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At least 271 records · Page 15

Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompanied by community-sourced guidelines, instructional templates, and peer support to use KBase within a classroom whether virtual or in-person.

59 BASIC BIOLOGICAL SCIENCES↗

Perspectives on AI Architectures and Codesign for Earth System Predictability

Abstract Recently, the U.S. Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER), and Advanced Scientific Computing Research (ASCR) programs organized and held the Artificial Intelligence for Earth System Predictability (AI4ESP) workshop series. From this workshop, a critical conclusion that the DOE BER and ASCR community came to is the requirement to develop a new paradigm for Earth system predictability focused on enabling artificial intelligence (AI) across the field, laboratory, modeling, and analysis activities, called model experimentation (ModEx). BER’s ModEx is an iterative approach that enables process models to generate hypotheses. The developed hypotheses inform field and laboratory efforts to collect measurement and observation data, which are subsequently used to parameterize, drive, and test model (e.g., process based) predictions. A total of 17 technical sessions were held in this AI4ESP workshop series. This paper discusses the topic of the AI Architectures and Codesign session and associated outcomes. The AI Architectures and Codesign session included two invited talks, two plenary discussion panels, and three breakout rooms that covered specific topics, including 1) DOE high-performance computing (HPC) systems, 2) cloud HPC systems, and 3) edge computing and Internet of Things (IoT). We also provide forward-looking ideas and perspectives on potential research in this codesign area that can be achieved by synergies with the other 16 session topics. These ideas include topics such as 1) reimagining codesign, 2) data acquisition to distribution, 3) heterogeneous HPC solutions for integration of AI/ML and other data analytics like uncertainty quantification with Earth system modeling and simulation, and 4) AI-enabled sensor integration into Earth system measurements and observations. Such perspectives are a distinguishing aspect of this paper. Significance Statement This study aims to provide perspectives on AI architectures and codesign approaches for Earth system predictability. Such visionary perspectives are essential because AI-enabled model-data integration has shown promise in improving predictions associated with climate change, perturbations, and extreme events. Our forward-looking ideas guide what is next in codesign to enhance Earth system models, observations, and theory using state-of-the-art and futuristic computational infrastructure.

54 ENVIRONMENTAL SCIENCES↗

AI-Enhanced Co-Design for Next-Generation Microelectronics: Innovating Innovation (Workshop Report)

The Artificial Intelligence Enhanced Co-Design for Next Generation Microelectronics virtual workshop was held April 4-5, 2023, and attended by subject matter experts from universities, industry, and national laboratories. This was the third in a series of workshops to motivate the research community to identify and address major challenges facing microelectronics research and production. The 2023 workshop focused on a set of topics from materials to computing algorithms, and included discussions on relevant federal legislation and such as the Creating Helpful Incentives to Produce Semiconductors and Science Act (CHIPS Act) which was signed into law in the summer of 2022. Talks at the workshop included edge computing in radiation environments, new materials for neuromorphic computing, advanced packaging for microelectronics, and new AI techniques. We also received project updates from several of the Department of Energy (DOE) microelectronics co-design projects funded in the fall of 2021, and from three of the Energy Frontier Research Centers (EFRCs) that had been funded in the fall of 2022. The workshop also conducted a set of breakout discussions around the five principal research directions (PRDs) from the 2018 Department of Energy workshop report: 1) define innovative material, device, and architecture requirements driven by applications, algorithms, and software; 2) revolutionize memory and data storage; 3) re-imagine information flow unconstrained by interconnects; 4) redefine computing by leveraging unexploited physical phenomena; 5) reinvent the electricity grid through new materials, devices, and architectures. We tasked each breakout group to consider one primary PRD (and other PRDs as relevant topics arose during discussions) and to address questions such as whether the research community has embraced co-design as a methodology and whether new developments at any level of innovation from materials to programming models requires the research community to reevaluate the PRDs developed back in 2018.

97 MATHEMATICS AND COMPUTING↗

Unraveling the Threads of Environmental Justice in Critical Mineral Extraction: A Framework for Regionalized Life Cycle Data

As we transition to a more sustainable energy system, the extraction and processing of critical minerals becomes increasingly important. However, these industries often raise concerns about environmental and social impacts, particularly in disadvantaged communities. To address these concerns, our research focuses on regionalizing environmental life cycle data to connect it with communities affected by mineral extraction. A framework was developed for collecting life cycle background data that supports the Justice40 Toolset, a market-based approach to evaluating net benefits and costs of critical mineral material recovery pathways. A goal was to alleviate public skepticism around mineral extraction processes, including secondary and unconventional feedstocks, by highlighting both environmental and social impacts. To achieve this, computational analysis and geospatial data science techniques were employed, such as within-scale and across-scale methods and proxy dataset usage. By doing so, we were able to develop a framework for identifying and disaggregating data down to regions small enough to support Justice40 goals. Our approach not only provides valuable tools fo insight into the environmental implications of mineral extraction but also helps policymakers evaluate the social impacts on local communities. This research contributes to a more just and equitable transition to a sustainable energy system, ensuring that marginalized voices are heard in decision-making process.

