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At least 73 records · Page 4
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DOE OSTI2024

Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum : Insights into the Origins of Paralytic Shellfish Toxins

Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of harmful algal bloom-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins produced by harmful algal blooms remain at best incomplete. The paralytic shellfish toxin saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from nonaxenic culture, coupled with a combination of short- and long-read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, paralytic shellfish toxin-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the paralytic shellfish toxin saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that paralytic shellfish toxin production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of paralytic shellfish toxin biosynthetic gene cluster diversity and suggests a mechanism for the origin of paralytic shellfish toxin biosynthetic genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B

Toxin B (TcdB) is a primary cause of Clostridioides difficile infection (CDI). This toxin acts by glucosylating small GTPases in the Rho/Ras families, but the structural basis for TcdB recognition and selectivity of specific GTPase substrates remain unsolved. Here, we report the cocrystal structures of the glucosyltransferase domain (GTD) of two distinct TcdB variants in complex with human Cdc42 and R-Ras, respectively. These structures reveal a common structural mechanism by which TcdB recognizes Rho and R-Ras. Furthermore, we find selective clustering of adaptive residue changes in GTDs that determine their substrate preferences, which helps partition all known TcdB variants into two groups that display distinct specificities toward Rho or R-Ras. Mutations that selectively disrupt GTPases binding reduce the glucosyltransferase activity of the GTD and the toxicity of TcdB holotoxin. These findings establish the structural basis for TcdB recognition of small GTPases and reveal strategies for therapeutic interventions for CDI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The galaxy–halo connection of emission-line galaxies in IllustrisTNG

ABSTRACT We employ the hydrodynamical simulation IllustrisTNG-300-1 to explore the halo occupation distribution (HOD) and environmental dependence of luminous star-forming emission-line galaxies (ELGs) at z ∼ 1. Such galaxies are key targets for current and upcoming cosmological surveys. We select model galaxies through cuts in colour–colour space allowing for a direct comparison with the Extended Baryon Oscillation Spectroscopic Survey and the Dark Energy Spectroscopic Instrument (DESI) surveys and then compare them with galaxies selected based on specific star formation rate (sSFR) and stellar mass. We demonstrate that the ELG populations are twice more likely to reside in lower density regions (sheets) compared with the mass-selected populations and twice less likely to occupy the densest regions of the cosmic web (knots). We also show that the colour-selected and sSFR-selected ELGs exhibit very similar occupation and clustering statistics, finding that the agreement is best for lower redshifts. In contrast with the mass-selected sample, the occupation of haloes by a central ELG peaks at ∼20 per cent. We furthermore explore the dependence of the HOD and the autocorrelation on environment, noticing that at fixed halo mass, galaxies in high-density regions cluster about 10 times more strongly than low-density ones. This result suggests that we should model carefully the galaxy–halo relation and implement assembly bias effects into our models (estimated at ∼4 per cent of the clustering of the DESI colour-selected sample at z = 0.8). Finally, we apply a simple mock recipe to recover the clustering on large scales (r ≳ 1 Mpc h−1) to within 1 per cent by augmenting the HOD model with an environment dependence, demonstrating the power of adopting flexible population models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Cosmological measurements from void-galaxy and galaxy-galaxy clustering in the Sloan Digital Sky Survey

We present the cosmological implications of measurements of void-galaxy and galaxy-galaxy clustering from the Sloan Digital Sky Survey (SDSS) Main Galaxy Sample (MGS), Baryon Oscillation Spectroscopic Survey (BOSS), and extended BOSS (eBOSS) luminous red galaxy catalogues from SDSS Data Release 7, 12, and 16, covering the redshift range 0.07 < $z$ < 1.0. We fit a standard ΛCDM cosmological model as well as various extensions, including a constant dark energy equation of state not equal to −1, a time-varying dark energy equation of state, and these same models allowing for spatial curvature. Results on key parameters of these models are reported for void-galaxy and galaxy-galaxy clustering alone, both of these combined, and all these combined with measurements from the cosmic microwave background (CMB) and supernovae (SN). For the combination of void-galaxy and galaxy-galaxy clustering, we find tight constraints of Ω m = 0.356 ± 0.024 for a base ΛCDM cosmology, Ω m = $0.391^{+0.028}_{-0.021}$, w = $-1.50^{+0.43}_{-0.28}$ additionally allowing the dark energy equation of state $w$ to vary, and Ω m = $0.331^{+0.067}_{-0.094}$, $w=-1.41^{+0.70}_{-0.31}$, and Ω k = $0.06^{+0.18}_{-0.13}$ further extending to non-flat models. The combined SDSS results from void-galaxy and galaxy-galaxy clustering in combination with CMB+SN provide a 30 per cent improvement in parameter Ω m over CMB+SN for ΛCDM, a 5 per cent improvement in parameter Ω m when $w$ is allowed to vary, and a 32 per cent and 68 per cent improvement in parameters Ω m and Ω k when allowing for spatial curvature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Oscillatory and Collective Dynamics of Gold‐Nanoparticle‐Laden Droplets Driven by Photothermal‐Induced Thermocapillarity

