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At least 163 records · Page 9

Imaging Bragg Edge Analysis TooLs for Engineering Structures (iBeatles)

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) provides pulsed neutrons with energies varying from epithermal to cold. In preparation for VENUS, the neutron imaging beamline to be located at beam port 10, we have performed a series of experiments focused on wavelength-dependent radiography and computed tomography for a broad range of applications, from materials science to biological tissues.One of the time-of-flight (TOF) techniques that is of interest to the scientific community is the 2-dimensional mapping of phases and average crystalline plane orientation in samples both ex-situ and during applied stresses such as tensile loading and heating. This technique is known as Bragg edgeimaging and relies on the identification of changes of transmission values, fitting of the edge to measure its displacement, and thus identify the shift in lattice parameter due to stresses. One of the challenges of TOF imaging measurements is the amount of data and the inability to observe Bragg edge shifts in real time during an experiment. Thus, we have been focusing on creating a Python-based interface that allows fast data processing and instantaneous mapping and fitting of the Bragg edges, and their evolution through time. Python libraries and Jupyter notebooks have been implemented to facilitate decision making during an experiment. The advantage of the notebooks is the possibility to guide an experiment as they can quickly process and display Bragg edge data. These notebooks can be used independently, or can be combined in a Python Graphical User Interface (GUI) tool called iBeatles. This interface permits visualization and fitting of the Bragg edges, and ultimately back-projects the fitting results onto the radiographs to display a strain map. Assuming data collection has sufficient statistics, the strain mapping analysis can be performed on a pixel-by-pixel basis. This development is a step forward toward a better user experience at the future VENUS beamline in terms of live feedback and productivity. Analysis that used to take days of switching between different applications can now be done in minutes within the

Bilheux, JeanChristophe [Oak Ridge National Labora↗

Digital image correlation and infrared thermography data for seven unique geometries of 304L stainless steel

Material Testing 2.0 (MT2.0) is a paradigm that advocates for the use of rich, full-field data, such as from digital image correlation and infrared thermography, for material identification. By employing heterogeneous, multi-axial data in conjunction with sophisticated inverse calibration techniques such as finite element model updating and the virtual fields method, MT2.0 aims to reduce the number of specimens needed for material identification and to increase confidence in the calibration results. To support continued development, improvement, and validation of such inverse methods—specifically for rate-dependent, temperature-dependent, and anisotropic metal plasticity models—we provide here a thorough experimental data set for 304L stainless steel sheet metal. The data set includes full-field displacement, strain, and temperature data for seven unique specimen geometries tested at different strain rates and in different material orientations. Commensurate extensometer strain data from tensile dog bones is provided as well for comparison. We believe this complete data set will be a valuable contribution to the experimental and computational mechanics communities, supporting continued advances in material identification methods.

36 MATERIALS SCIENCE↗

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗

High Energy Physics Network Requirements Review: Two-Year Update

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all its laboratories and facilities in the US and abroad. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet interconnects DOE national laboratories, user facilities, and major experiments so that scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large datasets, and access distributed data repositories. ESnet is specifically built to provide a range of network services tailored to meet the unique requirements of the DOE’s data-intensive science. In July 2023, the Energy Sciences Network (ESnet) and the High Energy Physics program (HEP) of the DOE SC organized an interim ESnet requirements review of HEP-supported activities, to follow up on the work started during the 2020 HEP Network Requirements Review. Preparation for these events included checking back with the key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare updates to their previously submitted case study documents, so that ESnet could update the understanding of any changes to the current, near-term, and long-term status, expectations, and processes that will support the science activities of the program.

