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At least 721 records · Page 40

Neutrino interaction vertex reconstruction in DUNE with Pandora deep learning

The Pandora Software Development Kit and algorithm libraries perform reconstruction of neutrino interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at the Deep Underground Neutrino Experiment, which will operate four large-scale liquid argon time projection chambers at the far detector site in South Dakota, producing high-resolution images of charged particles emerging from neutrino interactions. While these high-resolution images provide excellent opportunities for physics, the complex topologies require sophisticated pattern recognition capabilities to interpret signals from the detectors as physically meaningful objects that form the inputs to physics analyses. A critical component is the identification of the neutrino interaction vertex. Subsequent reconstruction algorithms use this location to identify the individual primary particles and ensure they each result in a separate reconstructed particle. A new vertex-finding procedure described in this article integrates a U-ResNet neural network performing hit-level classification into the multi-algorithm approach used by Pandora to identify the neutrino interaction vertex. The machine learning solution is seamlessly integrated into a chain of pattern-recognition algorithms. The technique substantially outperforms the previous BDT-based solution, with a more than 20% increase in the efficiency of sub-1 cm vertex reconstruction across all neutrino flavours.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

t -channel dark matter models – a whitepaper

This report, summarising work achieved in the context of the LHC Dark Matter Working Group, investigates the phenomenology of t -channel dark matter models, spanning minimal setups with a single dark matter candidate and mediator to more complex constructions closer to UV-complete models. For each considered class of models, we examine collider, cosmological and astrophysical implications. In addition, we explore scenarios with either promptly decaying or long-lived particles, as well as featuring diverse dark matter production mechanisms in the early universe. By providing a unified analysis framework, numerical tools and guidelines, this work aims to support future experimental and theoretical efforts in exploring t -channel dark matter models at colliders and in cosmology.

Arina, Chiara [Universite Catholique de Louvain, L↗

Testing T2K’s Bayesian constraints with priors in alternate parameterisations

Bayesian analysis results require a choice of prior distribution. In long-baseline neutrino oscillation physics, the usual parameterisation of the mixing matrix induces a prior that privileges certain neutrino mass and flavour state symmetries. Here we study the effect of privileging alternate symmetries on the results of the T2K experiment. We find that constraints on the level of CP violation (as given by the Jarlskog invariant) are robust under the choices of prior considered in the analysis. On the other hand, the degree of octant preference for the atmospheric angle depends on which symmetry has been privileged.

Bayesian Inference↗

Reconstruction of atmospheric neutrinos in DUNE’s horizontal-drift far-detector module

This paper reports on the capabilities in reconstructing and identifying atmospheric neutrino interactions in one of the Deep Underground Neutrino Experiment’s (DUNE) far detector modules, a liquid argon time projection chamber (LArTPC) with horizontal drift (FD-HD) of ionization electrons. The reconstruction is based upon the workflow developed for DUNE’s long-baseline oscillation analysis, with some necessary machine-learning models’ retraining and the addition of features relevant only to atmospheric neutrinos such as the neutrino direction reconstruction. Where relevant, the impact of the detection of the charged particles of the hadronic system is emphasized, and comparisons are carried out between the case when lepton-only information is considered in the reconstruction (as is the case for many neutrino oscillation experiments), versus when all particles identified in the LArTPC were included. Three neutrino direction reconstruction methods have been developed and studied for the atmospheric analyses: using lepton-only information, using all reconstructed particles, and using only correlations from reconstructed hits. The results indicate that incorporating more than just lepton information significantly improves the resolution of both neutrino direction and energy reconstruction. The angle reconstruction algorithms developed in this work result in no strong dependence on particle direction for reconstruction efficiencies or neutrino flavor identification. This comprehensive review of the reconstruction of atmospheric neutrinos in DUNE’s FD-HD LArTPC is the first step towards developing a first neutrino oscillation sensitivity analysis, which will ready DUNE for its first measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Systematics of the chemical freeze-out line in the high baryon density regime explored at SIS100

The systematic uncertainties of chemical freeze-out fits at SIS100 energies (Au+Au reactions at $\sqrt{s_{NN}}$ = 3 – 5 GeV) are studied using UrQMD simulations. Although hadron production in UrQMD does not occur on a sharp chemical freeze-out hyper-surface, the extracted fit quality is shown to be very good. The extracted chemical parameters depend on the selected hadron species as well as the underlying equation of state (EoS) of the matter. Including light nuclei and anti-protons in the fit increases the expected freeze-out temperature, while a stiffer EoS increases the obtained chemical potential. Similarly, the baryon densities extracted by the thermal fits depend on the choice of hadrons as well as the underlying equation of state. These results are important for the upcoming CBM@FAIR physics program and highlight that a degree of caution is advised when one relates the chemical freeze-out curve to features on the QCD phase diagram like the critical endpoint or a possible phase transition.

