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DOE OSTI2021

America Resilient Climate Conference

On April 14, 2021, scientists, policymakers, and other interested parties from research institutes, academia, and other organizations gathered together virtually at the America Resilient Climate Conference to discuss one of the most pressing challenges of the 21st century: building resilience to climate change. Climate change affects the security and health of all Americans. Coastal areas are enduring more frequent and severe flooding due to sea level rise and storm surge; western states and Alaska have experienced increasingly devastating wildfires, driven in part by hotter, drier, and longer fire seasons; and communities across the nation have suffered through extreme precipitation events and heat waves. Even if emissions are reduced aggressively in the near future, the world—and the United States—will continue to feel the impacts of climate change for decades to come, due to the continued accumulation of greenhouse gasses in the atmosphere. Consequently, it is essential to act now to protect natural and human assets from the gradual—as well as extreme—impacts of a changing climate. To build resilient communities, leaders and community members need science-based information about the potential impacts climate change will have decades into the future and for specific regions. Therefore, it is essential to develop high-resolution climate models that can project both various climate impacts and the interactions between earth system variables and humans down to regional and local scales. Collecting and curating data for such models and their computational requirements poses large challenges. In the future, artificial intelligence will be needed to increase their accuracy and reduce associated uncertainties. The investments in Earth system science and artificial intelligence made by the U.S. Department of Energy and other federal entities will be essential in addressing these challenges.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules

A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.

Naylor, Dan T.↗
DOE OSTI2021

Position Papers for the ASCR Workshop on Reimagining Codesign

On behalf of the Advanced Scientific Computing Research (ASCR) program in the US Department of Energy (DOE) Office of Science, we are organizing a Workshop on Reimagining Codesign (ReCoDe). Codesign is the process of jointly designing interoperating components of a computing system—in particular: applications, algorithms, system software, programming models, and the hardware on which they run. The goal is to maximize the overall performance, efficiency, and other desirable qualities of the system as a whole. Codesign is a standard methodology in the embedded-systems community, where space, power, and cost constraints are commonly pitted against execution speed for a tightly constrained feature set. Over the last decade, the DOE has invested in codesign efforts to foster the development of exascale computing systems for broad classes of scientific and engineering applications. The ReCoDe workshop hopes to explore how scientific applications of interest to the DOE can be accelerated through close interactions with hardware designers and software-stack developers, in which all components adapt to each other’s requirements and constraints. We want to answer the question of what are the key tools and methodologies for accomplishing codesign in today’s computing landscape, and what will be the highest impact targets for meeting DOE’s emerging mission requirements. This workshop aims to bring together DOE, industry, and academia to identify opportunities to build on past codesign successes and identify new areas that are either emerging or that may need reimagining for the future. We want to continue to find opportunities that can be pursued as a joint effort and continue to break down the traditional customer/vendor dichotomy with true partnerships. From this work, DOE will benefit from increased application performance relative to what stock hardware or existing general-purpose roadmaps can provide, and vendors will benefit from expanding their hardware’s capabilities to address needs they might have not otherwise anticipated and thereby create more widespread interest in their products. The workshop will be structured around a set of breakout sessions, with every attendee expected to participate actively in the discussions. Afterward, workshop attendees—from DOE, industry, and academia—will produce a report for ASCR that summarizes the findings made during the workshop.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Oak Ridge National Laboratory Annual Sustainability Report 2023

