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DOE OSTI2025

Cyanobacteria dynamically regulate phycobilisome-to-photosystem excitation energy transfer

In cyanobacteria and red algae, the phycobilisome (PBS) absorbs light and transfers its energy to the chlorophylls in photosystems II (PSII) and I (PSI). With the help of target analysis of time-resolved emission spectra measured at room temperature (RT) and at 77 K, we establish a general kinetic scheme for excitation energy transfer (EET) and trapping based upon a PBS-PSII-PSI megacomplex. At RT it is found that in the dark-adapted cells (State II), the terminal emitter of PBS, allophycocyanin APC680, transfers energy to PSII and PSI with equal rates of ≈50 ns −1 , and that spillover from PSII to PSI is present with rate ≈6 ns −1 . At 77 K, upon transition from State I to State II the EET rate from APC680 to PSII is constant, whereas the rate to PSI increases by 67%. This indicates that a structural change in EET distance in the PBS-PSII-PSI megacomplex underlies the state transition.

Science & Technology - Other Topics↗

DOE OSTI2021

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗

DOE OSTI2020

A Python Instrument Control and Data Acquisition Suite for Reproducible Research

Tools that standardize and automate experimental data collection are needed for greater confidence in research results. The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray experiments and collects an experimental record that facilitates complete reproducibility. Here, we show that the NSLS-II tools are not only useful for X-ray science at large-scale facilities by presenting an add-on package that adapts these tools for use in a small laboratory with common physics and electrical engineering instruments. The composite software suite eases and automates the execution of experiments, records extensive metadata, stores data in portable containers, and speeds up the analysis through tools for comprehensive searches. In total, this software suite increases the reproducibility of laboratory experiments. We demonstrate the software via the evaluation of two lock-in amplifiers-the miniature ADA2200 and the ubiquitous Stanford Research Systems (SRS) SR810. The frequency resolution, signal-to-noise ratio, and dynamic reserve of the lock-in amplifiers are measured and presented. The usage of the software suite is described throughout these measurements so that the reader can implement the tools in their lab.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Tailoring Crosslinks through Time─A Paradigm for Tough Hydrogels

The multidisciplinary applications of hydrogels have motivated a thorough exploration of the relationship between their structural and mechanical properties, i.e., spatial structure–function relationships, with particular regard to strength and toughness. While this approach has driven fundamental advancements in the design of robust hydrogel structures, further complementary perspectives are needed to enable holistic, rational design schemes that integrate considerations such as fabrication and advanced functions like response and adaptation. To these ends, this review focuses on the dynamics of temporal-function relationships and their fundamental bases in order to highlight how the dynamic regulation of polymer interactions programs: 1) polymer assembly and material structure; 2) response to deformation and fracture behavior; 3) dynamic modulation of properties and structural remodeling/self-healing. Here, by exploring this intersection of hydrogel formation, function, and remodeling, this review seeks to shed light on the fundamental relationship between molecular structure, material assembly, and performance in order to connect the emerging area of bioinspired materials processing with tough hydrogel design, and further provides a lasting inspiration and impetus for future hydrogel development that enables valuable scientific and technological advancements.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A review of materials used in tomographic volumetric additive manufacturing

Abstract Volumetric additive manufacturing is a novel fabrication method allowing rapid, freeform, layer-less 3D printing. Analogous to computer tomography (CT), the method projects dynamic light patterns into a rotating vat of photosensitive resin. These light patterns build up a three-dimensional energy dose within the photosensitive resin, solidifying the volume of the desired object within seconds. Departing from established sequential fabrication methods like stereolithography or digital light printing, volumetric additive manufacturing offers new opportunities for the materials that can be used for printing. These include viscous acrylates and elastomers, epoxies (and orthogonal epoxy-acrylate formulations with spatially controlled stiffness) formulations, tunable stiffness thiol-enes and shape memory foams, polymer derived ceramics, silica-nanocomposite based glass, and gelatin-based hydrogels for cell-laden biofabrication. Here we review these materials, highlight the challenges to adapt them to volumetric additive manufacturing, and discuss the perspectives they present. Graphical abstract

