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Genomes to Structure and Function Workshop Report 2022

The goal of the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Program is to achieve a predictive understanding of complex biological, earth, and environmental systems with the aim of advancing the nation’s energy and infrastructure security. (https://www.energy.gov/science/ ber/biological-and-environmental-research). To pursue this goal, collaborations among experts in diverse research areas that lead to multidisciplinary projects are indispensable. The roles of DOE’s User Facilities, which offer unique and powerful resources for such research projects, are evolving, and expectations for the facilities are increasing. To respond to Users’ needs, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) initiated the Facilities Integrating Collaborations for User Science (FICUS) program in 2014. This collaboration has grown into a popular and successful program, advancing more than 100 multidisciplinary projects to date. Similarly, the new interFacility collaborations among the JGI, EMSL, and User resources for BER structural biology and imaging at the Basic Energy Science (BES) Program’s synchrotron and neutron facilities are becoming essential for cutting-edge transdisciplinary science. To further explore the need for the BER research community to combine genomic, functional, and structural approaches to advance their research, an organizing committee was formed to develop and jointly host a 3-part workshop. The committee’s members represented seven DOE National Laboratory User Facilities (Appendix 1 lists the members). The “Genomes to Structure and Function” virtual workshop (see Appendices 2–5) was composed of three sessions. The first session, titled “Molecular Structures” (October 27– 28, 2021), highlighted diverse integrative experimental and computational approaches correlating structural data with sequencing and functional information, as well as predicting protein structures to model complex biological systems. The second session, “Intracellular Organization, and Material Synthesis and Decomposition” (December 15–16, 2021), covered imaging methods for observing, quantifying, and manipulating biosystems. The third session, “Imaging the Rhizosphere and Cellular Organization” (January 26–27, 2022) emphasized advanced and non-invasive imaging techniques applied to plant root-microbe-soil interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Best practices for experiments and reporting in photocatalytic CO 2 reduction

Visible-light-driven conversion of CO 2 to fuels and valuable compounds has experienced tremendous activity in recent years, aiming at storing solar energy into chemical bonds using CO 2 as a renewable feedstock, ultimately at massive scale. Despite these efforts, processes and catalytic systems are still at an early stage of development, with fundamental mechanistic challenges as pre-requisites for device design. In this context, collective efforts currently necessitate the exploration of a variety of approaches. On the other hand, an alignment of practices is required to ensure robustness, precision and accuracy of the results, as well as shared metrics and tools for advancing our understanding of the necessary processes. Here, this Perspective aims to provide guidelines and a framework towards these objectives.

photocatalysis↗

Oh, My Darling Clementine: A Detailed History and Data Repository of the Los Alamos Plutonium Fast Reactor

The Los Alamos Plutonium Fast Reactor, Clementine, provided the first fast neutron spectrum using a metallic plutonium fuel system and liquid mercury coolant. Clementine is often mentioned in the history of fast, metal-fueled, or metal-cooled designs, with little public information regarding the specifications or timeline. This paper contains a synopsis of each report regarding the development, operation, experimental results, failures, and subsequent disassembly of Clementine to explore this unique reactor within the context of modern advanced reactor development.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Qualification and Commissioning of Helium Flow Loop Experiment for Blanket Design Measurements

Sufficient cooling of plasma-facing materials remains an outstanding challenge in the design of fusion reactor blankets in commercial power demonstration plants. Due to its chemical inertness and low neutron interaction cross section, pressurized helium is a candidate coolant fluid for such systems; however, helium has a small thermal mass compared to liquid coolants, potentially reducing heat removal performance. To address this need, a number of heat transfer enhancements have been proposed to improve the cooling efficiency of such components, thereby decreasing pumping power needs and improving overall plant efficiency. Toward this end, a helium flow loop experiment (HFLE) has been designed and commissioned to test advanced passive heat transfer enhancements in unit-cell test sections, providing necessary data for model validation and subsequent system design. The HFLE is designed to provide flow of pressurized (up to 4 MPa) helium at flow rates up to 80 g/s, enabling heat transfer and pressure drop measurements in test pieces at Reynolds numbers in excess of 180 000. To explore the effects of novel and complex heat transfer enhancements, test sections are produced via additive manufacturing, providing geometries not typically obtainable by conventional machining. Here in this work, we present results from HFLE commissioning and the initial thermal-hydraulic tests of an additively manufactured rifled-rib test section. Results are compared to smooth pipe correlations, and plans are described for future HFLE measurements. These preliminary experiments indicate the utility of the HFLE for heat transfer enhancement testing and simulation validation activities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neutron reconstruction via blips in liquid argon time projection chambers