ORNL, managed under contract by UT-Battelle LLC, is DOE’s largest science and energy laboratory and, as such, executes the widest range of mission capabilities. Diverse expertise spans a broad range of scientific and engineering disciplines, enabling research and science achievements to accelerate the delivery of solutions to the marketplace. ORNL supports DOE’s national missions of scientific discovery, clean energy, and security. To execute these activities, ORNL has grown significantly over 80 years of continuous operations, consisting of facilities with commissioning dates ranging from the 1940s to the present—an extraordinary set of distinctive scientific facilities and equipment. The complexities of such a variety of facilities require teamwork among divisions, a wide variety of conservation projects, and creative strategies to achieve the desired energy and water savings. Such a diverse and unique set of major facilities, totaling over 5.5 million square feet, with 6,000 employees, requires an innovative plan to accomplish advancements in operational efficiencies. ORNL is tasked with the management of an extraordinary set of distinctive scientific facilities and equipment for DOE. ORNL is mission-driven, and its mission has grown substantially over the decades. ORNL’s core research capabilities provide broad science and technology support for DOE in the areas of energy, environment, and national security. Currently, ORNL is a world leader in materials, neutron, and nuclear science and engineering, and in high-performance computing and data analytics. ORNL’s vast portfolio of research facilities must be maintained and carefully upgraded to protect the nation’s investment in scientific analysis. The goal of sustainable and resilient operations is to enable more effective execution of ORNL’s science and technology mission. Sustainable operational practices and enhanced resilience strive for excellent results while remaining diligent in energy conservation, environmental stewardship, asset management, and community engagement. The Sustainable ORNL Program (Sustainable ORNL) Continuous improvements in operational and business processes must be integrated into the fabric of the ORNL culture to maximize the return from the investment made in modernizing facilities and equipment. The Sustainable ORNL program promotes the legacy of system-wide best practices, management commitment, and employee engagement that will lead ORNL into a future of efficient, resilient, and sustainable operations. ORNL leadership and Sustainable ORNL champions receive regular status reports on the progress of each project and focus area (i.e., roadmap) and periodic summary reports. More information can be found at the program’s website. The Sustainable ORNL roadmap structure endorses 15 vital roadmaps. The figure below summarizes the current project assignments and demonstrates that each project contributes to the wellbeing of the whole. Continuous employee engagement and regular status reports confirm the ideals of the program. The roadmap structure is not static; as the science mission advances and the needs of the organization evolve, the Sustainable ORNL roadmap structure elements are modified to align with developing priorities. In 2022, Sustainable ORNL made roadmap changes to better align ORNL to support new federal requirements that have been issued.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Laboratory earthquake forecasting: A machine learning competition

Earthquake prediction, the long-sought holy grail of earthquake science, continues to confound Earth scientists. Could we make advances by crowdsourcing, drawing from the vast knowledge and creativity of the machine learning (ML) community? We used Google’s ML competition platform, Kaggle, to engage the worldwide ML community with a competition to develop and improve data analysis approaches on a forecasting problem that uses laboratory earthquake data. The competitors were tasked with predicting the time remaining before the next earthquake of successive laboratory quake events, based on only a small portion of the laboratory seismic data. The more than 4,500 participating teams created and shared more than 400 computer programs in openly accessible notebooks. Complementing the now well-known features of seismic data that map to fault criticality in the laboratory, the winning teams employed unexpected strategies based on rescaling failure times as a fraction of the seismic cycle and comparing input distribution of training and testing data. In addition to yielding scientific insights into fault processes in the laboratory and their relation with the evolution of the statistical properties of the associated seismic data, the competition serves as a pedagogical tool for teaching ML in geophysics. The approach may provide a model for other competitions in geosciences or other domains of study to help engage the ML community on problems of significance.

58 GEOSCIENCES↗
DOE OSTI2023

Engineering Computational Practices (Rev. 1)

This manual will attempt to motivate the use of an automated build system for the purposes of computational science and engineering. As part of this motivation, the surrounding computational practices of version control, documen tation, compute environment management, and regression testing will also be addressed as applied to the practice of computational engineering. Specifically, this manual intends to motivate the adoption of these traditional software engineering practices for use in research and production engineering simulation projects. This manual is not the first such effort in the greater scientific computing community. In fact, the authors relied heavily on the lesson plans of the Software Carpentry, established to teach computing skills to researchers in 1998. As the intention for this manual is to lay out fundamental practices of engineering computing, it will not attempt to fully teach the underlying concepts and will instead reference the well designed lesson plans of the Software Carpentry. Where possible, this manual will explain to general computing practices and concepts and limit discussion of specific software implementations to examples or vehicles for practice in concrete application. The specific software taught by the Software Carpentry curriculum is an excellent starting point to learn the core concepts of computational engi neering. However, the authors have found that applications to engineering simulation and analysis require translation of these software development concepts into the language and workflows of computational engineers. Adopting these computational tools may require engineers to re-imagine their workflows in some combination of traditional engineer ing and software concepts. It has also been necessary to extend existing software build systems for engineering practices beyond the simple wrap ping of engineering software execution. Where necessary, examples of specific software and their method of extension to engineering simulations will be given, with reference to the User Manual for recommended practical use. Where this manual relies on specific implementation examples, it should be understood that the practicing engineer may find that different software is more amenable to their specific work. It is always the overall collection of computational practices is more important than any specific software implementation. The ability to recognize which concepts are implemented by a software package will make a practicing engineer agile to changing project needs, computing resources, numeric solvers, programming languages, and even available funding.