36 MATERIALS SCIENCE↗

DOE OSTI2021

Optically detected NMR in a diamond-anvil cell for geochemistry

Developments in quantum-information processing are being adapted to perform nuclear-magnetic resonance (NMR) measurements on solutions in very small volumes. Here we describe efforts to adapt the technology to a diamond-anvil cell (DAC), with the goal of conducting solution NMR measurements at elevated pressures and temperatures. At the center of the method is the use of diamonds that have a particular type of defect that pairs a nitrogen atom substitution for near-surface carbon with a vacancy. These NV sites have unpaired electrons that can be excited while conserving electron spins and the amount of light released upon decay of the excited state depends upon the orientation of the electron spin. Under certain conditions the NV centers can probe AC magnetic fields from nearby nuclei with exquisite sensitivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Graphical Optimization of Spectral Shift Reconstructions for Optical Backscatter Reflectometry

Optical backscatter reflectometry (OBR) is an interferometric technique that can be used to measure local changes in temperature and mechanical strain based on spectral analyses of backscattered light from a singlemode optical fiber. The technique uses Fourier analyses to resolve spectra resulting from reflections occurring over a discrete region along the fiber. These spectra are cross-correlated with reference spectra to calculate the relative spectral shifts between measurements. The maximum of the cross-correlated spectra—termed quality—is a metric that quantifies the degree of correlation between the two measurements. Recently, this quality metric was incorporated into an adaptive algorithm to (1) selectively vary the reference measurement until the quality exceeds a predefined threshold and (2) calculate incremental spectral shifts that can be summed to determine the spectral shift relative to the initial reference. Using a graphical (network) framework, this effort demonstrated the optimal reconstruction of distributed OBR measurements for all sensing locations using a maximum spanning tree (MST). By allowing the reference to vary as a function of both time and sensing location, the MST and other adaptive algorithms could resolve spectral shifts at some locations, even if others can no longer be resolved.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Integral Experiment Request 554 CED-1 Summary Report

This Critical Engineering Decision 1 report for the Integral Experiment Request 554 describes the effects of adding a commercially available neutron absorber material to a known light-water low-enriched uranium assembly. The assembly in question is the Seven Percent Critical Experiments at Sandia National Laboratories. The neutron absorber plates considered for the experiment are called Boralcan, which are made of boron carbide (B 4 C) particles embedded in 1100 aluminum alloy. The concentrations of B 4 C and 1100 aluminum, as well as the thickness and size of the plates, were changed, and the fuel rod configuration was adapted to ensure that the assembly would be critical in each case studied. A total of 10 critical configurations with a neutron absorber plate inserted are described in this report. No results of high-quality integral experiments involving neutron absorbers made with B 4 C and 1100 aluminum plates are currently publicly available. Sensitivity to the neutron absorber plate material definition, isotopes, and cross sections of specific regions and configurations are also analyzed. The study results indicate that these experiments are achievable with sufficiently low uncertainties and minimal modification to the assembly. The experimental uncertainty can be further decreased with an additional characterization of the plates by x-ray computerized tomography or neutron radiography methods.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Data-Driven Assessment of the Impact of Hurricanes Ian and Nicole: Natural and Armored Dunes in the Aftermath of Hurricanes on Florida’s Central East Coast

Hurricanes Ian and Nicole caused devastating destruction across Florida in September and November 2022, leaving widespread damage in their wakes. This study focuses on the assessment of barrier islands’ shorelines, encompassing natural sand dunes and dune vegetation as well as armored dunes with man-made infrastructure such as seawalls. High-resolution satellite imagery from Planet was used to assess the impacts of these hurricanes on the beach shorelines of Volusia, Flagler, and St. Johns Counties on the Florida Central East Coast. Shorefront vegetation was classified into two classes. Normalized Difference Vegetation Index (NDVI) values were calculated before the hurricanes, one month after Hurricane Ian, one month after Hurricane Nicole, and one-year post landfall. LiDAR (Light Detection and Ranging) was incorporated to calculate vertical changes in the shorelines before and after the hurricanes. The results suggest that natural sand dunes were more resilient as they experienced less impact to vegetation and elevation and more substantial recovery than armored dunes. Moreover, the close timeframe of the storm events suggests a compound effect on the weakened dune systems. This study highlights the importance of understanding natural dune resilience to facilitate future adaptive management efforts because armored dunes may have long-term detrimental effects on hurricane-prone barrier islands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Multipoint-BAX: a new approach for efficiently tuning particle accelerator emittance via virtual objectives

