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DOE OSTI2025

Effects of threshold resummation for large-x PDF in large momentum effective theory

Parton distribution functions (PDFs) at large x are challenging to extract from experimental data, yet they are essential for understanding hadron structure and searching for new physics beyond the Standard Model. Within the framework of the large momentum P z expansion of lattice quasi-PDFs, we investigate large x PDFs, where the matching coefficient is factorized into the hard kernel, related to the active quark momentum xP z , and the threshold soft function, associated with the spectator momentum (1 − x)P z . The renormalization group equation of the soft function enables the resummation of the threshold double logarithms α k ln 2k (1 − x), which is crucial for a reliable and controllable calculation of large x PDFs. Our analysis with pion valence PDFs indicates that perturbative matching breaks down when the spectator momentum (1 − x)P z approaches Λ QCD , but remains valid when both xP z and (1 − x)P z are much larger than Λ QCD . Additionally, we incorporate leading renormalon resummation within the threshold framework, demonstrating good perturbative convergence in the region where both spectator and active quark momenta are perturbative scales.

factorization↗

DOE OSTI2026

Measurement of the top quark pair production cross section in PbPb collisions at $\sqrt{s_{\mathrm{NN}}}=5.36$ TeV

The inclusive cross section for top quark pair ($\mathrm{t}\overline{\mathrm{t}}$) production in lead-lead (PbPb) collisions is reported for the first time at a center-of-mass energy per nucleon pair of 5.36 TeV. The analysis uses data corresponding to an integrated luminosity of 1.58 nb −1 collected by the CMS experiment at the CERN LHC in 2023. The $\mathrm{t}\overline{\mathrm{t}}$ production cross section, ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}={3.42}_{-0.51}^{+0.54}{\left(\mathrm{stat}\right)}_{-0.43}^{+0.50}\left(\mathrm{syst}\right)$ μb, is measured in dilepton final states using a fit to a multivariate discriminator that combines the decay electron and muon kinematic properties with the multiplicity of bottom quark jets. The result is consistent with perturbative quantum chromodynamics calculations at next-to-next-to-leading order (NNLO) accuracy employing several nuclear parton distribution functions. In addition, the Drell–Yan production cross section (σ DY ) for dilepton masses above 10 GeV and the ratio of $\mathrm{t}\overline{\mathrm{t}}$ to DY cross sections $\left({R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}\right)$ are found to be compatible with the NNLO predictions. The observables ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}$, σ DY , and ${R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}$ are measured separately for central and semicentral PbPb collisions to investigate for the first time the dependence of top quark production on the collision impact parameter.

Heavy Ion Experiments↗

DOE OSTI2026

Hydride and Seek: Comparing Crystallographic Hydride Placement Techniques with an Open-Shell Cobalt Complex

Locating hydrides is crucial in organometallic chemistry but difficult to do accurately using X-ray diffraction. Electron diffraction has been proposed as a way to overcome this problem but has not been systematically compared to neutron diffraction and to quantum crystallography (Hirshfeld atom refinement, HAR) to test this hypothesis. Here, we present a comparative analysis of methods for a terminal cobalt hydride complex by comparing a single-crystal neutron diffraction reference structure to results from single-crystal X-ray diffraction with and without Hirshfeld atom refinement (HAR, NoSpherA2), density functional theory (DFT), and electron diffraction (3D-ED/MicroED) refined under kinematical and dynamical formalisms. Conventional X-ray diffraction gives lower precision than neutron diffraction as expected. Despite expected improvements, HAR gives systematic deviation from the neutron benchmark. Interestingly, optimized DFT equilibrium geometries are closer to the neutron value than the value from HAR. On the other hand, electron diffraction with a high-quality data set coupled with dynamical refinement localizes the hydride in difference maps and gives excellent agreement with the neutron data. Dynamical refinement is crucial, as kinematical refinement does not allow assignment of a hydride peak. This cross-modal comparison defines the conditions under which 3D-ED/MicroED delivers high-precision metal–hydride distances for this open-shell cobalt hydride.

anions↗

DOE OSTI2024

Forming a database to study reversed magnetic shear from the National Spherical Torus eXperiment using machine learning

