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At least 595 records · Page 33

Neural networks to learn protein sequence–function relationships from deep mutational scanning data

Understanding the relationship between protein sequence and function is necessary to design new and useful proteins with applications in bioenergy, medicine, and agriculture. The mapping from sequence to function is tremendously complex because it involves thousands of molecular interactions that are coupled over multiple lengths and timescales. We show that neural networks can learn the sequence–function mapping from large protein datasets. Neural networks are appealing for this task because they can learn complicated relationships from data, make few assumptions about the nature of the sequence–function relationship, and can learn general rules that apply across the length of the protein sequence. We demonstrate that learned models can be applied to design new proteins with properties that exceed natural sequences.

59 BASIC BIOLOGICAL SCIENCES↗

Introduction to spectral line shape theory

Spectral line-shape models are an important part of understanding high-energy-density (HED) plasmas. Models are needed for calculating opacity of materials and can serve as diagnostics for astrophysical and laboratory plasmas. However, much of the literature on line shapes is directed toward specialists. This perspective makes it difficult for non-specialists to enter the field. We have two broad goals with this topical review. First, we aim to give information so that others in HED physics may better understand the current field. Additionally, this first goal may help guide future experiments to test different aspects of the theory. Second, we provide an introduction for those who might be interested in line-shape theory, and enough materials to be able to navigate the field and the literature. We give a high-level overview of line broadening process, as well as dive into the formalism, available methods, and approximations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Commercial, industrial, and institutional discount rate estimation for efficiency standards analysis: Sector-level data 1998–2021

Underlying each of the Department of Energy’s (DOE’s) federal appliance and equipment energy conservation standards are a set of complex analyses of the projected costs and benefits of regulation. Any new or amended standard must be designed to achieve significant additional energy conservation, provided that it is technologically feasible and economically justified (42 U.S.C. 6295(o)(2)(A)). DOE determines economic justification based on whether the benefits exceed the burdens, considering a variety of factors, including the economic impact of the standard on consumers of the product and the savings in lifetime operating cost compared to any increase in price or maintenance expenses (42 U.S.C. 6295(o)(2)(B)). As part of this determination, DOE conducts a Life-Cycle Cost (LCC) analysis, which models the combined impact of appliance first cost and operating cost changes on a representative commercial building sample in order to identify the fraction of customers achieving LCC savings or incurring net cost at the considered efficiency levels. Thus, the commercial discount rate value(s) used to calculate the present value of energy cost savings within the LCC model implicitly plays a role in estimating the economic impact of potential standard levels. This report provides an in-depth discussion of the commercial discount rate estimation process. It is an update to previous reports on estimating commercial discount rates from firm-level financial data (Fujita, 2016). Major topics covered in this report include: Discount rate estimation methods and rationale; -Data sources used and data limitations; -Discount rate distributions for use in standards analysis; -Discount rate estimation methods and distributions specific to the small business subgroup analysis. Going forward, this report will be updated as data allow and analyses necessitate.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Beyond the Standard Model physics prospects at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) is an international project for neutrino physics and proton-decay searches, currently in the design and planning stages. Once built, DUNE will consist of two detectors exposed to the world's most intense neutrino beam. The near detector at Fermilab will record neutrino interactions near the beginning of the beam line. The other, much larger, detector, comprising four 10-kton liquid argon time projection chambers (LArTPCs), will be installed at a depth of 1.5 km at the Sanford Underground Research Facility in South Dakota, about 1,300 km away from the neutrino source. The unique combination of the high-intensity neutrino beam, DUNE's high-resolution near detector system, and massive LArTPC far detector enables a variety of probes of Beyond-the-Standard-Model (BSM) physics, from the discovery of new particles (sterile neutrinos or dark matter), to precision tests of beyond the three-flavor mixing paradigm, non-standard neutrino interactions (NSIs), heavy neutral leptons, and the detailed study of rare processes (e.g., neutrino trident production). This article reviews these physics topics and discusses the prospects for their discovery at the DUNE experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tuning Electrogenerated Chemiluminescence Intensity Enhancement Using Hexagonal Lattice Arrays of Gold Nanodisks

