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At least 289 records · Page 16

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DOE OSTI2023

Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture

To meet the ever-increasing need for high-throughput screening in metabolic engineering, information-rich, fast screening methods are needed. Mass spectrometry (MS) provides an efficient and general approach for metabolite screening and offers the capability of characterizing a broad range of analytes in a label-free manner, but often requires a range of sample clean-up and extraction steps. Liquid extraction surface analysis (LESA) coupled MS is an image-guided MS surface analysis approach that directly samples and introduces metabolites from a surface to MS. Here, we combined the advantages of LESA–MS and an acoustic liquid handler with stable isotope-labeled internal standards. This approach provides absolute quantitation of target chemicals from liquid culture-dried droplets and enables high-throughput quantitative screening for microbial metabolites. In this paper, LESA–MS was successfully applied to quantify several different metabolites (itaconic acid, triacetic acid lactone, and palmitic acid) from different yeast strains in different mediums, demonstrating its versatility, accuracy, and efficiency across a range of microbial engineering applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Seasonality and Declining Intensity of Methane Emissions from the Permian and Nearby US Oil and Gas Basins

We quantify weekly methane emissions and trends from oil and gas production in the US Permian Basin for 2019-2023, and in nearby basins for 2022-2023, by analytical inversion of Tropospheric Monitoring Instrument (TROPOMI) satellite observations with the Integrated Methane Inversion (IMI) at 25 km resolution. Permian oil and gas emissions averaged 4.0 ± 1.1 Tg a-1 over 2019-2023, with large seasonal variation but little interannual variability. Methane intensity fell from 5.2 to 3.2% as production surged. Intensity in the New Mexico Permian fell from 4.5 to 2.1%, approaching the state's 2026 target of <2%. Emissions were on average 50 ± 10% higher in winter than summer, which we corroborate with Permian Basin Tower Network measurements, Insight M aircraft data, and GHGSat satellite observations. This seasonality may be driven in part by higher winter emissions from liquid storage tanks due to decreased separator efficiency in cold conditions. Similar but weaker seasonality along with decreasing emissions and intensities is found in weekly inversions for the Anadarko, Barnett, Eagle Ford, and Haynesville basins in 2022-2023. Our work suggests that better weatherization of oil and gas facilities could significantly reduce methane emissions.

Permian↗

DOE OSTI2026

Recent Weakening of the Global Radiative Feedback

Earth's climate stability, characterized by the global radiative feedback parameter (𝜆), varies decadally due to changing surface temperature patterns. Recent variations in 𝜆 are poorly understood as coordinated model simulations typically end in 2014. We apply a convolutional neural network trained on climate model simulations to observation-based surface temperature reconstructions to estimate variations in 𝜆 up to 2025. We find that 𝜆 reached a minimum (maximum stability) around the mid 1990s (𝜆 ≃ −3 Wm −2 /K), but has since weakened significantly (𝜆 ≃ −2 Wm −2 /K). We confirm these results with climate model simulations extended to 2022. The recent 𝜆 weakening is not significantly affected by El Niño Southern Oscillation or Pacific Decadal Oscillation. Attribution reveals that warming in the subtropical Northeast Pacific is an important driver of the recently weakened feedback, confirmed by targeted experiments in E3SMv2. Our approach enables near real-time monitoring of Earth's climate stability.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Mixed heavy metal stress induces global iron starvation response

Abstract Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Choreographing root architecture and rhizosphere interactions through synthetic biology

Abstract Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The influence of laser energy on deuterium emission characteristics from a Zircaloy-4 plasma