Davis, Tyler [NETL Site Support Contractor, Nation↗

Computational Modeling of Atmospheric Processes at Texas Southern University

Texas Southern University (TSU) is strengthening its research program in atmospheric chemistry and physics with a climate science emphasis by leveraging partnerships with the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Facility, Brookhaven National Laboratory (BNL), and the Tracking Aerosol Convection Interactions ExpeRiment (TRACER). This RDPP-supported program focuses on secondary organic aerosols (SOAs) and reactive atmospheric species that influence cloud formation, precipitation processes, and radiative forcing. SOAs play a critical role in cloud microphysics and Earth’s energy balance, yet the chemical and physical mechanisms governing SOA–cloud interactions remain a significant source of uncertainty in predictive climate models. Through computational modeling, observational data analysis, and national laboratory collaboration, this program develops a skilled cohort of students trained in atmospheric science, environmental data analysis, and climate-relevant modeling. These research experiences build technical competencies that are transferable to careers in government laboratories, academia, and industry. By engaging students from historically underrepresented communities in high-impact climate research, TSU expands participation in the atmospheric sciences workforce while contributing meaningful scientific insights to DOE-supported ARM research activities. This partnership strengthens national capacity in climate science and supports the development of the next generation of atmospheric researchers.

54 ENVIRONMENTAL SCIENCES↗

The SGI/Cray T3E: Experiences and Insights

The NASA Goddard Space Flight Center is home to the fifth most powerful supercomputer in the world, a 1024 processor SGI/Cray T3E-600. The original 512 processor system was placed at Goddard in March, 1997 as part of a cooperative agreement between the High Performance Computing and Communications Program's Earth and Space Sciences Project (ESS) and SGI/Cray Research. The goal of this system is to facilitate achievement of the Project milestones of 10, 50 and 100 GFLOPS sustained performance on selected Earth and space science application codes. The additional 512 processors were purchased in March, 1998 by the NASA Earth Science Enterprise for the NASA Seasonal to Interannual Prediction Project (NSIPP). These two "halves" still operate as a single system, and must satisfy the unique requirements of both aforementioned groups, as well as guest researchers from the Earth, space, microgravity, manned space flight and aeronautics communities. Few large scalable parallel systems are configured for capability computing, so models are hard to find. This unique environment has created a challenging system administration task, and has yielded some insights into the supercomputing needs of the various NASA Enterprises, as well as insights into the strengths and weaknesses of the T3E architecture and software. The T3E is a distributed memory system in which the processing elements (PE's) are connected by a low latency, high bandwidth bidirectional 3-D torus. Due to the focus on high speed communication between PE's, the T3E requires PE's to be allocated contiguously per job. Further, jobs will only execute on the user specified number of PE's and PE timesharing is possible but impractical. With a highly varied job mix in both size and runtime of jobs, the resulting scenario is PE fragmentation and an inability to achieve near 100% utilization. SGI/Cray has provided several scheduling and configuration tools to minimize the impact of fragmentation. These tools include PScheD (the political scheduler), GRM (the global resource manager) and NQE (the Network Queuing Environment). Features and impact of these tools will be discussed, as will resulting performance and utilization data. As a distributed memory system, the T3E is designed to be programmed through explicit message passing. Consequently, certain assumptions related to code design are made by the operating system (UNICOS/mk) and its scheduling tools. With the exception of HPF, which does run on the T3E, however poorly, alternative programming styles have the potential to impact the T3E in unexpected and undesirable ways. Several examples will be presented (preceeded with the disclaimer, "Don't try this at home! Violators will be prosecuted!")