Electrogenerated chemiluminescence (ECL) microscopy shows promise as a technique for mapping chemical reactions on single nanoparticles. The technique’s spatial resolution is limited by the quantum yield of the emission and the diffusive nature of the ECL process. To improve signal intensity, ECL dyes have been coupled with plasmonic nanoparticles, which act as nanoantennas. Here, we characterize the optical properties of hexagonal arrays of gold nanodisks and how they impact the enhancement of ECL from the coreaction of tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate and tripropylamine. Here, we find that varying the lattice spacing results in a 23-fold enhancement of ECL intensity because of increased dye-array near-field coupling as modeled using finite element method simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Frustration- and doping-induced magnetism in a Fermi–Hubbard simulator

Geometrical frustration in strongly correlated systems can give rise to a plethora of novel ordered states and intriguing magnetic phases, such as quantum spin liquids. Promising candidate materials for such phases can be described by the Hubbard model on an anisotropic triangular lattice, a paradigmatic model capturing the interplay between strong correlations and magnetic frustration. However, the fate of frustrated magnetism in the presence of itinerant dopants remains unclear, as well as its connection to the doped phases of the square Hubbard model. Here we investigate the local spin order of a Hubbard model with controllable frustration and doping, using ultracold fermions in anisotropic optical lattices continuously tunable from a square to a triangular geometry. At half-filling and strong interactions U/t ≈ 9, we observe at the single-site level how frustration reduces the range of magnetic correlations and drives a transition from a collinear Néel antiferromagnet to a short-range correlated 120° spiral phase. Away from half-filling, the triangular limit shows enhanced antiferromagnetic correlations on the hole-doped side and a reversal to ferromagnetic correlations at particle dopings above 20%, hinting at the role of kinetic magnetism in frustrated systems. Furthermore, this work paves the way towards exploring possible chiral ordered or superconducting phases in triangular lattices and realizing t–t' square lattice Hubbard models that may be essential to describe superconductivity in cuprate materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

Near-term tropical cyclone risk and coupled Earth system model biases

Most current climate models predict that the equatorial Pacific will evolve under greenhouse gas–induced warming to a more El Niño-like state over the next several decades, with a reduced zonal sea surface temperature gradient and weakened atmospheric Walker circulation. Yet, observations over the last 50 y show the opposite trend, toward a more La Niña-like state. Recent research provides evidence that the discrepancy cannot be dismissed as due to internal variability but rather that the models are incorrectly simulating the equatorial Pacific response to greenhouse gas warming. This implies that projections of regional tropical cyclone activity may be incorrect as well, perhaps even in the direction of change, in ways that can be understood by analogy to historical El Niño and La Niña events: North Pacific tropical cyclone projections will be too active, North Atlantic ones not active enough, for example. Other perils, including severe convective storms and droughts, will also be projected erroneously. While it can be argued that these errors are transient, such that the models’ responses to greenhouse gases may be correct in equilibrium, the transient response is relevant for climate adaptation in the next several decades. Given the urgency of understanding regional patterns of climate risk in the near term, it would be desirable to develop projections that represent a broader range of possible future tropical Pacific warming scenarios—including some in which recent historical trends continue—even if such projections cannot currently be produced using existing coupled earth system models.