Laser-produced plasma coupled with optical emission spectroscopy (OES) is a promising technique for detecting certain isotopes, with unique capabilities such as standoff and rapid detection and minimal to no sample preparation requirements. The key figure-of-merit for isotopic analysis using optical spectroscopy tools is the linewidth relative to the isotope shift. Although the isotopes of hydrogen (1H, 2H, and 3H) possess large isotopic shifts (1H–2H ≈ 180 pm, 1H–3H ≈ 240 pm), being a light element, the H transitions are susceptible to various broadening mechanisms in the plasma environment. One of the critical parameters that influence the linewidth of a transition in an LPP is the incident laser energy. In the present study, we evaluated the role of laser energy on plume expansion dynamics, deuterium emission intensity, and linewidth in a nanosecond laser-produced Zircaloy-4 plasma. The changes in 2Hα emission intensity and linewidth were investigated for varying laser fluence and time after plasma onset. Spatially resolved and spatially integrated OES were performed and compared to investigate the emission spectral features and linewidth of 2Hα. Monochromatic two-dimensional time-resolved imaging was also performed to understand the morphology of the deuterium and protium emission relative to all species in the plume. Our results showed that 1Hα and 2Hα emissions predominantly occur closer to the target. Measurements of 2Hα linewidth approached similar values at later times of plasma evolution regardless of the laser energy. The linewidths of the 2Hα transition showed insignificant differences between spatially resolved and spatially integrated measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

The long road to ignition: An eyewitness account

This paper reviews the many twists and turns in the long journey that culminated in ignition in late 2022 using the laser heated indirect-drive approach to imploding DT filled targets at the National Ignition Facility (NIF), located at the Lawrence Livermore National Laboratory (LLNL). We describe the early origins of the Laser Program at LLNL and key developments such as the paradigm shifting birth of high energy density physics (HEDP) studies with lasers, changes in choice of laser wavelength, and the development of key diagnostics and computer codes. Fulfilling the requirements of the multi-faceted Nova Technical Contract was a necessary condition for the approval of the NIF, but more importantly, the end of the Cold War and the cessation of nuclear testing were key catalysts in that approval, along with the ready-and-waiting field of HEDP. The inherent flexibility of the field of laser driven inertial confinement fusion played a fundamental role in achieving success at the NIF. We describe how the ultimately successful ignition target design evolved from the original “point design” target, through the lessons of experiment. All key aspects of that original design changed: The capsule's materials and size were changed; the hohlraum's materials, size, laser entrance hole size, and gas fills were also all changed, as were the laser pulse shapes that go along with all those changes. The philosophy to globally optimize performance for stability (by raising the adiabat and thus lowering the implosion convergence) was also key, as was progress in target fabrication, and in increasing NIF's energy output. The persistence of the research staff and the steadfast backing of our supporters were also necessary elements in this success. We gratefully acknowledge seven decades of researcher endeavors and four decades of the dedicated efforts of many hundreds of personnel across the globe who have participated in NIF construction, operation, target fabrication, diagnostic, and theoretical advances that have culminated in ignition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are “dual-action” inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

Science & Technology - Other Topics↗

DOE OSTI2025

Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan

Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.

A.Br.047 Vollum↗

DOE OSTI2020

Novel Hot-Spot Ignition Designs for Inertial Confinement Fusion with Liquid-Deuterium-Tritium Spheres

A new class of ignition designs is proposed for inertial confinement fusion (ICF) experiments. These designs are based on the hot-spot-ignition approach, but instead of conventional targets that comprise of spherical shells with thin frozen deuterium{tritium (DT) layers, homogeneous-density (solid or liquid) DT spheres are used where the lower-density central region and higher-density shell are created dynamically by appropriately shaping the laser pulse. These offer several advantages, including simplicity in target production and lower sensitivity to both laser imprint and physics uncertainty in shock interaction with the ice-vapor interface. The design evolution starts by launching an ~1-Mbar shock into a homogeneous DT sphere. After bouncing from the center, the reflected shock reaches the outer surface of the sphere and the shocked material starts to expand outward until its pressure drops below the ablation pressure. At this point, an adjustment shock is launched inward by supporting ablation pressure. This shock compresses the ablator and fuel, forming a shell. The shell is then accelerated and compressed by appropriately shaping the drive laser pulse, similar to the conventional thin-shell, hot-spot designs. Here, this paper demonstrates the feasibility of the new concept using hydrodynamic simulations and discusses the advantages and disadvantages of the concept compared with more-traditional ICF designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Dissolution of Additively Manufactured Mo Disks and Structures for Accelerator Based Production of Mo-99