Abstract Although beam emittance is critical for the performance of high-brightness accelerators, optimization is often time limited as emittance calculations, commonly done via quadrupole scans, are typically slow. Such calculations are a type of multipoint query , i.e. each query requires multiple secondary measurements. Traditional black-box optimizers such as Bayesian optimization are slow and inefficient when dealing with such objectives as they must acquire the full series of measurements, but return only the emittance, with each query. We propose a new information-theoretic algorithm, Multipoint-BAX , for black-box optimization on multipoint queries, which queries and models individual beam-size measurements using techniques from Bayesian Algorithm Execution (BAX). Our method avoids the slow multipoint query on the accelerator by acquiring points through a virtual objective , i.e. calculating the emittance objective from a fast learned model rather than directly from the accelerator. We use Multipoint-BAX to minimize emittance at the Linac Coherent Light Source (LCLS) and the Facility for Advanced Accelerator Experimental Tests II (FACET-II). In simulation, our method is 20× faster and more robust to noise compared to existing methods. In live tests, it matched the hand-tuned emittance at FACET-II and achieved a 24% lower emittance than hand-tuning at LCLS. Our method represents a conceptual shift for optimizing multipoint queries, and we anticipate that it can be readily adapted to similar problems in particle accelerators and other scientific instruments.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Biochemistry & Molecular Biology↗

DOE OSTI2026

F‐Box Protein‐Mediated Proteolytic Regulation of Phenylpropanoid Metabolism in Response to Biotic and Abiotic Stresses

Protein ubiquitination is a central regulatory mechanism governing plant growth, development and environmental adaptation. Ubiquitylomic studies have revealed that many enzymes in phenylpropanoid biosynthetic pathways are subject to ubiquitination. Increasing evidence indicates that specific F-box proteins target key enzymes in these pathways, including PAL, CCR, CAD, COMT and peroxidases in the lignin biosynthetic branch, and CHS in the flavonoid biosynthetic branch, thereby promoting their ubiquitination and selective degradation. These F-box proteins act in response to diverse developmental and environmental cues, including cellular carbon status, light quality and intensity, and biotic stresses (e.g., pathogen and insect attack). By regulating the stability and activity of both enzymes and regulatory proteins involved in phenylpropanoid biosynthesis, F-box proteins modulate the accumulation of simple phenolics and lignin polymers, ultimately contributing to plant resilience. This review summarizes recent advances in the characterization of F-box proteins involved in phenylpropanoid metabolism and their regulatory roles in response to biotic and abiotic stresses and identifies key knowledge gaps that limit mechanistic understanding of F-box protein-mediated proteolytic regulation of phenylpropanoid metabolism. In conclusion, insights into ubiquitin-mediated proteolytic control of phenylpropanoid metabolism offer promising avenues for enhancing bioactive phenolic production, advancing biofuel feedstock engineering and improving crop stress tolerance.