Bernard, Lisa Hamet↗

CP2K: An Electronic Structure and Molecular Dynamics Software Package - Quickstep: Efficient and Accurate Electronic Structure Calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension. TDK has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 716142). VRR has been supported by the Swiss National Science Foundation in the form of Ambizione grant No. PZ00P2 174227 and RZK by the Natural Sciences and Engineering Research Council of Canada (NSERC) through Discovery Grants (RGPIN-2016-0505). GKS and CJM are supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. UK based work was funded under the embedded CSE programme of the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk), grants eCSE03-011, eCSE06-6, eCSE08-9, eCSE13-17 and the EPSRC (EP/P022235/1) grant “Surface and Interface Toolkit for the Materials Chemistry Community". Computational resources were provided by the Swiss National Supercomputing Centre (CSCS) and Compute Canada. The generous allocation of computing time on the FPGA-based supercomputer “Noctua" at PC2 is kindly acknowledged.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An evaluation of risks associated with relying on Fortran for mission critical codes for the next 15 years

This document examines risks associated with relying on Fortran for codes critical to nuclear security into the late 2030s. The study was requested by the LANL ASC program office to support its decisions. To date, much of the discussion about the prospects for Fortran has tended to be informal and centered on questions (such as, “will the language be around in 20 years”) that are impossible to answer with any certainty. By focusing on estimates of the likelihood associated with different outcomes, rather than on specific predictions, we hope to clarify points of disagreement within the community and strengthen the analytic basis for reasoning about the future.

97 MATHEMATICS AND COMPUTING↗

Teaching Software Sustainability for High Performance Computing at ATPESC

The Argonne Training Program in Extreme Scale Computing (ATPESC) was started by Argonne National Laboratory with the objective of expanding the ranks of better-prepared users of high-performance computing (HPC) machines. One of the unique aspects of the program was inclusion of a track on software engineering and community codes. The inclusion was motivated by the observation that the projects with good software processes were better able to meet their scientific goals. Over the years, with greater awareness of software sustainability issues in the community, the track has evolved into a software productivity and sustainability track. In this paper we present our experience in choosing and disseminating the content related to the topic of software engineering in high performance computing science from the beginning of the program until now. We discuss the motivations and the reception of the tracks. We also document the evolution of the track over the years based on student feedback and also the growth of awareness about software productivity in high performance computing.

Dubey, Anshu↗

Ion Coulomb Crystals in Storage Rings for Quantum Information Science

Quantum information science is a growing field that promises to take computing into a new age of higher performance and larger scale computing as well as being capable of solving problems classical computers are incapable of solving. The outstanding issue in practical quantum computing today is scaling up the system while maintaining interconnectivity of the qubits and low error rates in qubit operations to be able to implement error correction and fault-tolerant operations. Trapped ion qubits offer long coherence times that allow error correction. However, error correction algorithms require large numbers of qubits to work properly. We can potentially create many thousands (or more) of qubits with long coherence states in a storage ring. For example, a circular radio-frequency quadrupole, which acts as a large circular ion trap and could enable larger scale quantum computing. Such a Storage Ring Quantum Computer (SRQC) would be a scalable and fault tolerant quantum information system, composed of qubits with very long coherence lifetimes. With computing demands potentially outpacing the supply of high-performance systems, quantum computing could bring innovation and scientific advances to particle physics and other DOE supported programs. Increased support of R$\&$D in large scale ion trap quantum computers would allow the timely exploration of this exciting new scalable quantum computer. The R$\&$D program could start immediately at existing facilities and would include the design and construction of a prototype SRQC. We invite feedback from and collaboration with the particle physics and quantum information science communities.

43 PARTICLE ACCELERATORS↗

Portable and Adaptable Neutron Diagnostics for Advancing Fusion Energy Science Addendum

Activation detectors developed at LLNL for measuring real-time neutron fluence from fusion sources are used in the broader fusion community. The recommended fluence operating range of this diagnostic is 5x10 2 – 1x10 6 n/cm2. The upper limit on this fluence range is set by the dead time caused by data transfer between the detector and data acquisition computer. Delaying the start of counting is a possible strategy to operate these detectors in higher fluences.

42 ENGINEERING↗

FAIR Data and Interpretable AI Framework for Architectured Metamaterials (Final Report)