The press-and-sinter approach for production of Mo targets has been successfully tested and demonstrated. The main advantage of this process is that it uses readily available technology and tools that have been tuned for production of various metal and metal oxide targets. However, certain target design specifications, such as dimensional accuracy of the diameter and thickness of the disks, are required for proper fit into a target holder and therefore place strict tolerances on sintered Mo disks intended for accelerator production. Furthermore, having a target composed of multiple disks poses certain challenges for post-irradiation processing, where there is a potential for spillage of individual disks during the manipulation for dissolution inside a processing hot cell. Additive manufacturing (AM), also referred to as 3D printing, provides capabilities to design and build a single-piece Mo target that provides the opportunity for better geometry for optimized production of Mo-99, improved cooling capability, and safer post-irradiation handling. A drawback of AM Mo structures is roughness of finished surfaces, which could reduce the effectiveness of gas cooling systems. Process development for AM Mo structures using selective laser melting is described in work by Gibson and Lowden. For post-irradiation processing, it is important to look at the dissolution behavior of AM Mo structures in comparison to readily dissolved press-and-sinter Mo targets. The dissolution behavior of press-and-sinter targets has been well documented in our previous reports. In this report, we discuss results of dissolution experiments conducted with AM Mo disks and structures (provided by Oak Ridge National Laboratory [ORNL]) in 50% hydrogen peroxide (H 2 O 2 ).

36 MATERIALS SCIENCE↗

DOE OSTI2022

Deep Generative Models for Materials Discovery and Machine Learning-Accelerated Innovation

Machine learning and artificial intelligence (AI/ML) methods are beginning to have significant impact in chemistry and condensed matter physics. For example, deep learning methods have demonstrated new capabilities for high-throughput virtual screening, and global optimization approaches for inverse design of materials. Recently, a relatively new branch of AI/ML, deep generative models (GMs), provide additional promise as they encode material structure and/or properties into a latent space, and through exploration and manipulation of the latent space can generate new materials. These approaches learn representations of a material structure and its corresponding chemistry or physics to accelerate materials discovery, which differs from traditional AI/ML methods that use statistical and combinatorial screening of existing materials via distinct structure-property relationships. However, application of GMs to inorganic materials has been notably harder than organic molecules because inorganic structure is often more complex to encode. In this work we review recent innovations that have enabled GMs to accelerate inorganic materials discovery. We focus on different representations of material structure, their impact on inverse design strategies using variational autoencoders or generative adversarial networks, and highlight the potential of these approaches for discovering materials with targeted properties needed for technological innovation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Conceptual Design of a HTS Dipole Insert Based on Bi2212 Rutherford Cable

The U.S. Magnet Development Program (US-MDP) is aimed at developing high-field accelerator magnets with magnetic fields beyond the limits of Nb 3 Sn technology. Recent progress with composite wires and Rutherford cables based on the first generation high-temperature superconductor Bi 2 Sr 2 CaCu 2 O 8-x (Bi2212) allows considering them for this purpose. However, Bi2212 wires and cables are sensitive to transverse stresses and strains, which are large in high-field accelerator magnets. This requires magnet designs with stress management concepts to control azimuthal and radial strains in the coil windings and prevent the degradation of the current carrying capability of Bi2212 conductor or even its permanent damage. This paper describes a novel stress management approach, which was developed at Fermilab for high-field large-aperture Nb 3 Sn accelerator magnets, and is now being applied to high-field dipole inserts based on Bi2212 Rutherford cables. The insert conceptual design and main parameters, including the superconducting wire and cable, as well as the coil stress management structure, key technological steps and approaches, test configurations and their target parameters, are presented and discussed.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

System and method for wave prediction

A method and system for prediction of wave properties include collecting time series data streams from one or more wave measurement devices and processing the data using a wave-prediction algorithm to identify the frequency components of the data and compute wave parameters. The wave-field is propagated in space and time to predict wave height, speed, and velocity at a target location. A sliding window approach is used to continuously update the prediction in real-time.