Hofmann, Emma Lilith [GSI Helmholtzzentrum für Sch↗

Exploring the QCD phase diagram through correlations and fluctuations

The exploration of the Quantum Chromodynamics (QCD) phase diagram is a central goal of relativistic heavy-ion collision experiments. This review focuses on the role of fluctuations and correlations as sensitive probes of the phase structure. We discuss theoretical advancements and experimental methodologies employed to map the QCD phase diagram, highlighting constraints derived from both lattice QCD calculations and existing experimental data. Key observables such as cumulants and factorial cumulants of conserved charges (e.g., net-proton, net-charge) are explored as promising signatures of phase transitions and the QCD critical point. We discuss how these quantities are measured experimentally and compared with theoretical predictions, addressing challenges and best practices for meaningful comparisons. Special attention is given to predictions and current experimental results at high baryon density, including recent findings from the STAR collaboration at RHIC. Finally, we identify open issues and future directions for fluctuation and correlation studies at lower collision energies, relevant for future measurements, for example by the CBM experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Optimized Tandem Catalyst Patterning for CO 2 Reduction Flow Reactors

Tandem catalysis involves two or more catalysts arranged in proximity within a single reaction vessel, with the aim of synergistically aligning the catalysts’ reaction pathways to maximize overall system performance. This study presents a proof of concept showing the integration of continuum transport modeling with design optimization in a simplified two-dimensional flow reactor setup for electrochemical CO 2 reduction. Ag catalysts provide the CO 2 ⟶ CO reaction capability, and Cu catalysts provide the CO ⟶ high-value products reaction capability. Given a set of input parameters, the optimization algorithm uses adjoint methods to modify the Ag/Cu surface patterning in order to maximize the current density toward high-value products, such as ethylene. The optimized designs yield significant performance enhancement especially at more negative applied voltages (i.e., stronger surface reactions) and for larger numbers of patterning sections. For an applied voltage of −1.7 V vs. SHE, the 12-section optimized design increases the current density toward ethylene by up to 65% compared to the unoptimized 2-section design. For the optimized cases, observed differences in the production and consumption of CO (the key intermediate species) and minimized zones of low CO reactant surface concentration on Cu sections explain the improved reactor performance.

CO2 reduction↗

Code Generators for Floating-Point Unit Design in Integrated Circuits (OpenFloat) v1.0

This IP provides a comprehensive set of code generators for various floating-point units (FPUs) essential for integrated circuit design and integration, targeting a broad spectrum of applications, including machine learning and scientific computing. The suite includes FP adders, multipliers, subtractors, dividers, reciprocals, exponentials, square roots, trigonometric functions (sine, cosine, arctangent), and more. It supports customizable hardware design parameters, such as precision (16, 32, 64, and 128 bits) and pipeline depths, offering users enhanced flexibility and productivity. The generated code is in an industry-standard hardware description language, ensuring compatibility with standard design flows, including simulation, verification, synthesis, and implementation on both field-programmable gate arrays (FPGAs) and application-specific integrated circuits (ASICs).

Shalf, JohnM. [Lawrence Berkeley National Laborato↗

A Roadmap for the Future of Systems Biology in Cancer Research

Cancer systems biology seeks to understand how cancer arises as a system of interconnected molecules, cells, and tissues, with the goal of understanding, predicting, and controlling the disease. In the last decade, the field has rapidly grown as advances in experimental, computational, and analytic technologies have improved our ability to capture and recapitulate the complexities of cancer at multiple scales. However, the field’s promise to understand how specific molecular changes give rise to altered cancer outcomes remains incompletely fulfilled. Fortunately, an opportunity exists to accelerate progress by better coordinating modeling and data-gathering efforts across the cancer systems biology community. This will create the foundation for building accurate, multiscale cancer models that can better predict and identify improved therapeutic interventions. Here, in this study, we outline some of the current challenges in cancer systems biology research, how they can be addressed, and actions that the community can take to accelerate progress in the field.

Modeling & Simulation↗

Evaluation and Intercomparison of Small Uncrewed Aircraft Systems Used for Atmospheric Research

Abstract Small uncrewed aircraft systems (sUAS) are regularly being used to conduct atmospheric research and are starting to be used as a data source for informing weather models through data assimilation. However, only a limited number of studies have been conducted to evaluate the performance of these systems and assess their ability to replicate measurements from more traditional sensors such as radiosondes and towers. In the current work, we use data collected in central Oklahoma over a 2-week period to offer insight into the performance of five different sUAS platforms and associated sensors in measuring key weather data. This includes data from three rotary-wing and two fixed-wing sUAS and included two commercially available systems and three university-developed research systems. Flight data were compared to regular radiosondes launched at the flight location, tower observations, and intercompared with data from other sUAS platforms. All platforms were shown to measure atmospheric state with reasonable accuracy, though there were some consistent biases detected for individual platforms. This information can be used to inform future studies using these platforms and is currently being used to provide estimated error covariances as required in support of assimilation of sUAS data into weather forecasting systems.