Neutrons are important final-state particles in neutrino interactions, yet they are not considered or reconstructed in most current neutrino liquid argon time projection chamber (LArTPC) physics analyses. In this paper, we present a simulation-based proof-of-concept study of neutron reconstruction in a generic LArTPC detector. Leveraging isolated, MeV-scale energy deposits, or blips, from neutron inelastic scattering, and using realistic blip response from published experimental results, we demonstrate the capability to identify neutrons and to reconstruct the direction and energy of the final-state neutron system in sub-GeV neutrino interactions. We then explore how neutron-related blip attributes can be used to improve physics studies of neutrino interactions, such as enhancing neutrino-antineutrino separation in atmospheric neutrinos and reverse-horn-current beam neutrinos. This study provides an initial quantification of LArTPC neutron reconstruction capabilities, which we expect to improve with future advancements in blip reconstruction, identification, and classification algorithms, as well as the modeling of neutrons.

Morquecho, Miguel Hernandez [Univ. of Minnesota, M↗

Natural Gas Community of the Future (Final Report)

Nicor Gas, a subsidiary of Southern Company Gas and its parent company Southern Company, is developing the concept of the Carbon-neutral, Affordable, Resilient, and Equitable Community ("CARE Community") to address the challenges of accessibility and affordability of grid-interactive efficient buildings in historically disadvantaged communities. The CARE Community is a new construction net-zero energy and carbon neutral residential neighborhood consisting of 50 homes with electricity and natural gas services in South Suburban Chicago, built as low-income affordable housing. The National Renewable Energy Laboratory (NREL) is assisting Southern Company to explore how energy efficiency, renewable technologies, and the reliability and resilience of natural gas can be combined and optimized in an islandable energy system as part of a broader effort to understand the role natural gas plays in future communities integrated with renewable energy and improved energy efficiency. The CARE Community will demonstrate how energy efficiency, distributed energy resources (DERs), and advanced controls can be combined with existing natural gas infrastructure to serve historically disadvantaged communities in a cold climate with low energy cost for affordable housing programs and enhanced resilience to withstand extreme weather. Homes will be a part of an islandable energy system, integrating multiple DER technologies such as solar panels, natural gas fuel cells, reciprocating natural gas engines, and battery storage. The CARE Community will provide a replicable template that affordable housing developers and energy companies can adopt throughout the United States. In this report, we present the design and modeling of the community and potential approaches for integrating DERs. We analyze and discuss annual simulations under normal operating conditions and week-long simulations under electric power grid outage conditions.

03 NATURAL GAS↗

Bill Savings vs. Backup Power: Evaluating operational tradeoffs for home solar+storage systems [Slides]

Adoption of residential solar photovoltaic+energy storage systems (PVESS) is driven by both bill savings opportunities and customer demand for backup power. Prior work by this team (Gorman et al., 2022; Gorman et al., 2023) explored PVESS backup power capabilities during long-duration power interruptions (e.g., due to severe weather events), when customers are assumed to be able to anticipate the event and charge their batteries in advance. In many cases, however, power interruptions are unpredictable (and often relatively short); for those types of events, a customer will typically set its battery to maintain some minimum capacity in reserve in case of an interruption, which reduces the capacity available for managing utility bills. This study evaluates this operational tradeoff to help customers and installers configure backup reserve settings, and to inform decision-making more generally about the customer value of backup power services compared to utility bill savings. This study utilizes Berkeley Lab’s PRESTO tool to produce stochastic simulations of (predominantly short-duration) power interruption events, and builds on an earlier case-study demonstrating PVESS backup performance during short-duration interruptions (Baik et al., 2023).