Science & Technology - Other Topics↗

Evaluating the Influence of Plants on Hydrologic Cycling: Quantifying and Validating the Role of Plant Processes and Stomatal Conductance (Final Report)

Plants can exert strong controls on water cycling, both locally and across the globe. The impacts are driven by how plants control the exchange of water and energy between the land and the atmosphere, which in turn are influenced by how plants photosynthesize and grow (e.g. biogeochemical cycling). Our team has shown previously that plant responses to increasing CO 2 in the atmosphere can influence the water cycle through changes in rainfall and the amount of water on land with implications for drought. Plant responses can also alter both average and extreme flow of water in rivers, with implications for freshwater availability and flood frequency. Although the impact of plant responses on water cycling has been demonstrated to exist, significant uncertainty remains in our understanding of the magnitude and form of the plant responses themselves, as well as their ultimate impact on water availability for people and ecosystems. In this project we worked to quantify the role of plant processes in regulating water cycling (e.g., precipitation, evapotranspiration, runoff, droughts, etc.). We addressed the following objectives: quantify the control of physiological vs. radiative effects on water cycling across many coupled models in idealized and realistic scenarios, as well as to quantify how our assumptions about leaf-level processes (e.g. coupling between stomatal conductance and photosynthesis), and organism-level processes (e.g. leaf area response to high CO 2 ) contributed to uncertainties and biases in water cycling. We focused on the impact of these processes on water cycling to assess the sensitivities of precipitation, evapotranspiration, and runoff to model assumptions about plant processes at the leaf, organism, and community level. As part of this project we used measurements of stable carbon isotopes to generate observationally based estimates of plant functioning during the historical period. This work is directly relevant to DOE’s primary scientific research questions in the RGMA topic area (b) on Biogeochemical processes, feedbacks, and interactions in the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative Power System Resilience Metrics and Evaluation Approach: Preprint

Power system resilience is an emerging topic and plays an essential role in helping power industry understand and respond to the increasing threats of extreme weather events. The first step of power system resilience analysis is to introduce metrics to quantify the resilience reasonably. Existing resilience metrics are typically restrained by the limited data for extreme event modeling and fall short in terms of physical interpretation and comparability. This paper develops novel quantitative metrics to evaluate power system resilience in pre- and post-event contexts. The developed metrics illustrate clear physical meanings and can be effectively used to compare resilience across different systems under different extreme events. Moreover, the developed metrics can be applied to both transmission and distribution systems. Simulation on a distribution system is employed to validate the effectiveness of the proposed resilience metrics and resilience evaluation approach.

power system resilience↗

Increasing Industry Involvement: A Solution from a Student's Perspective

Many engineering employers are finding that graduates are not sufficiently equipped to begin contributing productively when they exit a 4-year institution and enter the workforce. The Intern Professional Development Center (IPDC) is a proposed business model that exposes engineering undergraduates to industry-relevant knowledge, while providing them with working experience during their degree. Using a tri-stage approach, the IPDC engages with students early in their academic careers, provides continuous training and development opportunities, and finally connects the students with potential employers. The two topics most commonly under-represented in engineering programs are: - Familiarity with drafting software - Knowledge of relevant codes and standards. The Intern Professional Development Center (IPDC): A tri-stage solution for recruiting, training, and encouraging the workforce of tomorrow. An IPDC allows students to be active members of industry during their undergraduate careers, leading to: - Improved local talent retention; - Improved graduation and academic performance statistics; - Near-guarantee for post-graduation employment. In March of 2019, the first IPDC prototype began operating in the Tri-Cities, Washington. Since then, 3 undergraduate students have entered the IPDC at Stage 2, beginning with the standard training and professional development. Of those 3 students, 2 have already moved on to Stage 3, with successful ongoing internships with local employers. At a performance review for one of the IPDC's Stage 3 students after 90 days of employment, the direct manager said: 'How soon can we get another one?'.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Gerischer Electrochemistry Today