(A)biotic stress↗

DOE OSTI2022

Reducing the Overnight Capital Cost of Advanced Reactors Using Equipment-Level Seismic Protective Systems

Consideration of the effects of earthquake shaking on the design and construction of nuclear power plants adds substantially to the overnight capital cost, with anecdotal estimates as high as 35+%, attributed to additional construction materials, need for one-off and sub-optimal designs of equipment due to conflicting design choices, the high cost of seismic qualification of equipment, and regulatory review. Safety-critical equipment in large light water reactors is designed and qualified for seismic demands imposed by the supporting reactor building, optimal mechanical designs are not possible, and designs of a given piece of equipment may vary with height above grade. Similar negative impacts are expected for advanced reactors unless the seismic design paradigm is changed. The overarching goal of this transformational MEITNER project, which involved a multidisciplinary engineering team and designers of three fundamentally different advanced reactors, was to adapt proven seismic isolation and damping technologies to operationalize modular protective systems for safety-class equipment inside advanced reactor buildings. Such seismic protective systems would be tightly integrated into design development for reactor support systems and balance-of-plant construction. The adoption of the technology, which is widely used in non-nuclear sectors, would simplify plant design, enable the use of standardized equipment and buildings, optimized for operational performance, and reduce plant size and weight. The need for site-specific equipment would be eliminated, enabling identical equipment to be used across multiple plants sited across the US and economies of scale, and catalyzing new interest and investment. The equipment-based protective systems would allow siting of advanced reactors in regions of high seismic hazard.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Engineering quantitative stomatal trait variation and local adaptation potential by cis‐regulatory editing

Summary Cis‐regulatory element editing can generate quantitative trait variation that mitigates extreme phenotypes and harmful pleiotropy associated with coding sequence mutations. Here, we applied a multiplexed CRISPR/Cas9 approach, informed by bioinformatic datasets, to generate genotypic variation in the promoter ofOsSTOMAGEN, a positive regulator of rice stomatal density. Engineered genotypic variation corresponded to broad and continuous variation in stomatal density, ranging from 70% to 120% of wild‐type stomatal density. This panel of stomatal variants was leveraged in physiological assays to establish discrete relationships between stomatal morphological variation and stomatal conductance, carbon assimilation and intrinsic water use efficiency in steady‐state and fluctuating light conditions. Additionally, promoter alleles were subjected to vegetative drought regimes to assay the effects of the edited alleles on developmental response to drought. Notably, the capacity for drought‐responsive stomatal density reprogramming instomagenand two cis‐regulatory edited alleles was reduced. Collectively our data demonstrate that cis‐regulatory element editing can generate near‐isogenic trait variation that can be leveraged for establishing relationships between anatomy and physiology, providing a basis for optimizing traits across diverse environments.

Biotechnology & Applied Microbiology↗

DOE OSTI2023

Integral Experiment Request 554: CED-2 Summary Report

This report summarizes the critical experiment design 2 (CED-2) or final design study for Integral Experiment Request 554 (IER-554). This experiment describes the effects and importance of adding a commercially available neutron absorber material to a known light-water low-enriched uranium assembly. The assembly in question is the Seven Percent Critical Experiments (7uPCX) at Sandia National Laboratories. The neutron absorber plates considered for the experiment are known as Boralcan and are made of boron carbide (B 4 C) particles embedded in 1100 aluminum alloy. The concentrations of B 4 C and 1100 aluminum were changed as well as the thickness and the positions of the plates, and the fuel rod configuration was adapted to ensure that the assembly would be critical in each case studied. A total of 6 critical configurations, each with a neutron absorber plate inserted, are described in this report. No results of high-quality integral experiments involving neutron absorbers made with B 4 C and 1100 aluminum plates are currently publicly available. Sensitivity to the neutron absorber plate material definition, isotopes, and cross sections of specific regions and configurations are also analyzed. As part of the final design of the experiment, a safe plate holder made of 3003 aluminum was designed. The study results indicate that these experiments are achievable with sufficiently low uncertainties and minimal modification to the assembly, and the CED-3 phase can start when funding allows.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

New directions and principles for solvent extraction for recovery of lithium from aqueous brines and mineral leachates: A brief review