42 ENGINEERING↗
DOE OSTI2022

Novel Proposals for FAIR, Automated, Recommendable, and Robust Workflows

Lightning talks of the Workflows in Support of Large-Scale Science (WORKS) workshop are a venue where the workflow community (researchers, developers, and users) can discuss work in progress, emerging technologies and frameworks, and training and education materials. This paper summarizes the WORKS 2022 lightning talks, which cover five broad topics: data integrity of scientific workflows; a machine learning-based recommendation system; a Python toolkit for running dynamic ensembles of simulations; a cross-platform, high-performance computing utility for processing shell commands; and a meta(data) framework for reproducing hybrid workflows.

Abhinit, Ishan↗
DOE OSTI2022

Version [OpenIPSL 2.0.0] - [iTesla Power Systems Library (iPSL): A Modelica library for phasor time-domain simulations]

This paper describes Open-Instance Power System Library (OpenIPSL) version 2.0.0 and its most recent enhancements. This new version brings upgrades that include more robust models that are better documented, and example systems that illustrate certain functionalities to users. Repository and library documentations have been enhanced and expanded, and the library is now released under a new license. Changes are meant to foster user and developer communities, while providing more attractive frameworks for collaborative work to be carried out with the library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

140,142 Ce Neutron Cross Section Resolved Resonance Region Evaluation

A resolved resonance region evaluation of 140,142 Ce was conducted by Oak Ridge National Laboratory. Requested by the US Nuclear Criticality Safety Program, this evaluation is based on recent high-resolution transmission and capture high-resolution measurements of nat Ce and 142 Ce conducted at JRC-Geel at the Geel Linear Accelerator facility. It is also based on recently measured thermal constants available from the EX FOR database. Starting from the resonance parameters from the ENDF/B-VIII.0 library and following a preliminary R-matrix analysis, an updated set of resonance parameters and corresponding covariance in formation was derived by the fit of these experimental datasets using the Reich–Moore approximation of the R-matrix theory, as implemented in the SAMMY code system. The resolved resonance region upper energy limit for 140 Ce was kept at 200 keV, whereas the 142 Ce resonance region was extended from 13 to 26 keV. This new evaluation was found to be in good agreement not only with several integral quantities of interest to the reactor physics community, but also with the stellar Maxwellian-averaged cross section.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Towards exact finite temperature electronic structure in solids and molecules (Final Technical Report)

This report describes the University of Iowa portion of a project that is now continuing at Michigan State University. We are developing novel methods, algorithms, and software to enable simulations of molecules and materials at high temperature. This is a key challenge in chemistry and materials science. By refining an approach called Density Matrix Quantum Monte Carlo (DMQMC), we developed faster and more accurate ways to conduct these simulations. These advances will help us understand how temperature affects the behavior of electrons, chemical bonds, and phase transitions in solids and molecules. These breakthroughs are especially important for applications where light and heat drive chemical reactions, superconductivity, and materials used in energy and sensing. In addition, this project involved the development of the open-source HANDE-QMC software package, supporting the broader community in benchmarking and developing finite-temperature electronic structure methods.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Discovery of Signaling Small Molecules (e.g. quorum sensing molecules) from the Microbiome

Microbial communities are shaped through the interactions between their microbial members and the environment (microbe-microbe and host-microbe interactions). Signal transduction pathways in the microbiome are often modulated through the small molecule products of microbial biosynthetic gene clusters (BGCs). Advances in 16S rRNA profiling and shotgun metagenomics have revolutionized our understanding about the microbial composition of various communities and their BGCs. Environmental metagenomes contain thousands of BGCs with uncharacterized small molecule products that potentially play roles in signal transduction. The overarching aim of this proposal was to develop computational techniques for discovering these small molecules and characterizing their bioactivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

