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DOE OSTI2024

Gas Stopper Developments for Improved Purity and Intensity of Low-Energy, Rare Isotope Ion Beams (Final Technical Report)

This final technical report summarizes the work of the Michigan State University (MSU) team supported by grant # DE-SC0021423 awarded by the Office of Nuclear Physics, Department of Energy. Objectives: The successful fulfillment of the FRIB science mission hinges on ensuring the availability of fast, stopped, and reaccelerated beams consisting of rare isotopes. This project's research and development focus was dedicated to supporting the advancement and creation of a cutting-edge linear gas stopper. The primary aim is to efficiently convert the high-intensity fast beams of rare isotopes provided by FRIB into high-quality, low-energy beams. These beams are essential for conducting stopped beam experiments or for subsequent reacceleration. The overarching goal is to advance technology, aiming to increase the beam rate capability of the linear gas stopper for medium-to-heavy-mass rare isotopes by more than tenfold compared to the currently most effective gas stopper in operation, and to improve the purity of the delivered beams. Project Description: The existing technology employed in gas stopping devices designed for low-energy, rare-isotope beams presents limitations in both the purity of extracted beams and the intensities of injected beams. These limitations are incompatible with the requirements of the recently commissioned rare isotope beam facility, FRIB. Our research and development efforts, aligned with the previously outlined objectives, focused on addressing the most critical aspects for enhancing beam-rate capability and purity. Specifically, advanced particle-in-cell simulations were developed and integrated into a simulation pipeline to explore the efficacy of multi-layer RF carpets on increasing ion transport efficiency with high incoming beam rates that generate space charge fields which can limit it. We also explored the possibility of using a collision-induced-dissociation (CID) gas cell to break up molecular contaminant ions that are generated during the stopping process. A prototype CID gas cell was constructed and tested with beams from an offline ion source, validating the concept with the successful demonstration of breaking of molecular ions. The outcome of this research enabled the formulation a conceptual design for a next-generation linear gas stopping device specifically tailored for FRIB. This device is envisioned to deliver rare-isotope-ion beams at a rate of 10 8 particles per second or higher, accompanied by advancements in purity. Methods employed: This project leverages advancements in technologies initially designed for the Advanced Cryogenic Gas Stopper (ACGS), the current state-of-the-art linear gas stopper, through the use of new simulations and beam purification via collision-induced-dissociation. The methods include: 1. Development of a prototype low-energy, low-pressure CID gas stopper. This prototype features a thin, approximately 20 nm, Si 3 N 4 entrance window designed for dissociating stable and rare-isotope molecular ions. The goal is to enhance beam purification and overall efficiency. 2. Creation of Particle-in-cell (PIC) simulations to assess the advantages of multi-layer RF carpets and multi-point extraction for ion transport efficiency. These simulations rely on the 3DCylPIC package, specifically designed for studying devices of this nature. The goal is to quantify and mitigate ion transport losses due to space charge generated in the stopping process of large numbers of ions. 3. Perform ion transport simulations across an RF carpet using an 8-phase travelling wave and evaluate its performance. Compared to the 4-phase RF carpets used in ACGS, the 8-phase carpets will double the wavelength of the generated traveling wave allowing for larger maximum RF amplitudes that could result in improved ion transport efficiency for high-intensity incoming beams when large space charge fields are present. Impact: Tackling the primary challenges associated with transforming high-energy projectile fragment beams into low-energy beams—specifically, addressing efficiency and purity—holds significant promise for advancing FRIB science. This advancement will particularly impact precision mass measurements, laser spectroscopy of short-lived nuclei, and studies in astrophysics and nuclear reactions using reaccelerated beams. These domains play a crucial role in addressing key questions outlined in the 2023 NSAC long-range plan, spanning nuclear structure, nuclear astrophysics, and fundamental symmetries. Additionally, they contribute to addressing 10 out of the 17 benchmarks identified by the NRC RISAC. The development of a next-generation gas stopping device capable of delivering low-energy, rare-isotope beams at a rate of 10 8 particles per second, or more, with high purity holds the potential to unlock experiments that would otherwise be unfeasible. Furthermore, it is expected to reduce the time required for experiments at FRIB, thereby maximizing scientific output. The research and development activities performed as part of this project bolstered essential competencies at FRIB in beam physics and ion source technologies, provided valuable training opportunities for junior scientists.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine learning-driven predictive resource management in complex science workflows