14 SOLAR ENERGY↗

Artificial Intelligence Application to D and D - 20492

As aging facilities across the DOE complex await decommissioning, there is an ongoing need to understand any changes in the structural conditions. Many of these facilities were built over 50 years ago and, in some cases, these facilities have gone beyond the expected operational lifetime. Many facilities have been placed in a state of 'cold and dark,' sitting unused and awaiting decommissioning. Especially challenging are the aging facilities that provide unique operational/production capabilities to support critical DOE missions and cannot be shut down. In any of these scenarios, the structural integrity of these facilities may become compromised as time passes. It is critical that adequate inspections be performed on a continual basis and that the data collected undergoes sufficient analysis to support timely identification of any new or worsening structural issues as well as prompt needed maintenance and repairs to maintain the facilities in a safe condition. In recent days, Artificial Intelligence (AI) [1] and its application to various domains are growing at fast speed. FIU is performing research in this area and exploring the associated technologies to solve nuclear decommissioning problems. Artificial intelligence refers to the capability of a program to autonomously act, react and adapt to the working environment. AI enables the machine to behave like humans and perform the cognitive functions such as 'learning' and 'problem solving'. AI systems gradually moving from traditional approaches (algorithms and expert systems) towards more efficient and advanced technologies (machine learning [1] and deep learning [2] [3]). AI is the study of algorithms and statistical models that is being used by computers to perform specific tasks without using explicit instructions. FIU is working to develop a pilot-scale infrastructure to implement structural health monitoring using AI technologies with focus on machine learning, deep learning. This research is focused on Computer Vision/Image Classification area of AI applications. This can also be expanded to other areas of AI related to Object Recognition and Character Recognition in images. In addition to utilizing existing data sets, FIU will collect and investigate image and video data using FIU test-bed mockups to monitor structural health of the facility. Resulting data will be processed and analyzed using machine learning/deep learning technologies. The proposed pilot system is intended to serve as a starting point to engage the DOE field sites on related data sets and their decision making needs. It is anticipated that proposed machine learning/deep learning technologies can be effectively employed using anomaly detection to solve EM challenges in surveillance and maintenance of the D and D facilities. FIU will work with research stakeholders to identify applications at various sites and other DOE facilities. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Can the United States Maintain Its Leadership in High-Performance Computing? - A report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR Office

The United States (U.S.) is no longer the unambiguous leader in the vitally important field of high performance computing (HPC). Japan, the European Union (EU), and China have fielded systems that are on par with our fastest supercomputers. The supply chain for everything from semiconductors to scientific software is globally distributed. Yet our economic future and security depend critically on our ability to innovate faster than our competitors, and the speed of innovation depends increasingly on large-scale computational science and engineering and thus HPC. How should the United States respond to this challenge? This report seeks to initiate a new and potentially transformative national discussion on this vital question. The Department of Energy’s (DOE) Advanced Scientific Computing Research (ASCR) program is well-positioned to make informed, targeted decisions about where the United States should cooperate and where it should compete in the global market for scientific exploration and discovery. By setting its sights on problems critical to our nation and the world, by establishing productive new collaborations, and by making strategic investments, ASCR can restore and maintain U.S. scientific leadership in the critical areas described in this report while strengthening our research infrastructure and training a large, diverse cohort of scientists. In doing so, ASCR and its scientists will pave the way for a secure and prosperous future for America. For more than 30 years, the ASCR program has provided the HPC and networking capabilities and expertise needed to support DOE’s mission to advance the national, economic, and energy security of the United States. The program now faces the challenge of developing and deploying the next generation of HPC systems and technologies, as well as supporting the application of HPC and artificial intelligence (AI) technologies to a wide range of scientific and engineering research problems. Through its research and development efforts, the ASCR program must also advance the state of the art in HPC and accelerate the pace of scientific discovery and technological innovation. Fulfilling this promise will require significantly increased investments, as well as innovative policies and programs. This subcommittee is aware that we are making recommendations and calls for action at a time when federal resources are limited. We understand that a wide range of competing priorities must be balanced by the nation’s leaders and that there is a need to leverage resources in new ways and seek efficiencies in facilities and operations. However, we must not let these realities limit our imagination or silence our advocacy. The ASCR program is a key part of the U.S. research infrastructure and an important component of economic growth and U.S. competitiveness. ASCR has a responsibility to pursue its mission, including advanced scientific computing, applications of AI technologies, and the required advanced research facilities, with determination and enthusiasm. To fulfill the scientific enterprise’s responsibility to the nation, the ASCR program must not only develop and publish a clear vision with an associated list of goals, priorities, and recommendations but also demonstrate scientific leadership by consistently securing long-term funding. This will allow the program to build on its achievements to date, to realize its ambitious vision, and to make lasting contributions to the field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Investigating Kinetic Mechanisms of Soot Formation in Plasma Pyrolysis of Methane via Active Learning (Final Technical Report)