Droplets have long intrigued researchers due to their ability to exhibit complex and fascinating behavior when subjected to external stimuli. Here, a coupled oscillatory behavior of gold-nanoparticle-surfactant-laden aqueous droplets is investigated at an oil-oil interface stimulated by light. This study shows that the interaction between light and the droplets gives rise to a range of oscillatory modes, including bouncing and clustering, where droplets exhibit collective movement. From experiment and numerical simulations, this study elucidates the underlying mechanism: upon laser irradiation, gold nanoparticles convert light into heat, generating asymmetric thermal gradients that drive upward thermocapillary flows and a hydrodynamic force from photothermal convection. These forces compete with gravity and buoyancy to induce droplet bouncing, while the resulting asymmetric flow fields bias neighboring droplets toward the illuminated droplet, leading to clustering. These findings not only expand the library of dynamic droplet behavior but also offer insights into the potential applications of light-driven systems in materials science, soft robotics, and microfluidics.

Marangoni effect↗
DOE OSTI2023

Reproducibility of calculations on Li species with correlation-consistent basis sets

Here we have found that two different basis set series, both labeled cc-pVxZ, are widely available and widely used for calculation on Li compounds such that calculations that should be the same are different, causing a reproducibility problem. Here we study the magnitude of the disagreement of these nominally-the-same basis sets for wave function and density functional calculations of Li clusters. We find deviations among the basis sets of as large as 22 millihartrees. In most cases one obtains lower energies with the noncanonical choices. Therefore, it is important to specify which version of the basis set is used for calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Miscentring of optical galaxy clusters based on Sunyaev–Zeldovich counterparts

ABSTRACT The ‘miscentring effect’, i.e. the offset between a galaxy cluster’s optically defined centre and the centre of its gravitational potential, is a significant systematic effect on brightest cluster galaxy (BCG) studies and cluster lensing analyses. We perform a cross-match between the optical cluster catalogue from the Hyper Suprime-Cam (HSC) Survey S19A Data Release and the Sunyaev–Zeldovich cluster catalogue from Data Release 5 of the Atacama Cosmology Telescope (ACT). We obtain a sample of 186 clusters in common in the redshift range $0.1 \le z \le 1.4$ over an area of 469 deg$^2$. By modelling the distribution of centring offsets in this fiducial sample, we find a miscentred fraction (corresponding to clusters offset by more than 330 kpc) of ∼25 per cent, a value consistent with previous miscentring studies. We examine the image of each miscentred cluster in our sample and identify one of several reasons to explain the miscentring. Some clusters show significant miscentring for astrophysical reasons, i.e. ongoing cluster mergers. Others are miscentred due to non-astrophysical, systematic effects in the HSC data or the cluster-finding algorithm. After removing all clusters with clear, non-astrophysical causes of miscentring from the sample, we find a considerably smaller miscentred fraction, $\sim 10~\,\rm per\,cent$. We show that the gravitational lensing signal within 1 Mpc of miscentred clusters is considerably smaller than that of well-centred clusters, and we suggest that the ACT SZ centres are a better estimate of the true cluster potential centroid.

