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At least 253 records · Page 14

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

Viral delivery of recombinases activates heritable genetic switches in plants

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ~0.6kb to ~1.5kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. Here, an excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

59 BASIC BIOLOGICAL SCIENCES↗

Cooperative effects in thin dielectric layers: Long-range Dicke superradiance

The realization and control of collective quantum effects so far have predominantly focused on cold atomic ensembles. Quantum photonic platforms, with their engineered Green's functions and integration capability of advanced solid-state quantum emitters, provide opportunities to explore regimes of light-matter interaction beyond the scope of atomic systems. In this work, we demonstrate that embedding quantum emitters within a thin dielectric layer fundamentally alters their collective radiative behavior. The optical modes in the dielectric layer mediate long-range dipole-dipole interactions between emitters, enabling both total and directional superradiance between emitters separated by several wavelengths. Crucially, this mechanism supports Dicke superradiance even in parameter regimes where standard settings fail to support an interaction, unveiling a dimensionality-driven enhancement of cooperative effects. By bridging many-body quantum optics and photonic engineering, our work reveals a distinct interplay between surrounding dimensionality and collective quantum dynamics. Experimental realization of these predictions, readily achievable in solid-state quantum optics platforms, paves the way for scalable, directional quantum light sources and frontiers in many-body quantum optics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Baryon-baryon, meson-meson, and meson-baryon interactions in nonrelativistic QCD

Van der Waals potentials describing interactions between color-singlet mesons and/or baryons vanish at leading order in potential nonrelativistic quantum chromodynamics (pNRQCD). This result and constraints from Gauss’s law are used to prove that weakly coupled pNRQCD van der Waals potentials in generic non-Abelian gauge theories with only heavy quarks are too weak to form bound states whose color state is a product of color singlets. Quantum Monte Carlo calculations of four, five, and six quarks with equal masses provide numerical evidence that exotic color configurations are higher energy than products of color-singlet hadrons, suggesting that equal-mass fully heavy tetraquark, pentaquark, and hexaquark bound states do not exist at next-to-leading order in pNRQCD and at all orders in QCD-like theories in which all quark masses are asymptotically large. Mechanisms for generating hadron-hadron bound states are identified, which necessarily involve large quark-mass hierarchies, relativistic effects arising from the presence of sufficiently light quarks, or nonperturbative effects outside the scope of weakly coupled pNRQCD.

Effective field theory↗

New Constraints on Cosmic Ray-Boosted Dark Matter from the LUX-ZEPLIN Experiment

While dual-phase xenon time projection chambers have driven the sensitivity toward weakly interacting massive particles at the GeV/c 2 to TeV/c 2 mass scale, the scope for sub-GeV/c 2 dark matter particles is hindered by a limited nuclear recoil energy detection threshold. One approach to probe for lighter candidates is to consider cases where they have been boosted by collisions with cosmic rays in the Milky Way, such that the additional kinetic energy lifts their induced signatures above the nominal threshold. In this Letter, we report first results of a search for cosmic ray-boosted dark matter (CRDM) with a combined 4.2 metric ton/yr exposure from the LUX-ZEPLIN experiment. We observe no excess above the expected backgrounds and establish world-leading constraints on the spin-independent CRDM-nucleon cross section as small as 3.9×10 −33 cm 2 at 90% confidence level for sub-GeV/c 2 masses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Performance analysis of superconductor-constriction-superconductor transmon qubits

Here, this work presents a computational analysis of a superconducting transmon qubit design, in which the superconductor-insulator-superconductor (SIS) Josephson junction is replaced by a coplanar, superconductor-constriction-superconductor (ScS) nanobridge junction. Within the scope of Ginzburg-Landau theory, we find that the nanobridge ScS transmon has an improved charge dispersion compared to the SIS transmon, with a tradeoff of smaller anharmonicity. These calculations provide a framework for estimating the superconductor material properties and junction dimensions compatible with gigahertz frequency ScS transmon operation.

36 MATERIALS SCIENCE↗

Stability of fractional Chern insulators with a non-Landau level continuum limit

The stability of fractional Chern insulators is widely believed to be predicted by the resemblance of their single-particle spectra to Landau levels. Here we investigate the scope of this geometric stability hypothesis by analyzing the stability of a set of fractional Chern insulators that explicitly do not have a Landau level continuum limit. By computing the many-body spectra of Laughlin states in a generalized Hofstadter model, we analyze the relationship between single-particle metrics, such as trace inequality saturation, and many-body metrics, such as the magnitude of the many-body and entanglement gaps. We show numerically that the geometric stability hypothesis holds for Chern bands that are not continuously connected to Landau levels, as well as conventional Chern bands, albeit often requiring larger system sizes to converge for these configurations.

2-dimensional systems↗

Efficient quantum circuits based on the quantum natural gradient

Efficient preparation of arbitrary entangled quantum states is crucial for quantum computation. This is particularly important for noisy intermediate-scale quantum simulators relying on variational hybrid quantum-classical algorithms. To that end, we propose symmetry-conserving modified quantum approximate optimization algorithm (SCom-QAOA) circuits. The depths of these circuits depend not only on the desired fidelity to the target state but also on the amount of entanglement the state contains. The parameters of the SCom-QAOA circuits are optimized using the quantum natural gradient method based on the Fubini-Study metric. The SCom-QAOA circuit transforms an unentangled state into a ground state of a gapped one-dimensional Hamiltonian with a circuit depth that depends not on the system size but rather on the finite correlation length. In contrast, the circuit depth grows proportionally to the system size for preparing low-lying states of critical one-dimensional systems. Even in the latter case, SCom-QAOA circuits with depth less than the system size were sufficient to generate states with fidelity in excess of 99%, which is relevant for near-term applications. The proposed scheme enlarges the set of the initial states accessible for variational quantum algorithms and widens the scope of investigation of nonequilibrium phenomena in quantum simulators. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sketched Nanoscale KTaO 3 -Based Superconducting Quantum Interference Device