Previsic, Mirko↗

DOE OSTI2025

Integrated Molten Salt Reactor Modeling Capabilities in NEAMS Thermal Hydraulics Tools

The DOE neams program supports a full range of computational thermal fluids analysis capabilities and code developments for a broad range of advanced reactor concepts. The research and development approach under the thermal fluids technical area synergistically combines three length and time scales in a hierarchical multi-scale approach. To enable multi-scale thermal fluids capability using these codes, a key joint effort has been underway to develop an integrated system- and engineering-scale thermal fluids analysis capability, through integration of SAM and Pronghorn codes, both based on the MOOSE framework. This report summarizes recent advances in developing an integrated system- and engineering-scale modeling capability for the msr concept, which has gained significant interest in recent years. A consistent framework was established by coupling Pronghorn and SAM through the Saline interface, with thermophysical properties provided by the Molten Salt Thermal Property Database (MSTDB-TP). Further improvements were made to the coupling schemes and domain-overlapping strategies, enhancing the stability and robustness of multi-code simulations. Verification and validation efforts demonstrate the accuracy of this integration across a range of benchmark problems, including one-dimensional heated pipe flows, three-dimensional natural convection loops with evolving isotopic compositions, and \gls{msre} demonstration cases. Within Pronghorn, new capabilities were introduced to model corrosion and noble-metal plating phenomena, supported by an extended thermal-hydraulics framework and refined turbulence treatments. To capture two-phase flow behavior, a multiphase Euler–Euler model was implemented in Pronghorn, including advanced closure relations, high-resolution advection techniques, and capillary force reconstruction. Preliminary verification cases confirm the fidelity of the approach, while planned validation efforts target canonical multiphase benchmarks and application to msr components such as the msre pump bowl. Finally, updates to SAM’s msr mass transfer modeling were extended to consider noble gas migration into porous structures like graphite. The point kinetics model was updated to include reactivity feedback contributions from any defined species, such as xenon. The gas transport model was expanded for applicability to gas mixtures, bubble efflux phenomena, and species transport between liquid and gas phases. A selection of multi-scale Sherwood number correlations from MOSCATO/NekRS and multi-phase correlations from literature have been added for improved accuracy in calculating mass transfer coefficients. A companion effort on developing system-level redox corrosion has also been incorporated into SAM. Collectively, these enhancements strengthen the predictive capability of SAM and Pronghorn for simulating MSR thermal-hydraulics, corrosion, multiphase behavior, and fission-product transport, providing a more complete toolset for design, safety analysis, and licensing support of next-generation \gls{msr}s.

42 - ENGINEERING↗

DOE OSTI2026

In Vitro Selection of Antibodies Targeting Yersinia pestis Membrane Lipids Using Nanodisc-Based Antigen Presentation

Proteins are the most common targets for antibody discovery and vaccine development, but their sequence variability can limit the breadth of resulting antigens. Lipids represent an alternative class of antigens due to their structural conservation and roles in host–pathogen interactions. Here, we describe the development and optimization of an in vitro antibody selection workflow using lipid-containing nanodiscs as antigen presentation platforms to enable phage and yeast display selections under conditions adapted for these non-protein targets. Lipopolysaccharide (LPS) nanodiscs were first used as a model system to evaluate selection strategies, including competitive and subtractive approaches to reduce non-specific binders, yielding peptide and single-chain variable fragment (scFv) binders that were affinity matured to improve binding signals. The same approach was subsequently used to select scFv antibodies that recognize lipid nanodiscs prepared from Yersinia pestis membrane lipid extracts. These antibodies show binding to lipid nanodiscs derived from Y. pestis, with evidence of selectivity relative to control nanodiscs. Overall, this work establishes a workflow for antibody selection against lipid-containing nanodisc antigens and highlights practical considerations associated with these targets. The approach may be useful for generating affinity reagents to membrane-associated lipids, although further characterization is required to define antigen specificity and functional activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

System and process for purification of astatine-211 from target materials

A new column-based purification system and approach are described for rapid separation and purification of the alpha-emitting therapeutic radioisotope 211At from dissolved cyclotron targets that provide highly reproducible product results with excellent 211At species distributions and high antibody labeling yields compared with prior art manual extraction results of the prior art that can be expected to enable enhanced production of purified 211At isotope products suitable for therapeutic medical applications such as treatment of cancer in human patients.

O'Hara, Matthew J.↗