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DOE OSTI2024

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↗

DOE OSTI2023

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↗

NASA NTRS2011

Evaluating Cloud Computing in the Proposed NASA DESDynI Ground Data System

The proposed NASA Deformation, Ecosystem Structure and Dynamics of Ice (DESDynI) mission would be a first-of-breed endeavor that would fundamentally change the paradigm by which Earth Science data systems at NASA are built. DESDynI is evaluating a distributed architecture where expert science nodes around the country all engage in some form of mission processing and data archiving. This is compared to the traditional NASA Earth Science missions where the science processing is typically centralized. What's more, DESDynI is poised to profoundly increase the amount of data collection and processing well into the 5 terabyte/day and tens of thousands of job range, both of which comprise a tremendous challenge to DESDynI's proposed distributed data system architecture. In this paper, we report on a set of architectural trade studies and benchmarks meant to inform the DESDynI mission and the broader community of the impacts of these unprecedented requirements. In particular, we evaluate the benefits of cloud computing and its integration with our existing NASA ground data system software called Apache Object Oriented Data Technology (OODT). The preliminary conclusions of our study suggest that the use of the cloud and OODT together synergistically form an effective, efficient and extensible combination that could meet the challenges of NASA science missions requiring DESDynI-like data collection and processing volumes at reduced costs.

Benchmark↗

NASA NTRS1991

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

Keller, Richard M.↗

NASA NTRS1994

SI (Metric) handbook

This guide provides information for an understanding of SI units, symbols, and prefixes; style and usage in documentation in both the US and in the international business community; conversion techniques; limits, fits, and tolerance data; and drawing and technical writing guidelines. Also provided is information of SI usage for specialized applications like data processing and computer programming, science, engineering, and construction. Related information in the appendixes include legislative documents, historical and biographical data, a list of metric documentation, rules for determining significant digits and rounding, conversion factors, shorthand notation, and a unit index.

Artusa, Elisa A.↗

NASA NTRSDate not supplied

RadLab and the Environmental Data Application Dashboard: Graphical and Programming Interfaces for Interrogation of Space Telemetry Data

Sensors on the International Space Station (ISS) and multiple spacecraft elsewhere in Earth orbit and in deep space continuously monitor and collect environmental data, transmitting this information back to Earth. These data include ionizing radiation and, on the ISS, CO2, relative humidity levels, and temperature, and are of great importance to space biology research. Ionizing radiation in particular has been established in ground-based experiments as being correlated with increased risk of carcinogenesis and cardiovascular and neurological effects. Looking ahead to future long duration crewed missions beyond low Earth orbit, the ability to study how factors including CO2 levels, light cycle, temperature modulate the response to ionizing radiation and microgravity is essential. To date, access to these data has been fragmented across space agencies, spacecraft, and databases. To address this issue, NASA’s Open Science Data Repository (osdr.nasa.gov) has developed two Web applications: the Environmental Data Application (EDA) and a radiation-specific RadLab. Each consists of an API (application programming interface) and an associated GUI (graphical user interface) that provide single points of access to the data. To date, OSDR has focused on the sensors from payloads and radiation detectors located on the ISS. The Web applications process telemetry information and associated data, such as spacecraft location and orientation, from multiple international databases. The applications’ request syntax enables users to interrogate these data by craft, sensor type, time range, radiation type (galactic cosmic rays, solar particle events, the contribution of the South Atlantic Anomaly), facilitating arbitrary comparisons of original source data at varying time resolutions. The applications provide programmatic access for use in computational pipelines and GUIs for data visualization and exploration, making these data FAIR (Findable, Accessible, Interoperable, and Reusable), complementing the biological data contained in OSDR, and providing the space science community with a valuable resource for scientific analyses.

radiation↗

DOE OSTI2025

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↗

DOE OSTI2023

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↗

DOE OSTI2022

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↗

NASA NTRS2016

Technical Challenges and Lessons from the Migration of the GLOBE Data and Information System to Utilize Cloud Computing Service

The Global Learning and Observation to Benefit the Environment (GLOBE) Data and Information System supports an international science and education program with capabilities to accept local environment observations, archive, display and visualize them along with global satellite observations. Since its inception twenty years ago, the Web and database system has been upgraded periodically to accommodate the changes in technology and the steady growth of GLOBEs education community and collection of observations. Recently, near the end-of-life of the system hardware, new commercial computer platform options were explored and a decision made to utilize Cloud services. Now the GLOBE DIS has been fully deployed and maintained using Amazon Cloud services for over two years now. This paper reviews the early risks, actual challenges, and some unexpected findings as a result of the GLOBE DIS migration. We describe the plans, cost drivers and estimates, highlight adjustments that were made and suggest improvements. We present the trade studies for provisioning, for load balancing, networks, processing, storage, as well as production, staging and backup systems. We outline the migration teams skills and required level of effort for transition, and resulting changes in the overall maintenance and operations activities. Examples include incremental adjustments to processing capacity and frequency of backups, and efforts previously expended on hardware maintenance that were refocused onto application-specific enhancements.