Plasma pyrolysis of methane is an effective route for zero-carbon hydrogen production. Yet, soot generated from pyrolysis of hydrocarbons is detrimental to the climate and human health. There is ample experimental and theoretical evidence that suggests polycyclic aromatic hydrocarbons (PAHs) are the molecular precursors to soot particles. The reaction pathways of PAH formation are intricately dependent on a multitude of process parameters, whose kinetic mechanisms are not well-understood in plasma pyrolysis. This project aims to leverage advances in the kinetic modeling of soot formation in combustion, as well as in surrogate modeling and active learning, to systematically investigate the effects of process parameter on the kinetics of PAH formation in plasma pyrolysis of methane. To this end, we propose to use the PAH formation kinetics model developed by the PPPL/PU group based on the well-established ABF and HACA mechanisms, coupled with low-temperature plasma models. We will develop an active learning (AL) framework based on Bayesian optimization to systematically and data-efficiently explore the complex and multivariable parameter space of plasma pyrolysis in order to quantify the effects of plasma and feed parameters on the ABF and HACA kinetic pathways. AL is the branch of machine learning concerned with systematically querying samples from a system (experimental or computational) to train a data-driven model that maps design parameters to a performance criterion. We will use the data generated via AL to perform global sensitivity analysis, combined with uncertainty quantification, to elucidate the impact of different reaction pathways on minimizing formation of soot precursors. This study will result in an improved understanding of kinetics of PAH formation in plasma pyrolysis and can pave the way for more advanced mechanistic studies (e.g., soot nucleation mechanisms). Additionally, the findings will be useful for establishing practical strategies for increasing the pyrolysis efficiency and producing high-grade carbon for synthesis of nanomaterials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

New approaches to secondary metabolite discovery from anaerobic gut microbes

The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme & Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Advances in Colloidal InP-Based Quantum Dots for Photocatalytic Hydrogen Evolution

Photocatalytic materials for hydrogen generation are typically categorized into UV-absorbing metal oxides and visible-range semiconductors such as chalcogenides or perovskites, which often incorporate toxic elements. To address environmental concerns of the latter group, indium phosphide (InP)-based quantum dots (QDs) have recently emerged as a less toxic alternative. These nanocrystals (NCs) benefit from a broadband and tunable absorption spectrum, which is well matched for solar photochemistry, and offer suitable electronic characteristics to drive photoinduced charge separation. This perspective provides a comprehensive summary of the recent advancements in developing InP-based NCs with a focus on photocatalytic hydrogen production. We discuss synthetic strategies that enhance the catalytic activity of these materials and highlight key challenges that must be addressed to enhance their performance. Finally, we explore future research directions aimed at improving photocatalytic efficiency and integrating InP-based QDs into practical solar-to-fuel conversion systems.

Hydrogen↗

The Optical Stochastic Cooling Program at Fermilab

Recently, Optical Stochastic Cooling (OSC) became the first demonstrated method for ultra-high-bandwidth stochastic cooling. The initial experiments at Fermilab’s IOTA ring explored the essential physics of the method and demonstrated cooling, heating and manipulation of beams and single particles. Having been validated in practice, with continued development, OSC carries the potential for dramatic advances in the state-of-the-art performance and flexibility for beam cooling and control. The ongoing program at Fermilab is now focused on the development of an OSC system that includes high-gain optical amplification, which promises a two-order-of-magnitude increase in the strength of the OSC force. Here we review the progress and plans for the amplified OSC program. This includes detailed lattice designs and tracking simulations for the various experimental configurations, designs and status for the various hardware systems, and near-term operational plans and use cases.