Here, the collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained increasing importance in science experiments. Data processing workflows typically consist of multiple intricate steps, and the precise specification of resource requirements is crucial for each step to allocate optimal resources for effective processing. Estimating resource requirements in advance is challenging due to a wide range of analysis scenarios, varying skill levels among community members, and the continuously increasing spectrum of computing options. One practical approach to mitigate these challenges involves initially processing a subset of each step to measure precise resource utilization from actual processing profiles before completing the entire step. While this two-staged approach enables processing on optimal resources for most of the workflow, it has drawbacks such as initial inaccuracies leading to potential failures and suboptimal resource usage, along with overhead from waiting for initial processing completion, which is critical for fast-turnaround analyses. In this context, our study introduces a novel pipeline of machine learning models within a comprehensive workflow management system, the Production and Distributed Analysis (PanDA) system. These models employ advanced machine learning techniques to predict key resource requirements, overcoming challenges posed by limited upfront knowledge of characteristics at each step. Accurate forecasts of resource requirements enable informed and proactive decision-making in workflow management, enhancing the efficiency of handling diverse, complex workflows across heterogeneous resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Data Fusion to Enhance Quality Control and Analysis with Instruments at the Marine and Coastal Research Laboratory

Deploying environmental monitoring instruments in the marine environment can be challenging, facing challenges around device survivability, biofouling and corrosion, and consistent data collection. This project explores the use of data fusion – the process of integrating multiple data sources to produce more consistent, accurate, and useful information – to build a consistent long-term monitoring system at the Marine and Coastal Research Laboratory (MCRL) in Sequim, Washington. Unused instruments that had been acquired from past projects were inventoried and deployments planned on the MCRL pier and floating dock. A total of 8 instruments were deployed including a tide gauge, hydrophone, acoustic Doppler current profiler (ADCP), photosynthetically active radiation (PAR) sensors, meteorological station, and three water quality sensors. Deployments were planned to be well-protected around the pier structure and a maintenance schedule was created for cleaning and recalibration. An automated data pipeline was created to aggregate data on edge computers that push data to Amazon Web Services (AWS) cloud storage every 15 minutes, performing automated quality control and data transformations using the Time Series Data Analytical Toolkit (TSDAT). Continued efforts are underway to maintain this system into the future, take a data-driven approach to maintenance scheduling, improve the reliability of the system, and share the data with a variety of end-users.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Enabling Dark Energy Measurements from DESI and LSST (Final Technical Report)

This grant enabled efforts to lead the Survey Validation of the Luminous Red Galaxy (LRG) sample for DESI, entailing intensive work to prepare target samples, test their performance with DESI data, and validate that the requirements of the survey for this key sample are met. Luminous Red Galaxies represent the gold standard target class for Baryon Acoustic Observation experiments to study Dark Energy. It also funded work to co-leading the Follow-up Task Force within the LSST Dark Energy Science Collaboration (LSST DESC), which is intended to help develop collaborations with external groups and to produce cross-working group proposals for telescope time, policy proposals and white papers as needed in order to help the collaboration obtain and make use of complementary data which will strengthen LSST Dark Energy constraints. The PI has been particularly engaged in efforts to obtain access to spectroscopic training sets for LSST photometric redshifts in the first years of the survey, which requires developing relationships with groups that are obtaining such data for other purposes. This group has evolved into an External Synergies working group within DESC, also co-led by the PI. These groups have developed white papers for Astro2020, letters of intent and white papers for Snowmass2021, and a response to a DOE-NASA RFI. It also has enabled smaller contributions to improving LSST DESC pipeline infrastructure for photometric redshifts.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

pmartR 2.0 : A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes

The pmartR (https://github.com/pmartR/pmartR) package was designed for the quality control (QC) and analysis of mass spectrometry (MS) data, tailored to specific characteristics of proteomic (isobaric or labelled), metabolomic, and lipidomic datasets. Since its initial release, the tool has been expanded to address the needs of its growing userbase and now includes QC and statistics for nuclear magnetic resonance (NMR) metabolomic data, and leverages the DESeq2, edgeR, and limma-voom R packages for some transcriptomic data analyses. These improvements have made progress towards a unified omics processing pipeline for ease of reporting and streamlined statistical purposes. The package’s statistics and visualization capabilities have also been expanded by adding support for paired data and by integrating pmartR with the trelliscopejs R package for the quick creation of trellis displays (https://github.com/hafen/trelliscopejs). Here, we present relevant examples of each of these enhancements to pmartR and highlight how each new feature benefits the omics community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Automated Strain Construction for Biosynthetic Pathway Screening in Yeast