Ding, Jupiter (ORCID:0000000296119799)↗
DOE OSTI2025

The hierarchical growth of bright central galaxies and intracluster light as traced by the magnitude gap

Using a sample of 2800 galaxy clusters identified in the Dark Energy Survey across the redshift range 0.20 < z < 0.60, we characterize the hierarchical assembly of bright central galaxies (BCGs) and the surrounding intracluster light (ICL). To quantify hierarchical formation we use the stellar mass–halo mass (SMHM) relation, comparing the halo mass, estimated via the mass–richness relation, to the stellar mass within the BCG + ICL system. Moreover, we incorporate the magnitude gap (M14), the difference in brightness between the BCG (measured within 30 kpc) and fourth brightest cluster member galaxy within 0.5 $R_{200,c}$, as a third parameter in this linear relation. The inclusion of M14, which traces BCG hierarchical growth, increases the slope and decreases the intrinsic scatter, highlighting that it is a latent variable within the BCG + ICL SMHM relation. Moreover, the correlation with M14 decreases at large radii. However, the stellar light within the BCG + ICL transition region (30 –80 kpc) most strongly correlates with halo mass and has a statistically significant correlation with M14. Since the transition region and M14 are independent measurements, the transition region may grow due to the BCG’s hierarchical formation. Additionally, as M14 and ICL result from hierarchical growth, we use a stacked sample and find that clusters with large M14 values are characterized by larger ICL and BCG + ICL fractions, which illustrates that the merger processes that build the BCG stellar mass also grow the ICL. Furthermore, this may suggest that M14 combined with the ICL fraction can identify dynamically relaxed clusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Eridanus II: A Fossil from Reionization with an Off-center Star Cluster

In this work, we present deep Hubble Space Telescope (HST) photometry of the ultra-faint dwarf galaxy Eridanus II (Eri II). Eri II, which has an absolute magnitude of M V = -7.1, is located at a distance of 339 kpc, just beyond the virial radius of the Milky Way. We determine the star formation history of Eri II and measure the structure of the galaxy and its star cluster. We find that a star formation history consisting of two bursts, constrained to match the spectroscopic metallicity distribution of the galaxy, accurately describes the Eri II stellar population. The best-fit model implies a rapid truncation of star formation at early times, with >80% of the stellar mass in place before z ~ 6. A small fraction of the stars could be as young as 8 Gyr, but this population is not statistically significant; Monte Carlo simulations recover a component younger than 9 Gyr only 15% of the time, where they represent an average of 7 ± 4% of the population. These results are consistent with theoretical expectations for quenching by reionization. The HST depth and angular resolution enable us to show that Eri II’s cluster is offset from the center of the galaxy by a projected distance of 23 ± 3 pc. This offset could be an indication of a small (~50–75 pc) dark matter core in Eri II. Moreover, we demonstrate that the cluster has a high ellipticity of and is aligned with the orientation of Eri II within 3° ± 6°, likely due to tides. The stellar population of the cluster is indistinguishable from that of Eri II itself.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Constraints on MeV dark matter and primordial black holes: Inverse Compton signals at the SKA

Here we investigate the possibilities for probing MeV dark matter (DM) particles and primordial black holes (PBHs) (for masses ~ 10 15 –10 17 g) at the upcoming radio telescope SKA, using photon signals from the Inverse Compton (IC) effect within a galactic halo. Pair-annihilation or decay of MeV DM particles (into e + e - pairs) or Hawking radiation from a population of PBHs generates mildly relativistic e ± which can lead to radio signals through the IC scattering on low energy cosmic microwave background (CMB) photons. We study the ability of SKA to detect such signals coming from nearby ultra-faint dwarf galaxies Segue I and Ursa Major II as well as the globular cluster ω-cen and the Coma cluster. We find that with ~ 100 hours of observation, the SKA improves the Planck constraints on the DM annihilation/decay rate and the PBH abundance for masses in the range ~ 1 to few tens of MeV and above 10 15 to 10 17 g, respectively. Importantly, the SKA limits are independent of the assumed magnetic fields within the galaxies. Previously allowed regions of diffusion parameters of MeV electrons inside a dwarf galaxy that give rise to observable signals at the SKA are also excluded. For objects like dwarf galaxies, predicted SKA constraints depend on both the DM and diffusion parameters. Independent observations in different frequency bands, e.g., radio and γ-ray frequencies, may break this degeneracy and thus enable one to constrain the combined parameter space of DM and diffusion. However, the constraints are independent of diffusion parameters for galaxy clusters such as Coma.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