54 ENVIRONMENTAL SCIENCES↗

Assimilation of a Coordinated Fleet of Uncrewed Aircraft System Observations in Complex Terrain: EnKF System Design and Preliminary Assessment

Abstract Uncrewed aircraft system (UAS) observations collected during the 2018 Lower Atmospheric Process Studies at Elevation—a Remotely Piloted Aircraft Team Experiment (LAPSE-RATE) field campaign were assimilated into a high-resolution configuration of the Weather Research and Forecasting Model using an ensemble Kalman filter. The benefit of UAS observations was assessed for a terrain-driven (drainage and upvalley) flow event that occurred within Colorado’s San Luis Valley (SLV) using independent observations. The analysis and prediction of the strength, depth, and horizontal extent of drainage flow from the Saguache Canyon and the subsequent transition to upvalley and up-canyon flow were improved relative to that obtained both without data assimilation (benchmark) and when only surface observations were assimilated. Assimilation of UAS observations greatly improved the analyses of vertical variations in temperature, relative humidity, and winds at multiple locations in the northern portion of the SLV, with reductions in both bias and the root-mean-square error of roughly 40% for each variable relative to the benchmark run. Despite these noted improvements, some biases remain that were tied to measurement error and/or the impact of the boundary layer parameterization on vertically spreading the observations, both of which require further exploration. The results presented here highlight how observations obtained with a fleet of profiling UAS improve limited-area, high-resolution analyses and short-term forecasts in complex terrain.

54 ENVIRONMENTAL SCIENCES↗

Assimilation of a Coordinated Fleet of Uncrewed Aircraft System Observations in Complex Terrain: Observing System Experiments

Uncrewed aircraft system (UAS) observations from the Lower Atmospheric Profiling Studies at Elevation–A Remotely-Piloted Aircraft Team Experiment (LAPSE-RATE) field campaign were assimilated into a high-resolution configuration of the Weather Research and Forecasting (WRF) Model. The impact of assimilating targeted UAS observations in addition to surface observations was compared to that obtained when assimilating surface observations alone using observing system experiments (OSEs) for a terrain-driven flow case and a convection initiation (CI) case observed within Colorado’s San Luis Valley (SLV). The assimilation of UAS observations in addition to surface observations results in a clear increase in skill for both flow regimes over that obtained when assimilating surface observations alone. For the terrain-driven flow case, the UAS observations improved the representation of thermal stratification across the northern SLV, which produced stronger upvalley flow over the eastern half of the SLV that better matched the observations. For the CI case, the UAS observations improved the representation of the pre-convective environment by reducing dry biases across the SLV and over the surrounding terrain. This led to earlier CI and more organized convection over the foothills that spilled outflows into the SLV, ultimately helping to increase low-level convergence and CI there. In addition, the importance of UAS capturing an outflow that originated over the Sangre de Cristo Mountains and triggered CI is discussed. These outflows and subsequent CI were not well captured in the simulation that assimilated surface observations alone. We report that observations obtained with a fleet of UAS are shown to notably improve high-resolution analyses and short-term predictions of two very different mesogamma-scale weather events.

54 ENVIRONMENTAL SCIENCES↗

Near-Cloud Atmospheric Ingredients for Deep Convection Initiation

A lack of routine environmental observations located near deepening cumulus congestus clouds limits verification of important theorized and simulated updraft–environment interaction processes occurring during deep convection initiation (CI). We analyze radiosonde profiles collected during several hundred CI events near a mountain range in central Argentina during the CACTI field campaign. Statistical analyses illustrate environmental conditions supporting radar-observed CI outcomes that span a spectrum of convective cell depths, widths, and durations, as well as events lacking precipitating convection. Tested environmental factors include a large variety of sounding-derived measurements of CAPE, CIN, moisture, terrain-relative winds, vertical shear, and lifted parcel properties, with supplemental model reanalysis of background larger-scale vertical motion. CAPE and CIN metrics do not consistently differentiate CI success from failure. Only a few environmental factors contain consistent monotonic relationships among the spectrum of cloud depths achieved during CI: (i) the depth and strength of background ascent, and (ii) the component of low-level flow oriented parallel to the ridgeline. These metrics suggest that the ability of the surrounding flow to lift parcels to their LFC and terrain-modified flow are consistently relevant processes for CI. Low- to midlevel relative humidity strongly discriminated between CI and non-CI events, likely reflecting entrainment-driven dilution processes. However, we could not confidently conclude that relative humidity similarly discriminated robust from marginal CI events. Circumstantial evidence was found linking cell width, an important cloud property governing the probability of CI, to LCL height, boundary layer depth, depth and magnitude of the CIN layer, and ambient wind shear.