Semiconductor photoelectrochemistry is a dynamic and interdisciplinary field at the forefront of research in solar fuels, energy conversion, and catalysis. Here, this Perspective captures the collective insights from the second Gerischer Electrochemistry Today Symposium, held at Colorado State University in Fort Collins, CO, in August 2024, which convened leading researchers, early-career scientists, and industry partners to define the critical next steps for the field. Through interactive sessions, technical talks, panel discussions, and training initiatives─including a Semiconductor Electrochemistry Bootcamp─the symposium emphasized three pillars of advancement: (i) facilitating the exchange of new ideas in semiconductor electrochemistry and charge separation; (ii) fostering the development of future researchers, research topics, and participation in the semiconductor workforce; and (iii) building community. This Energy Focus distills key themes from the meeting and identifies major knowledge gaps in the following areas: mechanisms of charge separation and recombination, role of defects and disorder, dynamic and operando characterization methods, interfacial chemistry and surface passivation, theoretical and modeling limitations, and standardization and benchmarking. The inclusive and collaborative structure of the symposium enabled the generation of this comprehensive report that will serve as a roadmap for fundamental and applied research in the rapidly evolving field of semiconductor electrochemistry over the next decade.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Operation and Maintenance of PV Systems: Data Science, Analysis, and Standards

This effort improves the effectiveness and reduce uncertainty in O&M cost through four primary objectives/tasks: 1) institutionalize standards for reliability and availability reporting for large PV power plants; 2) bridge systemic O&M knowledge gaps around important topics affecting O&M; 3) characterize systemic failure modes and patterns and accelerate O&M experiential learning cycles using field data; and 4) establish a baseline understanding of UPVS O&M cost drivers. Key results of this effort include publication of IEC standards, published topical papers on O&M topics, training, and characterize field data for climate- and service-related patterns (additional details below). Integrating these results serves to reduce performance risk and facilitate improvement in the way solar projects are operated and maintained. Results are well received and two publications are among the most successful SETO publications at NREL ("Model of Operation and Maintenance Costs for Photovoltaic Systems with over 40,000 downloads and "Best Practices in Operation and Maintenance of PV Systems, 3rd Ed." with over 90,000 downloads).

14 SOLAR ENERGY↗

The effects of anthropogenic and volcanic aerosols and greenhouse gases on twentieth century Sahel precipitation

Abstract There is little scientific consensus on the importance of external climate forcings—including anthropogenic aerosols, volcanic aerosols, and greenhouse gases (GHG)—relative to each other and to internal variability in dictating past and future Sahel rainfall. We address this query by relating a 3-tiered multi-model mean (MMM) over the Climate Model Intercomparison Project phase 5 “twentieth century” and pre-Industrial control simulations to observations. The comparison of single-forcing and historical simulations highlights the importance of anthropogenic and volcanic aerosols over GHG in generating forced Sahel rainfall variability in models. However, the forced MMM only accounts for a small fraction of observed variance. A residual consistency test shows that simulated internal variability cannot explain the residual observed multidecadal variability, and points to model deficiency in simulating multidecadal variability in the forced response, internal variability, or both.

54 ENVIRONMENTAL SCIENCES↗

Learning local and semi-local density functionals from exact exchange-correlation potentials and energies

Finding accurate exchange-correlation (XC) functionals remains the defining challenge in density functional theory (DFT). Despite 40 years of active development, attaining general purpose chemical accuracy is still elusive with existing functionals. We present a data-driven pathway to learn the XC functional by using the exact density, XC energy, and XC potential. While the exact densities are obtained from accurate configuration interaction (CI), the exact XC energies and XC potentials are obtained via inverse DFT calculations on the CI densities. We demonstrate how simple neural network (NN)–based local density approximation (LDA) and generalized gradient approximation (GGA), trained on just five atoms and two molecules, provide remarkable improvement in total energies and densities. Particularly, the NN-based GGA functional attains similar accuracy as the higher rung SCAN meta-GGA on various thermochemistry datasets. These results underscore the promise of using the XC potential in modeling XC functionals and can pave the way for systematic learning of increasingly accurate XC functionals.

Science & Technology - Other Topics↗

Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model

For the past 50 years, researchers have sought molecular models that can accurately reproduce water’s microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima near 223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ~208 K. A local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is found to be the most probable hydrogen-bonding topology at all temperatures. Further, this work suggests that MB-pol may provide predictive capability for studies of liquid water’s physical properties across broad ranges of thermodynamic states, including the so-called water’s “no man’s land” which is difficult to probe experimentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