97 MATHEMATICS AND COMPUTING↗

A new database website for nuclear level densities

We introduce a new open-access, web-based database (http://nld.ascsn.net), Current Archive of Nuclear Density of Levels (CANDL), that hosts experimental nuclear level density (NLD) datasets from a variety of techniques and energy ranges. Built using the Dash framework in Python, the database is designed to be interactive and user-friendly, allowing researchers to search, visualize, fit, and export NLD data with minimal effort. This resource includes data extracted from evaporation spectra, Oslo method variants, and other experimental techniques that cover excitation energies beyond the neutron resonance region. The database supports on-the-fly fitting with two widely-used phenomenological models—the Constant Temperature (CT) model and the Back-Shifted Fermi Gas (BSFG) model—selected for their simplicity and computational efficiency. Future versions aim to include additional datasets and model types, as well as easy-to-use interfaces to data science techniques. Here, this platform offers a vital tool for the nuclear physics, astrophysics, medicine, and reactor design communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quantum Optimization: Potential, Challenges, and the Path Forward

Recent advances in quantum computers are demonstrating the ability to solve problems at a scale beyond brute force classical simulation. As such, a widespread interest in quantum algorithms has developed in many areas, with optimization being one of the most pronounced domains. Across computer science and physics, there are a number of algorithmic approaches, often with little linkage. This is further complicated by the fragmented nature of the field of mathematical optimization, where major classes of optimization problems, such as combinatorial optimization, convex optimization, non-convex optimization, and stochastic extensions, have devoted communities. With these aspects in mind, this work draws on multiple approaches to study quantum optimization. Provably exact versus heuristic settings are first explained using computational complexity theory — highlighting where quantum advantage is possible in each context. Then, the core building blocks for quantum optimization algorithms are outlined to subsequently define prominent problem classes and identify key open questions that, if answered, will advance the field. The effects of scaling relevant problems on noisy quantum devices are also outlined in detail, alongside meaningful benchmarking problems. We underscore the importance of benchmarking by proposing clear metrics to conduct appropriate comparisons with classical optimization techniques. Lastly, we highlight two domains – finance and sustainability – as rich sources of optimization problems that could be used to benchmark, and eventually validate, the potential real-world impact of quantum optimization.

97 MATHEMATICS AND COMPUTING↗

Predictive coarse-grained (CG) modeling of morphologies in polymer nanocomposites with specific and directional intermolecular interactions (Final Report)

The overarching goal of the proposed work was to develop predictive models for investigating structure and dynamics in soft materials with chemistries that have specific and directional molecular interactions. The motivation behind studying materials with specific and directional interactions lies in the many desirable features these interactions provide when designing novel soft materials. Soft materials with specific and direction interactions (such as hydrogen bonds or H-bonds) can have a) thermally reversible phase behavior with different functions with varying temperature, b) precisely tuned nanostructure with desirable geometries that afford unique physical properties (e.g., color response, mechanical properties) and c) well-mixed/blended morphologies that are useful for variety of applications in energy field (e.g., materials for batteries require use of blended polymers where one domain gives superior mechanical properties and one domain promotes electrical conduction). Notably, biology makes extensive use of specific and directional interactions, in many cases based on H-bonds, to construct materials with precisely defined architectures and properties. Engineered soft materials with precisely tuned nanostructures and improved processiblity through thermoresponsive phase behavior are useful in numerous applications that are relevant to the Department of Energy (DOE) including high efficiency electronic devices, light-weight high-strength composite materials for batteries and fuel cells, and polymer membranes for separations, etc. While past computational studies have been tremendously useful in understanding molecular phenomena and guiding synthesis of new macromolecular soft materials for a wide variety of applications, the inability to capture small scale specific and directional interactions alongside macromolecular length and time scales represented a key limitation of most studies to date. Our work in this project addressed this grand challenge in computational materials chemistry, i.e., ability to model the anisotropic, directional, and specific interactions that govern the behavior of many macromolecular soft matter systems of interest, thus, has greatly expanded the predictive potential of simulations. Specifically the key outcomes were: successful development of new coarse-grained (CG) polymer models to study generic and specific polymer chemistries in which hydrogen-bonding interactions are dominant. These CG models were then used in molecular simulations to study structure and thermodynamics in polymer nanocomposites and blends; some studies were conducted in collaboration with experimentalists. We also published a perspective and a viewpoint which included some of the work we completed in this DOE project; we believe these perspective and viewpoint articles guide other researchers in the soft materials community on how to extend the computational approaches and models we have developed for the purposes of their studies.