EpiCast: Simulating Epidemics with Extreme Detail

In early 2020, COVID-19 swept the globe. Governments attempted to “flatten the curve” through business shutdowns and stay-at-home orders, but the United States was hit hard. By the end of March, mere months after the virus first emerged in humans 7,000 miles away, the U.S. had recorded 192,300 cases and 5,300 deaths. While this unprecedented disaster sent shockwaves through every level of society and clouded an uncertain future, state and local governments turned to computational and mathematical epidemiology researchers to help formulate intervention strategies to limit the spread of the disease. Traditional forecasting models provided a reasonable understanding of how the near future was likely to look, but local policy makers and public health communities still struggled to understand how potential mitigations ought to be implemented. Decision makers needed a way to measure the impact of their policy choices—they needed better technology. EpiCast answered the call, bringing urgently needed answers to policymakers grappling with how to adjust school and business schedules. EpiCast is modeling software that generates a synthetic, representative population to simulate infectious disease transmission in the United States with extreme detail and granularity. The software models human behavior combined with community-specific information to provide a fine-grained preview of the effect of potential mitigation strategies for decision makers.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Information and Statistics in Nuclear Experiment and Theory (ISNET)

As with all empirical sciences, nuclear physics operates in the virtuous cycle of the scientific method: observations inspire theoretical models; models lead to new predictions; predictions are tested in experiments; experiments lead to new observations; and so on. Evaluating what we are inferring, and how certain we are of it, is key to this process. These requirements, and a general interest in applying novel statistical, mathematical, and computational techniques, led to the formation of a dedicated research community entitled “Information and Statistics in Nuclear Experiment and Theory (ISNET)” (https://isnet-series.github.io/), which now includes more than 300 members. While the community’s interests lean toward nuclear theory, the unifying theme for this group is the inference of knowledge from data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Bioimaging Capabilities to Enable Mapping of the Neural Connections in a Complex Brain

DOE’s Office of Science (SC), through its BRAIN Initiative Working Group, convened a virtual roundtable on November 2-4, 2020, to develop a conceptual framework for the capabilities needed to enable an interdisciplinary community of researchers to fully map the neural connections initially in the brain of a mouse and ultimately in the brain of a human. Over 30 researchers and programmatic observers from diverse scientific backgrounds, including those working in both the basic and applied sciences, participated in the roundtable and conceptualized forward-leaning ideas. In developing the framework, participants were asked to address questions under the three themes: connectome requirements, bioimaging technology, and computing and data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Developing and Distributing HEP Software Stacks with Spack

The Computational Science and AI Directorate at Fermilab is using Spack to support the development efforts of a large number of scientific programmers, in many independent projects and experiments. While independent, these projects share many dependencies. They are typically under continuous and fairly rapid development. They have to support deployment on diverse hardware. This is a different context than is typical for the management of HPC software, where Spack was born. To support our community, we have created a model that enables users to develop code with greater efficiency than is possible with Spack’s current development facilities. In this talk we will present: - a brief introduction to the science we support (particle physics) - how the code we work with is naturally organized into several layers of packages - how we are using Spack to manage those layers - how we leverage the layering to provide efficient support for developers, using our Spack extension “MPD”. - some suggestions for changes or additions to Spack to make such work easier.

Knoepfel, Kyle J. [Fermilab]↗
DOE OSTI2023

Importance of ice nucleation and precipitation on climate with the Parameterization of Unified Microphysics Across Scales version 1 (PUMASv1)

Cloud microphysics is critical for weather and climate prediction. In this work, we document updates and corrections to the cloud microphysical scheme used in the Community Earth System Model (CESM) and other models. These updates include a new nomenclature for the scheme, now called Parameterization of Unified Microphysics Across Scales (PUMAS), and the ability to run the scheme on graphics processing units (GPUs). The main science changes include refactoring an ice number limiter and associated changes to ice nucleation, adding vapor deposition onto snow, and introducing an implicit numerical treatment for sedimentation. We also detail the improvements in computational performance that can be achieved with GPU acceleration. We then show the impact of these scheme changes on the (a) mean state climate, (b) cloud feedback response to warming, and (c) aerosol forcing. We find that corrections are needed to the immersion freezing parameterization and that ice nucleation has important impacts on climate. We also find that the revised scheme produces less cloud liquid and ice but that this can be adjusted by changing the loss process for cloud liquid (autoconversion). Furthermore, there are few discernible effects of the PUMAS changes on cloud feedbacks but some reductions in the magnitude of aerosol–cloud interactions (ACIs). Small cloud feedback changes appear to be related to the implicit sedimentation scheme, with a number of factors affecting ACIs.

54 ENVIRONMENTAL SCIENCES↗