Jarvis, J. [Fermilab]↗

Roadmap to Automated Mobility Systems: Informing the Planning of a Sustainable, Resilient Transportation Ecosystem for Dallas/Fort Worth International Airport

The National Renewable Energy Laboratory (NREL) developed this report to provide Dallas/Fort Worth International Airport (DFW) assistance toward a vision that considers the maturation and proliferation of mobility automation, electrification, and infrastructure integrated with Internet of Things (IoT) technologies as they present themselves on the path to 2035. In planning ongoing infrastructure investments, DFW has goals to accommodate and leverage these enabling technologies toward greater sustainability and enhanced traveler and employee experiences, ensuring that infrastructure investments are fully utilized into the future. The objective of this document is to assist DFW to anticipate and envision future airport access by travelers, employees, and goods by examining existing needs and exploring opportunities enabled by technology that informs longer-term infrastructure planning. The vast infrastructure of DFW, which includes buildings, roadways, and other physical structures, as well as growing digital and energy network infrastructures, requires long-term planning and strategy to fully leverage technology advancement and avoid abandoning assets due to functional obsolescence.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Industrial Locomotive Inventory Analysis

Due to their captive and local operations, industrial locomotives present a unique potential to reduce energy consumption and associated costs through application of advanced locomotive technologies. However, until now, there has been no data source for the number, size (hp), usage, and energy consumption of these locomotives, which limits the ability to design and implement a research, development, and deployment strategy. This research addresses this gap by developing the first national inventory of locomotives in industrial use and provides a tool to explore the energy and emissions associated with this transportation segment.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Multiscale Electricity Modeling for Evaluating Carbon Capture and Sequestration Technologies (MEME-CCS)

This effort employs and adapts a rigorous multiscale electricity modeling platform at the National Renewable Energy Laboratory (NREL) to evaluate carbon capture and sequestration (CCS) and negative emissions technologies (NET) from the ARPA-E FLECCS program. NREL's modeling platform includes the Regional Energy Deployment System (ReEDS) electric sector capacity expansion model, which projects future electricity generation mixes at sub-state-level resolution that are downscaled to the unit-level to enable hourly, zonal or nodal electricity production cost modeling in the PLEXOS model. The ReEDS-PLEXOS modeling suite is well-established for examining electric sector futures with high renewable energy penetrations, energy storage, electrification, and distributed generation. The key advancement proposed herein utilizes collaboration with CCS experts at the University of Wyoming (U.WY) and the FLECCS technology development teams to create innovative methods for representing CCS and NET in the ReEDS and PLEXOS models. Expanded technology options and new operational parameterizations are integrated into these models to allow an unprecedented combination of scope and resolution for exploring the future of CCS and NET. The resulting capabilities permit wide-ranging scenario analysis to assess CCS and NET deployment under alternative scenarios of CO2 prices and competitiveness of flexible CCS and NET technologies. We demonstrate sample deployment and operational outcomes to show how these models are being used to assess the future potential for FLECCS technologies and their impacts on the U.S. electricity system. These products will help an emerging CCS/NET industry in the United States by providing economics-driven guidance to technology developers while informing policy and investment decisions in the public and private sectors.

capacity expansion↗

Designing the Protocols for Programmable Ammonia Catalysis

Programmable catalysis can provide a more energy-efficient and cost-effective route to enhancing commercial ammonia production, a key process in the advancement of renewable energy technologies and the manufacture of fertilizers and basic chemicals. This work explores the computational discovery of optimal forcing protocols to drive such dynamic catalysis models. By employing matrix-free time-stepper methods, coupled with an optimization approach, that integrates Bayesian optimization with a Bayesian continuation strategy to efficiently discover the periodic steady states of such periodically forced systems, we enable the discovery of complex optimal catalyst strain waveforms, while ensuring robust solver convergence. We demonstrate the flexibility of our approach to discover optimized forcing protocols under varying physical constraints on strain modulation or other catalyst operating parameters. We show that these can have a temporal structure more complex than simple step functions. In order to detect undesirable catalytic loops that may correlate with overall reduced performance, we perform a study using graph-theoretical analysis to investigate the dynamics of catalytic kinetic networks formed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