Automation accelerates the Design-Build-Test-Learn (DBTL) cycle for synthetic biology; however, most strain construction pipelines lack robotic integration. Here, in this study, we present the workflow design and source code for a modular, integrated protocol that automates the Build step in Saccharomyces cerevisiae. We programmed the Hamilton Microlab VANTAGE to integrate off-deck hardware via its central robotic arm, enabling automated steps that increased throughput to 2,000 transformations per week. We developed a user interface with the Hamilton VENUS software to support on-demand parameter customization. As a proof of concept, we screened a gene library in an engineered yeast strain producing verazine, a key intermediate in the biosynthesis of steroidal alkaloids. Our pipeline rapidly identified pathway bottlenecks and genes that enhanced verazine production by 2.0- to 5-fold. This technical note provides resources for synthetic biologists designing yeast workflows for biofoundries to screen libraries for pathway discovery/optimization, combinatorial biosynthesis, and protein engineering.

automation↗
DOE OSTI2025

Intersection of Hydrologic Change and Hydropower in the United States: Needs for Future Research and Practice

Hydropower is crucial for electric‐grid stability in the context of variable renewables but faces threats from changing hydrology. Here, we summarize the state of the science at the intersection of hydropower operations and planning, hydrologic science, and climate. We focus on the United States, outlining research, development, and training needs. Key knowledge gaps include the risk that intensification of compound extreme events poses to future generation, as well as uncertainties surrounding greenhouse gas emissions from hydropower reservoirs with relevance to hydropower's role in energy decarbonization. Quantifying such impacts and reducing uncertainty are critical where possible, but remaining irreducible or deep uncertainty will require new approaches. Future monitoring and modeling methods must provide a better understanding of the complexity inherent in large watersheds that is critical to managing both hydropower and watersheds in the context of hydrologic change. Yet, research and development will have little impact if they do not inform practice. Standardization and consolidation of platforms are essential for data, modeling, and tool translation to local scales and small operators. An enhanced industry‐academia dialog is pivotal for fostering a robust pipeline of hydropower professionals. Collaboration among researchers, policymakers, authorities, and industry stakeholders emerges as a recurring theme, highlighting the imperative for collective efforts.

13 HYDRO ENERGY↗
DOE OSTI2022

Mining Air for Fuels and Fine Chemicals

The Intergovernmental Panel on Climate Change’s 2021 report underscores that Direct Air Capture (DAC) is an essential component to limiting global warming to 2 °C, yet separating CO 2 from air and its subsequent concentration for conversion into carbon neutral fuels/chemicals or permanent storage remains energy intensive and costly. Further, most DAC technologies rely on repetitive capture and release cycles that reduces the amount of time the DAC materials are able to collect CO 2 and increases wear and tear. Moisture swing (MS) sorption within anion exchange materials utilizes differences in relative humidity to capture and concentrate CO 2 up to 500-fold with negligible energy inputs and low-cost sorbents. Molecular modeling predicts that membranes with a dry and wet side would actively transport CO 2 from its dry side to its wet side against a counter flow of H 2 O evaporating on the dry side, however, existing MS materials are too brittle to be processed into membranes to test this hypothesis. This project brought together experts in DAC materials and design, techno-economic analysis and project management at Arizona State University (ASU), polymer processing at University of Texas at Austin (UTA) and modeling gas transport and exchange at Norther Arizona University (NAU) to develop hollow fiber membranes that use energy from water evaporation to continuously pump CO 2 from air against a concentration gradient to the membranes interior and requiring significantly less energy than current DAC technologies. While this project did not meet its ultimate objectives of demonstrating an active CO 2 pumping membrane, a number of key accomplishments were made in developing low-cost, flexible anion exchange membranes (AEM) at 3.5 m 2 scale, characterizing the ionic and molecular transport within MS materials, and developing several analytical and mathematical models of the MS and pumping process leading to new fundamental knowledge about key rate limiting steps of CO 2 flux in anion exchange membranes at low water activity. Technoeconomic models show that if CO 2 fluxes ≥ 25 µmol CO 2 m -2 s -1 (membrane surface area) are achieved that cost ≤ $\$$100/tonne CO 2 captured, purified and compressed to pipeline quality is possible. The knowledge gained in this research will guide future research in developing new materials toward overcoming these rate limiting steps that in turn could enable transformative and disruptive DAC technologies needed for capturing gigatons of CO 2 per year needed to limiting global warming to 2 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High-throughput native mass spectrometry as experimental validation for in silico drug design