36 MATERIALS SCIENCE↗

A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory

In the search for a sustainable approach for software ecosystems that supports experimental and observational science (EOS) across Oak Ridge National Laboratory (ORNL), we conducted a survey to understand the current and future landscape of EOS software and data. This paper describes the survey design we used to identify significant areas of interest, gaps, and potential opportunities, followed by a discussion on the obtained responses. The survey formulates questions about project demographics, technical approach, and skills required for the present and the next five years. The study was conducted among 38 ORNL participants between June and July of 2021 and followed the required guidelines for human subjects training. We plan to use the collected information to help guide a vision for sustainable, community-based, and reusable scientific software ecosystems that need to adapt effectively to: i) the evolving landscape of heterogeneous hardware in the next generation of instruments and computing (e.g. edge, distributed, accelerators), and ii) data management requirements for data-driven science using artificial intelligence.

Bernholdt, David↗

Experiential findings for sustainable software ecosystems to support experimental and observational science

In the search for a sustainable approach for software ecosystems that supports experimental and observational science (EOS) across Oak Ridge National Laboratory (ORNL), we conducted a survey to understand the current and future landscape of EOS software and data. This paper describes the survey design we used to identify significant areas of interest, gaps, and potential opportunities, followed by a discussion on the obtained responses. The survey formulates questions about project demographics, technical approach, and skills required for the present and the next five years. Here, the study was conducted among 38 ORNL participants between June and July of 2021 and followed the required guidelines for human subjects training. We plan to use the collected information to help guide a vision for sustainable, community-based, and reusable scientific software ecosystems that need to adapt effectively to: (i) the evolving landscape of heterogeneous hardware in the next generation of instruments and computing (e.g. edge, distributed, accelerators), and (ii) data management requirements for data-driven science using artificial intelligence.

97 MATHEMATICS AND COMPUTING↗

pyRMG: A framework for high-throughput, large-cell DFT calculations on supercomputers

Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density functional theory (DFT) code’s grid-decomposition approach scales nearly linearly with the number of graphics processing units (GPUs), even for simulations exceeding thousands of atoms. This scalability makes RMG a compelling tool for high-throughput DFT studies of materials that would otherwise be bottlenecked in other codes (for example, by global fast Fourier transforms in plane-wave DFT). However, the limited workflow infrastructure for RMG has thus far constrained its adoption to a small user community. In this work, we present pyRMG, a Python package designed to streamline the setup and execution of RMG DFT calculations. Built on the pymatgen and ASE (Atomic Simulation Environment) computational materials science Python packages, pyRMG automates input generation and convergence checking, and it integrates with modern job schedulers (e.g., Flux) on leadership-class platforms such as Frontier and Perlmutter. Here, we demonstrate pyRMG for a high-throughput study of strain effects in 2D 2L-Bi 2 Se 3 /2L-NbSe 2 heterostructures, which offers chemical insights into this system and shows that RMG-based workflows can converge with limited user intervention.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

HL-LHC Computing Review Stage 2, Common Software Projects: Data Science Tools for Analysis

This paper was prepared by the HEP Software Foundation (HSF) PyHEP Working Group as input to the second phase of the LHCC review of High-Luminosity LHC (HL-LHC) computing, which took place in November, 2021. It describes the adoption of Python and data science tools in HEP, discusses the likelihood of future scenarios, and recommendations for action by the HEP community.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nuclear Physics Network Requirements Review Report

The Energy Sciences Network (ESnet) is the Office of Science’s high-performance network user facility, delivering highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the U.S. Department of Energy (DOE) science mission by connecting each and every DOE lab and its user facilities. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) Program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet connects DOE national laboratories, user facilities, and major experiments so scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large data sets, and access distributed data repositories. While ESnet provides network connectivity, it cannot be characterized as an internet service provider as it is specifically built to provide a range of network services that are tailored to meet the unique requirements of DOE’s data-intensive science.

97 MATHEMATICS AND COMPUTING↗

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds

Abstract Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.