GEANT4 parameter tuning using Professor

The GEANT4 toolkit is used extensively in high energy physics to simulate the passage of particles through matter and to predict effects such as detector efficiencies and smearing. GEANT4 uses many underlying models to predict particle interaction kinematics, and uncertainty in these models leads to uncertainty in high energy physics measurements. The GEANT4 collaboration recently made free parameters in some models accessible through partnership with GEANT4 developers. We present a study of the impact of varying parameters in three GEANT4 hadronic physics models on agreement with thin target datasets and describe fits to these datasets using the Professor model tuning framework [1]. We find that varying parameters produces substantially better agreement with some datasets, but that more degrees of freedom are required for full agreement. This work is a first step towards a common framework for propagating uncertainties in GEANT4 models to high energy physics measurements, and we outline future work required to complete that goal.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Timing of pulsars in the globular cluster omega centauri

We present the timing of the first five millisecond pulsars discovered in the globular cluster Omega Centauri and the discovery of a pulsar with a spin period of 3.68 ms. With a timing baseline of ~3.5 yr we are able to measure the derivative of the spin frequency ($\dot{\nu }$) for the first five pulsars. Upper limits on the pulsar line-of-sight acceleration are estimated and compared with predictions based on analytical models of the cluster. We find that PSRs J1326-4728B and D show large negative accelerations, which are in tension with the minimum acceleration predicted by analytical models. We searched for pulsed γ-ray signals using 14.3 yr of data from the Fermi Large Area Telescope. Although we found no evidence for γ-ray pulsations, PSRs J1326-4728A, B, C, and E are associated with X-ray sources. This suggests that the observed γ-ray emission from Omega Centauri is likely caused by the emission of the ensemble of MSPs. Finally, the linearly polarized emission from PSR J1326-4728A yields a rotation measure of -18 ± 8 rad m -2 .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

FPGA-based tracking for the CMS Level-1 trigger using the tracklet algorithm

The high instantaneous luminosities expected following the upgrade of the Large Hadron Collider (LHC) to the High-Luminosity LHC (HL-LHC) pose major experimental challenges for the CMS experiment. A central component to allow efficient operation under these conditions is the reconstruction of charged particle trajectories and their inclusion in the hardware based trigger system. There are many challenges involved in achieving this: a large input data rate of about 20–40 Tb/s; processing a new batch of input data every 25 ns, each consisting of about 15,000 precise position measurements and rough transverse momentum measurements of particles (“stubs”); performing the pattern recognition on these stubs to find the trajectories; and producing the list of trajectory parameters within 4 µs. Here, this paper describes a proposed solution to this problem, specifically, it presents a novel approach to pattern recognition and charged particle trajectory reconstruction using an all-FPGA solution. The results of an end-to-end demonstrator system, based on Xilinx Virtex-7 FPGAs, that meets timing and performance requirements are presented along with a further improved, optimized version of the algorithm together with its corresponding expected performance.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Introducing a Markov chain-based time calibration procedure for multi-channel particle detectors: application to the SuperFGD and ToF detectors of the T2K experiment

Inter-channel mis-synchronisation can be a limiting factor to the time resolution of high performance timing detectors with multiple readout channels and independent electronics units. In these systems, time calibration methods employed must be able to efficiently correct for minimal mis-synchronisation between channels and achieve the best detector performance. We present an iterative time calibration method based on Markov Chains, suitable for detector systems with multiple readout channels. Starting from correlated hit pairs alone, and without requiring an external reference time measurement, the method solves for fixed per-channel offsets, with precision limited only by the intrinsic single-channel resolution. A mathematical proof that the method is able to find the correct time offsets to be assigned to each detector channel in order to achieve inter-channel synchronisation is given, and it is shown that the number of iterations to reach convergence within the desired precision is controllable with a single parameter. Numerical studies are used to confirm unbiased recovery of true offsets. Finally, the application of the calibration method to the Super Fine-Grained Detector (SuperFGD) and the Time of Flight (TOF) detector at the upgraded T2K near detector (ND280) shows good improvement in overall timing resolution, demonstrating the effectiveness in a real-world scenario and scalability.