This research program established a transformative framework for the discovery and design of mechanical metamaterials, which are architected structures engineered to control physical phenomena like sound and vibration in ways natural materials cannot. To overcome the traditional reliance on trial-and-error, the project developed an interpretable Artificial Intelligence (AI) framework that moves beyond "black box" models to reveal the specific geometric patterns—such as "unit-cell templates"—that govern a material’s performance. A major breakthrough was the development of a hierarchical design method, which allows a single material to block vibrations across multiple frequency ranges simultaneously by layering patterns at different scales without them interfering with one another. This was further expanded to include irregular, graph-based designs that use spanning tree algorithms to ensure structural connectivity while allowing for customized, direction-dependent properties like stiffness and acoustic impedance. Beyond design, the project addressed the practicalities of real-world production by developing uncertainty quantification techniques that account for manufacturing defects and material variability, reducing the need for expensive physical testing by orders of magnitude. To speed up the discovery process, the team implemented Gaussian Process Regression and other surrogate models that provide accurate performance predictions at a fraction of the traditional computational cost. The AI-generated designs were successfully validated through fabrication of physical samples and wave propagation experiments, confirming their ability to accurately guide or reflect waves as predicted. By contributing these tools and high-quality FAIR benchmark datasets to the wider scientific community, this work provides a scalable foundation for advancing technologies in aerospace vibration control, medical imaging, and noise reduction.

36 MATERIALS SCIENCE↗

The Multiphysics on Advanced Platforms Project

In 2015, the Lawrence Livermore National Laboratory started development of next-generation multiphysics simulation capabilities for the National Nuclear Security Administration under the Advanced Technologies Development and Mitigation (ATDM) element of the Advanced Simulation and Computing program in collaboration with the Exascale Computing Project (ECP). A key driver for this effort across the NNSA tri-lab was the emergence of advanced high performance computing (HPC) architectures based on heterogeneous compute capabilities, including GPU based systems, as part of the national drive toward exascale computing platforms at multiple Department of Energy (DOE) facilities. Developing a multiphysics code capable of meeting the various simulation needs of the NNSA as defined by the current generation of integrated codes (or ICs), initially developed as part of the Accelerated Strategic Computing Initiative (ASCI) program beginning in 1996, and able to scale to the current 100 petaflop class pre-exascale systems, as well the forthcoming exaflop class computers, is a daunting challenge. To accomplish this ambitious goal, LLNL has embraced two key themes: use of high-order numerical methods and a modular approach to code development. The LLNL next generation effort is organized under the Multi-Physics on Advanced Platforms Project (MAPP). A foundational component of MAPP is the Axom computer science (CS) toolkit which provides infrastructure for the development of modular, performance portable, multi-physics application codes. MARBL is a next-generation application code built on the Axom base to address the modeling needs of the high energy density physics (HEDP) community for simulating high-explosive, magnetic or laser driven experiments such as inertial confinement fusion (ICF), pulsed-power magneto-hydrodynamics (MHD), equation of state (EOS) and material strength studies as part of the NNSA’s stockpile stewardship program (SSP).

97 MATHEMATICS AND COMPUTING↗

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗

Models and Methods for Sparse (Hyper)Network Science in Business, Industry, and Government

The authors are hosting an AMS sponsored Mathematics Research Community (MRC) focusing on two themes that have garnered intense attention in network models of complex relational data: (1) how to faithfully model multi-way relations in hypergraphs, rather than only pairwise interactions in graphs; and (2) challenges posed by modelling networks with extreme sparsity. Here we introduce and explore these two themes and their challenges. In this work, we hope to generate interest from researchers in pure and applied mathematics and computer science.

97 MATHEMATICS AND COMPUTING↗

Roadmap on electronic structure codes in the exascale era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.

36 MATERIALS SCIENCE↗

Survey of Deep Learning and Physics-Based Approaches in Computational Wave Imaging

Computational wave imaging (CWI) extracts hidden structure and physical properties of a volume of material by analyzing wave signals that traverse that volume. Applications include seismic exploration of the Earth’s subsurface, acoustic imaging and nondestructive testing (NDT) in material science, and ultrasound computed tomography (USCT) in medicine. Current approaches for solving CWI problems can be divided into two categories: those rooted in traditional physics and those based on deep learning. Physics-based methods stand out for their ability to provide high-resolution and quantitatively accurate estimates of acoustic properties within the medium. However, they can be computationally intensive and are susceptible to ill-posedness and nonconvexity typical of CWI problems. Machine learning (ML)-based computational methods have recently emerged, offering a different perspective to address these challenges. Diverse scientific communities have independently pursued the integration of deep learning in CWI. This review discusses how contemporary scientific ML techniques, and deep neural networks in particular, have been developed to enhance and integrate with traditional physics-based methods for solving CWI problems. We present a structured framework that consolidates existing research spanning multiple domains, including computational imaging, wave physics, and data science. This study concludes with important lessons learned from existing ML-based methods and identifies technical hurdles and emerging trends through a systematic analysis of the extensive literature on this topic.

42 ENGINEERING↗