GLOBE↗

NASA NTRS2017

Technical Challenges and Lessons from the Migration of the GLOBE Data and Information System to Utilize Cloud Computing Service

GLOBE Data↗

NASA NTRS2011

AstroBetter: A Blog and Wiki for Professional Astronomers

AstroBetter.com is a multi-contributor blog and wiki website designed for information sharing among professional astronomers. The goal of the site is to increase the productivity of astronomers by creating a centralized location for tips and tools of our multifaceted trade. Our content includes topics related to data reduction and analysis, general computing, writing papers and proposals, giving talks, teaching, career planning, productivity, organization, and diversity and equity in science and education. While we have several contributors, the site is intended to be community driven and we encourage everyone to publish to the wiki, submit guest posts, suggest post ideas, and to comment on blog entries. One of our primary goals is to consolidate and reduce the transient nature of the astronomy community's collective knowledge base by having an active wiki. Currently, the most common way to share astro-centric tools and tips that are not appropriate for a published paper, is to put them on an individual's website. However, the average astronomer's website will have at least four different addresses over the course of their career and only the site owner can edit the content. As a result, information on personal websites goes stale very quickly and deal links to such sites abound. It is our hope that community maintained wikis, such as the one hosted on AstroBetter, will gradually replace the personal website. In this poster we introduce the contributors to AstroBetter, show statistics about our current readership, give excerpts of some of our most popular posts and wiki entries, and show how anyone can add or edit content on the wiki. The goal of this poster is to spread the work about AstroBetter and increase our community of readers and wiki editors, because together, we can AstroBetter.

Rigby, Jane↗

NASA NTRSDate not supplied

RadLab: Graphical and Programming Interfaces for Interrogation of Space Telemetry Data

Sensors on multiple spacecraft in and beyond low Earth orbit continuously monitor and collect space radiation data and transmit it back to Earth. These data are of vast importance to space biology research, as ionizing radiation affects living organisms—astronauts and non-human experiment subjects alike—placing them at higher risk of carcinogenesis, degenerative diseases, and radiation sickness. Therefore, knowledge of the biological effects of space radiation is essential for planning future crewed missions beyond low Earth orbit. The RadLab project, initiated by GeneLab and ALSDA (the Open Science Data Repository; OSDR) and sponsored by the NASA Human Research Program, is a new effort aimed at connecting dosimetry data from radiation detectors located on the International Space Station (ISS), as well as other spacecraft. To date, access to these data has been fragmented across space agencies and databases; to address this issue, we have developed an application programming interface (API) and an associated graphical user interface (GUI) designed to provide a single point of access to the data. As of now, OSDR has focused on the detectors located on the ISS, with the long-term goal to establish a self-sustained portal receiving continuous updates through APIs connecting to multiple radiation databases of varying scope, as well as individual investigator contributions. The RadLab API implements a request syntax enabling users to query data by craft, sensor type, timespan, etc, allowing for arbitrary combinations of original source data, thus providing programmatic access for use in computational pipelines, while the GUI facilitates data visualization and exploration, making these data FAIR (Findable, Accessible, Interoperable, and Reusable), complementing the biological data contained in OSDR, and providing the space science community with a valuable resource for scientific analyses.

radiation↗

DOE OSTI2022

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↗

DOE OSTI2023

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↗

DOE OSTI2026

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↗

DOE OSTI2022

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↗

NASA NTRSDate not supplied

A Newly Developing Community-Oriented Data System from NASA GES DISC

Data services are essential to facilitate data access and to aid efficiency of conducting research and application activities. With emerging technologies such as cloud computing and AI/ML (Artificial Intelligence/Machine Learning) leading the pace of the data world, the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), home to the permanent archive for multidisciplinary Earth Observation (EO) geospatial data to study atmospheric composition, weather and climate variability, and water and energy cycles is no exception.Interfacing directly with users as part of data center work, we understand the challenges for the required time and effort to discover, visualize, and analyze large varieties and quantities of Earth Observation information for research, monitoring, and decision-making, largely due to the existing data and information systems aim to support experienced users, but has been proved difficult for non-earth scientists and new users that are unfamiliar with the variety of formats and structures in which data, metadata, and information are stored, as well as the required methods to use them. To address these challenges, I will update our latest activities with regard to water-and energy-related products and community-oriented and user-friendly services at the GES DISC, including our plans for the emerging technologies.

Jennifer Wei↗