calibration and fitting methods↗
DOE OSTI2026

Protonation Dynamics of Confined Ethanol–Water Mixtures in H-ZSM-5 from Machine Learning-Driven Metadynamics

Zeolites are indispensable heterogeneous catalysts in industrial chemical processes, valued for their strong Brønsted acidity, well-defined microporous frameworks, and tunable pore structures. Their catalytic activity arises primarily from Brønsted acid sites (BAS), typically present as bridging hydroxyl groups (Si–OH–Al). Under aqueous reaction conditions, these protons interact dynamically with water and alcohol molecules, leading to complex solvation and protonation behavior within confined pores. In this study, we investigate the protonation equilibrium occurring between ethanol and water at the BAS of acidic zeolites under varying hydration levels, i.e., C2H5OH–(H2O)n, n=1–4. Local structure was analyzed through an adaptive-learning global optimization algorithm, while enhanced sampling molecular dynamics simulations with Well-Tempered Metadynamics (WMetaD) and machine learning interatomic potentials (MLPs) provide free-energy surfaces (FES) at variable hydration levels. The results reveal a strong dependence of proton localization on the degree of hydration. At low hydration (1 water molecule), the proton resides predominantly on ethanol; with 2 water molecules, it shifts toward water, and at higher hydration (3 or more water molecules), it becomes extensively delocalized over the water cluster. These findings underscore the critical role of solvation in modulating acid site behavior and suggest that a minimum of three water molecules is necessary to fully stabilize the proton on water within the zeolite framework. This solvation threshold has significant implications for catalytic processes, particularly in biomass conversion reactions where alcohol protonation is a key step in dehydration mechanisms.

machine learning↗
DOE OSTI2022

Highly Structured Water Networks in Microhydrated Dodecaborate Clusters

Here, we report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B 12 X 12 2– ·nH 2 O (X = H, F, or I; n = 1–6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B 12 X 12 2– bases, illustrating the evident solute specificity. Because B–H···H–O dihydrogen bonds are stronger than O···H–O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B 12 H 12 2– . As a comparison, the hydrated B 12 F 12 2– clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B 12 I 12 2– share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Cosmological constraints from the tomography of DES-Y3 galaxies with CMB lensing from ACT DR4

We present a measurement of the cross-correlation between the MagLim galaxies selected from the Dark Energy Survey (DES) first three years of observations (Y3) and cosmic microwave background (CMB) lensing from the Atacama Cosmology Telescope (ACT) Data Release 4 (DR4), reconstructed over ∼ 436 deg 2 of the sky. Our galaxy sample, which covers ∼ 4143 deg 2 , is divided into six redshift bins spanning the redshift range of 0.20 < z <1.05. We adopt a blinding procedure until passing all consistency and systematics tests. After imposing scale cuts for the cross-power spectrum measurement, we reject the null hypothesis of no correlation at 9.1σ. We constrain cosmological parameters from a joint analysis of galaxy and CMB lensing-galaxy power spectra considering a flat ΛCDM model, marginalized over 23 astrophysical and systematic nuisance parameters. We find the clustering amplitude S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.75 +0.04 -0.05 . In addition, we constrain the linear growth of cosmic structure as a function of redshift. Our results are consistent with recent DES Y3 analyses and suggest a preference for a lower S 8 compared to results from measurements of CMB anisotropies by the Planck satellite, although at a mild level (< 2σ) of statistical significance.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Parametrizing the detector response with neural networks

In high energy physics, characterizing the response of a detector to radiation is one of the most important and fundamental experimental tasks. In many cases, this task is accomplished by parameterizing summary statistics of the full detector response probability density. The parameterized detector response can then be used for calibration as well as for directly improving physics analysis sensitivity. This paper reports on how to parameterize summary statistics of the detector response using neural networks. Specifically, neural networks are powerful tools for incorporating multidimensional data and the loss function used during training determines which summary statistic is learned. One common summary statistic that has not been combined with deep learning (as far as the authors are aware) is the mode. A neural network-based approach to mode learning is proposed and empirically demonstrated in the context of high energy jet calibrations. Altogether, the neural network-based toolkit for detector response parameterization can enhance the utility of data collected at high energy physics experiments and beyond.

47 OTHER INSTRUMENTATION↗