In this project, we developed automated workflows for both experimental validation and computational prediction of protein-ligand interactions. The ultimate goal is to establish an integrated pipeline for high throughput design of inhibitors to enzymes relevant to all areas of biological research. Our experimental approach is based on native mass spectrometry (native MS), which measures accurate masses and quantify the relative abundance of protein-ligand complexes to define binding affinity. We set up an in-house built autosampler with highly flexible configurations to minimize the manual steps for high throughput native MS. In parallel, we also performed manual native MS to characterize the binding of substrates and inhibitors of SARS-Cov-2 nonstructural protein nsp10/16 in order to optimize the experimental parameters for future automation. On the computational side, we streamlined the pipeline to achieve minimal manual intervention for predicting enzyme inhibitors via simulation, using the same nsp10/16 system as an example. Using the native MS method we examined 8 top-ranked designed compounds, 2 of which showed weak binding of ~50 µM. The information from native MS experiment provided critical insights and the foundation for a fully integrated workflow for enzyme inhibitor design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plant Cell Biology International Meeting 2022

There is a strong need to develop the knowledge base that will enable the rational design of improved crop species for sustainable agriculture and biomass production. To attain this goal, researchers must learn how plant cells integrate metabolism and cellular dynamics during growth and in response to environmental challenges. Meeting these goals require data sharing and the development and training of faculty, post-doctoral fellows, graduate and undergraduate students in state-of-the-art quantitative integrative cell biology methods. The inaugural Plant Cell Biology International (PCBI) meeting capitalized on the interaction between two well-established plant cell biology communities across the Atlantic, the Midwest Plant Cell Dynamics (PCD) and the European Network for Plant Endomembrane Research (ENPER) and provided a framework to meet these goals. The conference took place in person successfully during August 1-5th 2022 in Crete, Greece. The conference offered opportunities for undergraduate and graduate students, postdocs, young investigators across the globe to present their results and interact across different disciplines. The conference provided an open and inclusive forum for oral presentations that allowed all labs to share research results. It was attended over 80 % by students, postdocs and young investigators. Workshops on best practices for image acquisition and processing pipelines, publication guidelines by scientific journal editors, professional development and well-being benefited the participants at large. Overall, this was the inaugural joint Plant Cell Biology International conference that for the first time officially brought together plant cell biologists to discuss opportunities and challenges in the field to gain a mechanistic understanding of complex biological processes and advance sustainable agriculture. Due to its success, it was rescheduled for 2025 in Crete, to continue strengthening the plant cell biology community and exchanging knowledge and expertise across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hierarchical Inference with Bayesian Neural Networks: An Application to Strong Gravitational Lensing

In the past few years, approximate Bayesian Neural Networks (BNNs) have demonstrated the ability to produce statistically consistent posteriors on a wide range of inference problems at unprecedented speed and scale. However, any disconnect between training sets and the distribution of real-world objects can introduce bias when BNNs are applied to data. This is a common challenge in astrophysics and cosmology, where the unknown distribution of objects in our universe is often the science goal. In this work, we incorporate BNNs with flexible posterior parameterizations into a hierarchical inference framework that allows for the reconstruction of population hyperparameters and removes the bias introduced by the training distribution. We focus on the challenge of producing posterior PDFs for strong gravitational lens mass model parameters given Hubble Space Telescope–quality single-filter, lens-subtracted, synthetic imaging data. We show that the posterior PDFs are sufficiently accurate (statistically consistent with the truth) across a wide variety of power-law elliptical lens mass distributions. We then apply our approach to test data sets whose lens parameters are drawn from distributions that are drastically different from the training set. We show that our hierarchical inference framework mitigates the bias introduced by an unrepresentative training set's interim prior. Simultaneously, we can precisely reconstruct the population hyperparameters governing our test distributions. Our full pipeline, from training to hierarchical inference on thousands of lenses, can be run in a day. The framework presented here will allow us to efficiently exploit the full constraining power of future ground- and space-based surveys (https://github.com/swagnercarena/ovejero).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Neural architecture codesign for fast physics applications

We develop a pipeline to streamline neural architecture codesign for physics applications to reduce the need for ML expertise when designing models for novel tasks. Our method employs neural architecture search and network compression in a two-stage approach to discover hardware efficient models. This approach consists of a global search stage that explores a wide range of architectures while considering hardware constraints, followed by a local search stage that fine-tunes and compresses the most promising candidates. We exceed performance on various tasks and show further speedup through model compression techniques such as quantization-aware-training and neural network pruning. We synthesize the optimal models to high level synthesis code for FPGA deployment with the hls4ml library. Additionally, our hierarchical search space provides greater flexibility in optimization, which can easily extend to other tasks and domains. We demonstrate this with two case studies: Bragg peak finding in materials science and jet classification in high energy physics, achieving models with improved accuracy, smaller latencies, or reduced resource utilization relative to the baseline models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