Achieving a long-lived reversed magnetic shear (RMS) target plasma in the National Spherical Torus eXperiment Upgrade will require developing various sustainment scenarios. To help with the ongoing plasma control efforts, the development of a new analysis for the motional Stark effect (MSE) diagnostic using a machine learning algorithm, namely, MSE-ML, is described. MSE-ML will be used to identify patterns during RMS discharges, some of which suffer magnetohydrodynamic (MHD) events resulting in current redistribution and monotonic q-profiles. A database consisting of q and magnetic shear profiles is being constructed primarily based on the existing National Spherical Torus eXperiment data with equilibrium reconstructions constrained by the magnetic field pitch angle profile measured using the multi-channel MSE diagnostic. An unsupervised k-means clustering of the data is developed to study the RMS formation as a function of time. The initial clustering from the q-profiles shows significant differences in both amplitude and the duration of the RMS period. As a goal, the clustering results that detect and distinguish shots with substantial and sustained RMS are to be used as a preprocessing step in a supervised algorithm to identify the underlying conditions that lead to long-lasting improved confinement with RMS. Another aim of the MSE-ML study is to identify precursors of RMS-destroying MHD events in either derived data such as the q-profile or directly measured data such as the magnetic field pitch angle profile.

Uzun-Kaymak, I. U. (ORCID:0000000276251493)↗

DOE OSTI2026

Transfer learning for analysis of collective and non-collective Thomson scattering spectra

Thomson scattering (TS) diagnostics provide reliable, minimally perturbative measurements of fundamental plasma parameters, such as electron density (⁠n e ) and electron temperature (⁠T e ⁠). Deep neural networks can provide accurate estimates of ⁠n e and T e when conventional fitting algorithms may fail, such as when TS spectra are dominated by noise, or when fast analysis is required for real-time operation. Although deep neural networks typically require large training sets, transfer learning can improve model performance on a target task with limited data by leveraging pre-trained models from related source tasks, where select hidden layers are further trained using target data. We present five architecturally diverse deep neural networks, pre-trained on synthetic TS data and adapted for experimentally measured TS data, to evaluate the efficacy of transfer learning in estimating n e and T e in both the collective and non-collective scattering regimes. We evaluate errors in n e and T e estimates as a function of training set size for models trained with and without transfer learning, and we observe decreases in model error from transfer learning when the training set contains ≲ 200 experimentally measured spectra.

Artificial neural networks↗

DOE OSTI2025

Sm 2 Ru 3 Sn 5 : A Noncentrosymmetric Cubic Member of the Ln 2 M 3 X 5 Family

An optimized synthetic method is presented for Sm 2 Ru 3 Sn 5 and investigate its physical properties and electronic structure. Sm 2 Ru 3 Sn 5 is prepared by arc-melting stoichiometric ratios of the elements and is confirmed by single crystal and powder X-ray diffraction. An antiferromagnetic transition is observed at T N = 3.8 K. A modified Curie-Weiss fit to the data in the range 50–150 K yields a Curie-Weiss temperature: θ CW = −36.6 K and an effective magnetic moment: μ eff = 0.83 μ B , in agreement with a Sm 3+ oxidation state. Field-dependent magnetization up to H = 7 T at 2 K shows a maximum response of 0.06 μ B , which is significantly lower than the expected Sm 3+ saturation moment (0.71 μ B ). Resistivity measurements indicate metallic behavior, and analysis of the magnetic entropy from the heat capacity reveals a doublet ground state due to crystal electric field splitting. The electronic structure and density of states are calculated with density function theory and further supported by the local density approximation with dynamical mean-field theory. Finally, the experimental and computational results highlight localized Sm 3+ moments and suggest a possible interplay between Ruddelman–Kitel–Kasuya–Yosida and Kondo interactions, positioning Sm 2 Ru 3 Sn 5 as a promising material for studying topology and complex physical phenomena.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Measurements of electroweak production of a photon in association with two jets in proton-proton collisions at $\sqrt{s}=13$ TeV

The first observation of electroweak production of a photon in association with two forward jets in proton-proton collisions is presented. The measurement uses data recorded by the CMS experiment at the LHC during 2016–2018 at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138 fb −1 . The analysis is performed in a region enriched in photon production via vector boson fusion, with a requirement on the transverse momentum of the photon to exceed 200 GeV. The cross section is measured to be ${202}_{-32}^{+36}$ fb, at a significance with respect to the null hypothesis that exceeds five standard deviations. This is in agreement with the standard model prediction of ${177}_{-12}^{+13}$ fb. Differential cross sections are measured as a function of various observables. Limits are set on dimension-6 effective field theory operators that contribute to the WW γ interaction. The observed 95% confidence intervals for the corresponding Warsaw basis Wilson coefficients c W and c HWB are [−0.11, 0.16] and [−1.6, 1.5], respectively.