59 BASIC BIOLOGICAL SCIENCES↗

PhILMs: Collaboratory on Mathematics and Physics-Informed Learning Machines for Multiscale and Multiphysics Problems

The landscape of computational science and engineering is continually evolving, with the challenge of high-dimensional regression problems standing as a significant hurdle in numerous scientific endeavors. Addressing this challenge, our research, funded by this award, has led to the development of an innovative computational framework known as Probabilistic Partition of Unity Networks (PPOU-Nets). This initiative represents a collaborative effort to harness the potential of mathematics and physics-informed machine learning in tackling multiscale and multiphysics problems prevalent in high-dimensional spaces. Through this work, we have proposed a novel methodology that seamlessly integrates adaptive dimensionality reduction and a mixture of experts model, thereby facilitating a more efficient and accurate approximation of complex functions. This research effort has not only advanced the state of computational science but also opened new avenues for exploration in quantum computing and beyond. This report outlines the motivation, methodology, key findings, and implications of our work, underscoring our contributions to the broader scientific community and the potential pathways for future research.

97 MATHEMATICS AND COMPUTING↗

Bioimaging Science Program Principal Investigator Meetings Proceedings (2021)

As part of the 2021 Biological Systems Science Division (BSSD) Principal Investigator (PI) Meeting, the Bioimaging Science program (BSP), within BSSD's Biomolecular Characterization and Imaging Science portfolio, held its annual PI meeting virtually February 22–23. BSP's mission is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. BSP convenes annual PI meetings to bring together its contributing investigators to review progress and current state-of-the-art bioimaging research. Holding the BSP meeting as part of the broader BSSD PI meeting allowed researchers to interact with the extended Genomic Science program community. This convergence provided a platform for networking and exchange of ideas, helping to forge new multidisciplinary collaborations among investigators from the two sister programs. An important highlight of the BSP meeting was the keynote presentation “Enhancing Fluorescence Microscopy with Computation” by Dr. Hari Shroff of the NIH National Institute of Biomedical Imaging and Bioengineering. All the BSP PIs made presentations describing their research focus and progress, and these were followed by roundtable discussions of each project. The meeting’s proceedings provide an outline of the program’s current state and potential future directions and opportunities.

59 BASIC BIOLOGICAL SCIENCES↗

The 2022 applied physics by pioneering women: a roadmap

Abstract Women have made significant contributions to applied physics research and development, and their participation is vital to continued progress. Recognizing these contributions is important for encouraging increased involvement and creating an equitable environment in which women can thrive. This Roadmap on Women in Applied Physics, written by women scientists and engineers, is intended to celebrate women’s accomplishments, highlight established and early career researchers enlarging the boundaries in their respective fields, and promote increased visibility for the impact women have on applied physics research. Perspectives cover the topics of plasma materials processing and propulsion, super-resolution microscopy, bioelectronics, spintronics, superconducting quantum interference device technology, quantum materials, 2D materials, catalysis and surface science, fuel cells, batteries, photovoltaics, neuromorphic computing and devices, nanophotonics and nanophononics, and nanomagnetism. Our intent is to inspire more women to enter these fields and encourage an atmosphere of inclusion within the scientific community.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings

As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.

59 BASIC BIOLOGICAL SCIENCES↗

Enabling modern data discovery for atmospheric measurements

The Atmospheric Radiation Measurement (ARM) user facility is a US Department of Energy Office of Science user facility that is managed and operated through a collaborative effort led by nine US Department of Energy national laboratories. The ARM Data Center, located at Oak Ridge National Laboratory, is responsible for the timely collection, processing, and delivery of data products to the scientific community. The ARM Data Center holds more than 11,000 data products, including metadata collected from field campaigns, instruments, value-added products, and principal investigator–contributed data. These data sets are checked for successful transfer (for most data, this transfer is carried out automatically via the network; however, some of the largest data sets and some of the most remote sites require manual shipping of hard disks) and both the data and metadata are processed to a standard format, which is an ARM-standardized structure, via the Network Common Data Form. The Network Common Data Form is a self-describing binary format with many compatible software tools. Once processed, the data are cataloged, stored in the ARM Data Archive, and made discoverable through association with an array of metadata-characterizing information, such as location and measurement classification. These metadata enable powerful search capabilities through the ARM Data Center Data Discovery interface. This paper discusses the workflow of how the new discovery system has been redesigned from user requirements and how the data are distributed to the scientific community.

54 ENVIRONMENTAL SCIENCES↗