Storm environments↗

The Potential Roles of Preexisting Airmass Boundaries on a Tornadic Supercell Observed by TORUS on 28 May 2019

On 28 May 2019, a tornadic supercell, observed as part of Targeted Observation by UAS and Radars of Supercells (TORUS) produced an EF-2 tornado near Tipton, Kansas. The supercell was observed to interact with multiple preexisting airmass boundaries. These boundaries and attendant air masses were examined using unoccupied aircraft system (UAS), mobile mesonets, radiosondes, and dual-Doppler analyses derived from TORUS mobile radars. The cool-side air mass of one of these boundaries was found to have higher equivalent potential temperature and backed winds relative to the warm-side air mass; features associated with mesoscale air masses with high theta-e (MAHTEs). It is hypothesized that these characteristics may have facilitated tornadogenesis. The two additional boundaries were produced by a nearby supercell and appeared to weaken the tornadic supercell. This work represents the first time that UAS have been used to examine the impact of preexisting airmass boundaries on a supercell, and it provides insights into the influence environmental heterogeneities can have on the evolution of a supercell.

54 ENVIRONMENTAL SCIENCES↗

The landscape of regulatory element evolution in a C4 perennial grass

Gene regulatory evolution is a well-known source of phenotypic diversity and adaptive evolution. Although cis-regulatory elements (CREs) play a vital role in gene expression evolution, the molecular evolution of CREs remains mostly unknown due to the difficulty in identifying and characterizing these functional elements. Comparative genomic analyses of noncoding DNA can be leveraged to identify conserved noncoding sequences (CNS), many of which may harbor functional CREs conserved by purifying selection. However, purely computational inference of CREs from putative CNS can be erroneous due to the complex genomic architecture in plants. One promising experimental approach to identify CREs is by profiling accessible chromatin regions (ACRs) that are often associated with the location of CREs. In this study, we use comparative genomics along with the profiling of ACRs to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses. We identified sets of CNS that varied in relationship to the degree of evolutionary divergence among the studied taxa, including identifying core-Panicoid-CNS. We augmented this analysis by profiling ACRs in Panicum hallii ecotypes using ATAC-seq. ACRs had low SNP density at the summit, harbored a high frequency of core-Panicoid-CNS, and were enriched with expression QTL. These data help to annotate the P. hallii genome for putative functional elements and suggest that a large proportion of these ACRs are evolving under purifying selection. Turnover in CNS and ACR between ecotypes of P. hallii identifies a small set of putatively divergent CREs that may underlie differences in gene regulation between genotypes from inland and coastal habitats. In summary, we profiled ACRs in Panicoid grasses and integrated this data with our putative CNS prediction framework, which provides unique insight into patterns of polymorphism and divergence in CREs in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that anti- viral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

Background: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3). Results: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. Conclusions: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection.

59 BASIC BIOLOGICAL SCIENCES↗

Optimal load attachment of a deeply embedded ring anchor in clay

A Deeply Embedded Ring Anchor (DERA) system has been developed as a cost-effective solution for mooring arrays of floating offshore wind turbines (FOWTs) to the seabed. The DERA boasts several key features, including its versatility in various soil types, compact size, compatibility with diverse mooring systems, multi-line potential, and robust performance even under unintentional loading conditions. While prior preliminary studies have provided valuable insights into how the DERA can enhance cost-effectiveness by offering a high load capacity, these studies have predominantly focused on optimizing anchor performance under translational horizontal and vertical loading. However, to design the DERA optimally, we must also consider its ability to handle inclined loading conditions in addition to lateral and axial loadings. Due to its shorter length compared to a conventional caisson, the DERA has less resistance to moments, making it more sensitive to horizontal load capacity and the optimal load attachment depth concerning load angle. For this reason, our study introduces an analytical approach to evaluate the effects of inclined loading on anchor performance, utilizing the previously validated upper bound plastic limit analysis (PLA) method. In investigating the optimal load attachment of the DERA, this paper conducts a parametric study to analyze how factors such as load attachment depth, anchor aspect ratio, and load inclination affect the DERA’s load capacity. Our findings indicate that PLA can serve as a valuable analytical tool for assessing the ultimate load capacity of the DERA, particularly under inclined loading conditions.

42 ENGINEERING↗