electroweak interaction↗

DOE OSTI2025

Using the optimal combined index weight ratio to improve the probability of anomaly detection in big area additive manufacturing

Big Area Additive Manufacturing (BAAM) of composites requires significant time, energy, and material, so it is critical to reduce production inefficiencies to make functional parts without multiple iterations. Statistical process control coupled with Principal Component Analysis (PCA) is a powerful technique that provides a quick, computationally inexpensive, and intuitive way for operators to detect defects that form in a manufacturing process without massive datasets. Recently, a combined index that is a weighted sum of the Hotelling's T 2 and squared residual error statistics has been proposed that can be monitored in one chart, improving interpretation accuracy and simplicity. However, the literature does not offer a formal method to optimise the weights. Here, we introduce two new approaches to the traditional weight selection approach using simulated and BAAM image data. Approach 1 uses a theoretically motivated optimum inspired by probabilistic principal component analysis. Approach 2 systematically varies the ratio of the weights to find the optimum. We show that approach 1 delivers optimal anomaly detection performance in select cases while approach 2 fares better in practice. Surprisingly, we also show that choosing a more complex PCA model has a minimal negative impact on anomaly detection performance compared to a more simplistic model.

3-dimensional printing↗

DOE OSTI2024

Development of a Method for Shape Optimization for a Gas Turbine Fuel Injector Design Using Metal-Additive Manufacturing

Adjoint shape optimization has enabled physics-based optimal designs for aerodynamic surfaces. Additive manufacturing (AM) makes it possible to manufacture complex shapes. However, there has been a gap between optimal and manufacturable surfaces due to the inherent limitations of commercial computational fluid dynamics (CFD) codes to implement geometric constraints during adjoint computation. In such cases, the design sensitivities are exported and used to perform constrained shape modifications using parametric information stored in computer aided design (CAD) files to satisfy manufacturability constraints. However, modifying the design using adjoint methods in CFD solvers and performing constrained shape modification in CAD can lead to inconsistencies due to different shape parameterization schemes. This paper describes a method to enable the simultaneous optimization of the fluid domain and impose AM manufacturability constraints, resolving one of the key issues of geometry definition for isogeometric analysis. Similar to a grid convergence study, the proposed method verifies the consistencies between shape parameterization techniques present within commercial CAD and CFD software during mesh movement as a part of the adjoint shape optimization routine. By identifying the appropriate parameters essential to a shape optimization study, the error metric between the different parameterization techniques converges to demonstrate sufficient consistencies for justifiable exchange of data between CAD and CFD. For the identified shape optimization parameters, the error metric to measure the deviation between the two parameterization schemes lies within the AM laser-powder bed fusion (L-PBF) process tolerance. Additionally, comparison for subsequent objective function calculations between iterations of the optimization loop showed acceptable differences within 1% variation between the modified geometries obtained using the two parameterization schemes. This method provides justification for the use of multiphysics guided adjoint design sensitivities computed in CFD software to perform shape modifications in CAD to incorporate AM manufacturability constraints during the shape optimization loop such that optimal designs are also additively manufacturable.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2026

Final SeaQuest Results on the Flavor Asymmetry of the Proton Light-Quark Sea with Proton-Induced Drell-Yan Process

The Fermilab E906/SeaQuest collaboration performed measurements of the Drell-Yan process using 120 GeV proton beams bombarding liquid hydrogen and liquid deuterium targets. A combined analysis of all collected data was performed to obtain the final results for the 𝜎 𝑝⁢𝑑 /2⁢𝜎 𝑝⁢𝑝 Drell-Yan cross section ratio covering the kinematic region of 0.13 < 𝑥 <0.45. The 𝑥 dependencies of $\bar{d}$(𝑥)/$\bar{𝑢}$⁡(𝑥) and $\bar{d}$(𝑥) $-$ $\bar{𝑢}$⁡(𝑥) are extracted from these cross section ratios. It is found that $\bar{d}$(𝑥) is greater than $\bar{𝑢}$⁡(𝑥) over the entire measured 𝑥 range, with improved statistical accuracy compared to previous measurements. The new results on $\bar{d}$(𝑥)/$\bar{𝑢}$⁡(𝑥) and $\bar{d}$(𝑥) $-$ $\bar{𝑢}$⁡(𝑥) are compared to various parton distribution functions and theoretical calculations.