Increasing demand for lithium for manufacturing of batteries is fueling the unprecedented search for improved recovery and alternative sources. Wider source distribution, lower energy consumption, and greater sustainability make extraction of lithium from brines, both natural and process-derived, an attractive alternative to mineral ores. Solvent extraction, used industrially for production of metals, salts, and pharmaceuticals, has been investigated as a methodology for lithium recovery for several decades. However, industrial application of solvent extraction for lithium recovery has so far been limited. In contrast, direct lithium extraction using adsorbents based on inorganic minerals has rapidly advanced from research to commercialization. A comparison of solvent extraction processes to adsorption highlights these issues and explains the preference for adsorbents. Although the application of solvent extraction has been criticized for use of large amounts of acid, alkali, and organic solvents, steady progress has been made to improve its potential for industrial lithium production, spurred on generally by the advantages of solvent extraction in selectivity and throughput. Previously developed beta-diketone, organophosphate, and crown ether ligands are being adapted and improved. Their novel use with ionic liquids, deep eutectic solvents, and membrane technologies promises to expand capabilities for extraction of lithium from dilute aqueous sources while improving sustainability. Possibilities for further discovery and innovation abound. In this review, we provide a unique perspective from the field of solvent extraction starting with fundamentals such as ion-transfer theory and apply them to understanding lithium selectivity and extraction behavior. In conclusion, the results are cast in the light of the practical realities of developing economical solvent extraction processes.

Brine↗

DOE OSTI2021

Preparing Lamellae from Vitreous Biological Samples using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography

Presented here is a protocol for preparing cryo-lamellae from plunge-frozen grids of Plasmodium falciparum-infected human erythrocytes, which could easily be adapted for other biological samples. The basic principles for preparing samples, milling, and viewing lamellae are common to all instruments and the protocol can be followed as a general guide to on-grid cryo-lamella preparation for cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). Electron microscopy grids supporting the cells are plunge-frozen into liquid nitrogen-cooled liquid ethane using a manual or automated plunge freezer, then screened on a light microscope equipped with a cryo-stage. Frozen grids are transferred into a cryo-scanning electron microscope equipped with a focused ion beam (cryoFIB-SEM). Grids are routinely sputter coated prior to milling, which aids dispersal of charge build-up during milling. Alternatively, an e-beam rotary coater can be used to apply a layer of carbon-platinum to the grids, the exact thickness of which can be more precisely controlled. Once inside the cryoFIB-SEM an additional coating of an organoplatinum compound is applied to the surface of the grid via a gas injection system (GIS). This layer protects the front edge of the lamella as it is milled, the integrity of which is critical for achieving uniformly thin lamellae. Regions of interest are identified via SEM and milling is carried out in a step-wise fashion, reducing the current of the ion beam as the lamella reaches electron transparency, in order to avoid excessive heat generation. A grid with multiple lamellae is then transferred to a transmission electron microscope (TEM) under cryogenic conditions for tilt-series acquisition. A robust and contamination-free workflow for lamella preparation is an essential step for downstream techniques, including cellular cryoEM, cryoET, and sub-tomogram averaging. Development of these techniques, especially for lift-out and milling of high-pressure frozen samples, is of high-priority in the field.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Accelerating data acquisition with FPGA-based edge machine learning: a case study with LCLS-II

New scientific experiments and instruments generate vast amounts of data that need to be transferred for storage or further processing, often overwhelming traditional systems. Edge machine learning (EdgeML) addresses this challenge by integrating machine learning (ML) algorithms with edge computing, enabling real-time data processing directly at the point of data generation. EdgeML is particularly beneficial for environments where immediate decisions are required, or where bandwidth and storage are limited. In this paper, we demonstrate a high-speed configurable ML model in a fully customizable EdgeML system using a field programmable gate array (FPGA). Our demonstration focuses on an angular array of electron spectrometers, referred to as the ‘CookieBox,’ developed for the Linac Coherent Light Source II project. The EdgeML system captures 51.2 Gbps from a 6.4 GS s −1 analog to digital converter and is designed to integrate data pre-processing and ML inside an FPGA. Our implementation achieves an inference latency of 0.2 µs for the ML model, and a total latency of 0.4 µs for the complete EdgeML system, which includes pre-processing, data transmission, digitization, and ML inference. The modular design of the system allows it to be adapted for other instrumentation applications requiring low-latency data processing.

97 MATHEMATICS AND COMPUTING↗