of the computation. Central to our approach is a novel layout of instructions grouped into basic blocks that displays a looping structure in an intuitive way. We add to this disassembly representation a unique block-based mini-map that leverages our layout and shows context across thousands of disassembly instructions. Finally, we embed our disassembly visualization in a web-based tool, DisViz, which adds dynamic linking with source code across the entire application. DizViz was developed in collaboration with program analysis experts following design study methodology and was validated through evaluation sessions with ten participants from four institutions. Participants successfully completed the evaluation tasks, hypothesized about compiler optimizations, and noted the utility of our new disassembly view. Our evaluation suggests that our new integrated view helps application developers in understanding and navigating disassembly code.

Computer science↗

Quantitative Scanning Transmission Electron Microscopy for Materials Science: Imaging, Diffraction, Spectroscopy, and Tomography

Scanning transmission electron microscopy (STEM) is one of the most powerful characterization tools in materials science research. Due to instrumentation developments such as highly coherent electron sources, aberration correctors, and direct electron detectors, STEM experiments can examine the structure and properties of materials at length scales of functional devices and materials down to single atoms. STEM encompasses a wide array of flexible operating modes, including imaging, diffraction, spectroscopy, and 3D tomography experiments. This review outlines many common STEM experimental methods with a focus on quantitative data analysis and simulation methods, especially those enabled by open source software. The hope is to introduce both classic and new experimental methods to materials scientists and summarize recent progress in STEM characterization. The review also discusses the strengths and weaknesses of the various STEM methodologies and briefly considers promising future directions for quantitative STEM research.

36 MATERIALS SCIENCE↗

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms

Background: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. Results: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. Conclusions: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.

59 BASIC BIOLOGICAL SCIENCES↗

HPC for the EEC: Industrial Trade Tools for the Aging Energy Infrastructure

The petrochemical and refining sectors are challenged with reliably delivering safer and cleaner energy to US consumers, while meeting an ever-growing global demand. The petrochemical and refining infrastructure in the USA is aging, and corrosion and damage mechanisms are constant threats to mechanical integrity, safety, and profitability. However, governments and industry stakeholders are reluctant to replace or upgrade the existing infrastructure due to the immense cost. To better understand and mitigate the risks of aging energy infrastructure, strong technical analysis capabilities, combined with optimized monitoring and decision making, is critical. Today, this is accomplished via complex simulations and data analysis. To this end, advanced High-Performance-Computing (HPC) software will be leveraged and integrated in easy-to-use industrial trade tools, to lower the barrier for new users, increase the ease of access for experienced users, and allow for smarter decisions to be made in the midstream and downstream energy sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

SIERRA/Aero User Manual - Version 4.56

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

SIERRA/Aero Theory Manual - Version 4.56

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

SIERRA/Aero Theory Manual - Version 4.58

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

SIERRA/Aero User Manual - Version 4.58

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