Leung, C. H. [University of Illinois at Urbana-Cha↗

DOE OSTI2024

Properties of the 256 Db decay chain

Experiments were performed at Lawrence Berkeley National Laboratory's 88-Inch Cyclotron Facility to study the decays of neutron-deficient dubnium isotopes. These isotopes were produced in the 206 Pb( 51 V, xn) 255,256 Db reaction, and excitation functions were measured. This article reports on the observed properties of the 256 Db decay chain. The produced 256 Db nuclei were separated from unreacted-beam material and reaction byproducts with the Berkeley Gas-filled Separator (BGS) before being implanted into a double-sided silicon strip detector at the BGS focal plane. Decay properties of 256 Db and its daughters were then extracted from the analysis of correlations between implanted Db nuclei with α decay chains and spontaneous fission (SF) events. In total, 86 decay chains and 38 SF events were observed, giving increased statistics as compared to previous studies. In conclusion, improved decay data are presented for 256 Db and its daughter isotopes 252 Lr, 252 No, 248 Md, 248 Fm, 244 Es, and 244 Cf.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Joint Inversion of Regional Waveform, First-Motion Polarity, and Synthetic Aperture Radar Surface Displacement for the Fourth and Sixth North Korean Declared Nuclear Explosions

Here, this study analyzed the Democratic People’s Republic of Korea’s (DPRK) fourth (DPRK4, 6 January 2016 M w 4.49) and sixth (DPRK6, 7 September 2017 M w 5.2) declared nuclear tests, employing a joint seismic and Interferometric Synthetic Aperture Radar (InSAR) inversion to improve understanding of these events and enhance moment tensor (MT) inversion capabilities. The recent efforts have focused on employing seismic waveform and InSAR geodetic deformation data separately to analyze these and the previous nuclear tests (e.g., Chiang et al., 2018; Myers et al., 2018; Wang et al., 2018). Building upon our previous work (Chi-Durán et al., 2021), we performed a joint regional waveform, first-motion (FM) polarity, and surface displacement inversion, which demonstrated improved source-type discrimination, a revised MT solution with reduced scalar moment uncertainty, and an independently constrained location. In this article, we build on the previous results for DPRK6 by including an analysis using a four-layered velocity model with free-surface topography to compute the near-source static deformation Green’s functions. The model consists of a 50 m basalt layer (⁠V P = 2.07 km/s, V S = 1.2 km/s⁠), a 250 m stratified volcanic deposit layer (⁠V P = 1.73 km/s, V S = 1.0 km/s⁠), a 700 m weathered granodiorite layer (⁠V P = 2.5 km/s, V S = 1.3 km/s⁠⁠), and a granodiorite half-space (⁠V P = 5.35 km/s, V S = 3.09 km/s⁠⁠). The half-space shares the velocity of the regional MDJ2 velocity model (Ford et al., 2010), which has proven effective for waveform inversion in the region. This model considers the range of reported values for various lithologies and weathering effects. Our findings show that using the layered velocity model enhances the recovery of source location and depth for both the explosions by improving fits and reducing uncertainties. The joint inversion also improves source-type discrimination and better constrains the scalar seismic moment necessary for downstream yield estimation.

58 GEOSCIENCES↗

DOE OSTI2026

Glauber-theory analysis of nuclear reactions on a 12 C target with variational Monte Carlo wave functions

The application of Glauber theory has been playing an increasingly important role with the study of unstable or exotic nuclei. Its adaptation to medium and high-energy nucleus-nucleus collisions is severely limited because one has to evaluate the matrix elements of multiple-scattering operators. The extraction of physical observables has been done using ‘approximate’ Glauber theory whose validity is hard to evaluate. Here, we perform a full calculation of the matrix elements using Monte Carlo integration and analyze the elastic differential cross sections and the total reaction cross sections for p+¹²C, ⁴,⁶He+¹²C, and ¹²C+¹²C collisions. We use the variational Monte Carlo wave functions for ⁴,⁶He and ¹²C obtained by using realistic two- and three-nucleon potentials. We demonstrate the performance of the Glauber-theory calculations by comparing with available experimental data. We further discuss the accuracy of the conventional approximate methods in the light of the cumulant expansion for Glauber’s phase-shift function.

Horiuchi, W. [Osaka Metropolitan University (Japan↗

DOE OSTI2024

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Searching for Neutrino Tridents in the NOvA Near Detector

This dissertation presents a search for neutrino trident production in the NOvA near detector through the coherent ``dimuon" channel: $\nu_\mu +\hspace{1pt}\text{X} \rightarrow \nu_\mu + \mu^- + \mu^+ +\hspace{1pt}\text{X}$. Trident production is a rare, purely electroweak process with sensitivity to physics beyond the Standard Model. The theoretical background, motivation for studying the process, and previous experimental measurements are reviewed. The analysis uses data collected by the NOvA near detector (ND) from Fermilab's Neutrinos at the Main Injector (NuMI) beam between November 2014 and February 2024, corresponding to an exposure of $25.5\times 10^{20}$ protons on target. The ND is a segmented tracking calorimeter located 800~m from the beam target, receiving neutrinos with a mean energy of 2~GeV. A multi-pass background reduction strategy is implemented, including the development of a novel dimuon-specific tracking technique. Trident candidates are identified using a boost ed decision tree classifier trained on simulated signal and background events. Limited background Monte Carlo statistics necessitate the use of functional fits to sideband data, which are extrapolated to estimate backgrounds in the signal region. The unblinded data contain 9 trident-like events, with an estimated background of 5.66 $\pm$ 5.15 events. This yields a best fit estimate of 3.34 tridents compared to the Standard Model prediction of 4.66. A profiled Feldman-Cousins method is used to determine a 90\% confidence interval of [0,9.1] on the number of signal events, corresponding to an upper limit of 1.95$\times$ the Standard Model prediction. This result represents the lowest energy search for trident events to date, and the first experimental contribution to the process in 27 years.

Bowles, Reed Scott [Indiana U.]↗

DOE OSTI2024

Theory of Ion-Mediated Segmental Localization, Activated Structural Relaxation, and the Glass Transition in Polymerized Ionic Liquids

Here we combine polymer integral equation theory for structural correlations with a force-level theory for activated segmental relaxation to construct a microscopic theory for how ions modify the onset of segmental localization, the polymer alpha relaxation time, and glass transition temperature, T g , in dry polymerized ionic liquids (PolyILs). Our most important findings concerning the behavior of T g are (i) a weak dependence on anion–cation Coulomb attraction strength due to strong decoupling of ion and segmental dynamics, (ii) strong reduction with increasing mobile ion size due to both plasticization effects and weakening of ion-modified monomer caging, and (iii) increase with backbone rigidity and intrachain dynamic cooperativity. We quantitatively estimate T g variations as ion size and polymer static and dynamic rigidity are widely varied. The experimental data of 19 PolyILs are organized into a specific pattern consistent with the theoretical predictions with glass transition temperatures varying over a very wide range (~250 K) as observed experimentally. Based on the theoretical results, suggestions are made concerning the search for high conductivity Li- or Na-based PolyILs based on further lowering of T g via new polymer synthesis. Calculations of the alpha time as a function of packing fraction reveal the dynamic fragility increases for larger mobile ions, a more flexible backbone, and/or a smaller degree of intrachain dynamic cooperativity, as a consequence of the increasing importance of collective elasticity in determining the activation barrier. An analysis of transient segmental localization and a crossover to activated dynamics reveals similar, but not identical, trends as predicted at the laboratory vitrification timescale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Statistical relationships across epigenomes using large-scale hierarchical clustering

Recent advances in genomics and sequencing platforms have revolutionized our ability to create immense data sets, particularly for studying epigenetic regulation of gene expression. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given nonlinear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine learning for discerning infectivity and susceptibility. In this study, we explore over 3000 epigenomes of uninfected individuals and provide a framework to characterize the relationships among epigenetic modifiers, their modifiers, genetic loci, and specific immune cell types across all chromosomes using hierarchical clustering. Hierarchical clustering of epigenomic data revealed consistent epigenetic patterns across chromosomes, demonstrating that variation due to epigenetic modifiers is greater than variation between cell types. Gene Ontology and KEGG pathway analyses indicated significant enrichment of genes involved in chromatin remodeling, mRNA splicing, immune responses, and the regulation of microRNAs and snoRNAs. Epigenetic modifiers frequently formed biologically relevant clusters, including the cohesin complex, RNA Polymerase II transcription factors, and PRC2 complex members. These clustering behaviors remained consistent across all chromosomes, supported by entropy analysis and high Adjusted Rand Index scores, indicating robust cross-chromosomal similarity. Co-occurrence analysis further revealed specific sets of modifiers that consistently appeared together within clusters, reflecting shared biological functions and interactions. Validation using another dataset confirmed the reproducibility of these clustering patterns and modifier co-occurrence relationships, underscoring the reliability and generalizability of the methodology.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

59 BASIC BIOLOGICAL SCIENCES↗