The discovery of two-dimensional superconductivity in LaAlO 3 /KTaO 3 (111) and (110) interfaces has raised significant interest in this system. In this paper, we report the first successful fabrication of a direct current superconducting quantum interference device (dc-SQUID) in the KTO system. The key device elements, superconducting weak links, are created by conductive atomic force microscope lithography, which can reversibly control the conductivity at the LAO/KTO (110) interface with nanoscale resolution. The periodic modulation of the SQUID critical current 𝐼 c ⁡(𝐵) with magnetic field corresponds well with our theoretical modeling, which reveals a large kinetic inductance of the superconducting two-dimensional electron gas in KTO. The kinetic inductance of the SQUID is tunable by electrical gating from the back, due to the large dielectric constant of KTO. The demonstration of weak links and SQUIDs in KTO broadens the scope for exploring the underlying physics of KTO superconductivity, including the role of spin-orbit coupling, pairing symmetry, and inhomogeneity. It also promotes KTO as a versatile platform for a growing family of quantum devices, which could be applicable in the realm of quantum computing and information.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Defect Complexes in CrSBr Revealed Through Electron Microscopy and Deep Learning

Atomic defects underpin the properties of van der Waals materials, and their understanding is essential for advancing quantum and energy technologies. Scanning transmission electron microscopy is a powerful tool for defect identification in atomically thin materials, and extending it to multilayer and beam-sensitive materials would accelerate their exploration. Here, we establish a comprehensive defect library in a bilayer of the magnetic quasi-1D semiconductor CrSBr by combining atomic-resolution imaging, deep learning, and calculations. We apply a custom-developed machine learning work flow to detect, classify, and average point vacancy defects. This classification enables us to uncover several distinct Cr interstitial defect complexes, combined Cr and Br vacancy defect complexes, and lines of vacancy defects that extend over many unit cells. We show that their occurrence is in agreement with our computed structures and binding energy densities, reflecting the intriguing layer interlocked crystal structure of CrSBr. Our ab initio calculations show that the interstitial defect complexes give rise to highly localized electronic states. These states are of particular interest due to the reduced electronic dimensionality and magnetic properties of CrSBr and are, furthermore, predicted to be optically active. Our results broaden the scope of defect studies in challenging materials and reveal new defect types in bilayer CrSBr that can be extrapolated to the bulk and to over 20 materials belonging to the same FeOCl structural family.

deep learning↗

Constant-Depth Preparation of Matrix Product States with Adaptive Quantum Circuits

Adaptive quantum circuits, which combine local unitary gates, midcircuit measurements, and feedforward operations, have recently emerged as a promising avenue for efficient state preparation, particularly on near-term quantum devices limited to shallow-depth circuits. Matrix product states (MPS) comprise a significant class of many-body entangled states, efficiently describing the ground states of one-dimensional gapped local Hamiltonians and finding applications in a number of recent quantum algorithms. Recently, it has been shown that the Affleck-Kennedy-Lieb-Tasaki state—a paradigmatic example of an MPS—can be exactly prepared with an adaptive quantum circuit of constant depth, an impossible feat with local unitary gates alone due to its nonzero correlation length [Smith , PRX Quantum 4, 020315 (2023)]. In this work, we broaden the scope of this approach and demonstrate that a diverse class of MPS can be exactly prepared using constant-depth adaptive quantum circuits, outperforming theoretically optimal preparation with unitary circuits. We show that this class includes short- and long-ranged entangled MPS, symmetry-protected topological (SPT) and symmetry-broken states, MPS with finite Abelian, non-Abelian, and continuous symmetries, resource states for MBQC, and families of states with tunable correlation length. Moreover, we illustrate the utility of our framework for designing constant-depth sampling protocols, such as for random MPS or for generating MPS in a particular SPT phase. We present sufficient conditions for particular MPS to be preparable in constant time, with global on-site symmetry playing a pivotal role. Altogether, this work demonstrates the immense promise of adaptive quantum circuits for efficiently preparing many-body entangled states and provides explicit algorithms that outperform known protocols to prepare an essential class of states. Published by the American Physical Society 2024

Smith, Kevin C. (ORCID:0000000223971518)↗

Floquet-engineered fast SNAP gates in weakly coupled circuit-QED systems

Superconducting cavities with high quality factors, coupled to a fixed-frequency transmon, provide a state-of-the-art platform for quantum information storage and manipulation. The commonly used selective number-dependent arbitrary phase ( SNAP ) gate faces significant challenges in ultrahigh-coherence cavities, where the weak dispersive shifts necessary for preserving high coherence typically result in prolonged gate times. Here, in this work, we propose a protocol to achieve high-fidelity SNAP gates that are orders of magnitude faster than the standard implementation, surpassing the speed limit set by the bare dispersive shift. We achieve this enhancement by dynamically amplifying the dispersive coupling via sideband interactions, followed by quantum optimal control on the Floquet-engineered system. We also present a unified perturbation theory that explains both the gate acceleration and the associated benign drive-induced decoherence, corroborated by Floquet-Markov simulations. These results pave the way for the experimental realization of high-fidelity, selective control of weakly coupled, high-coherence cavities, and expanding the scope of optimal control techniques to a broader class of Floquet quantum systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Search for the Rare Decay 𝐷 0 → 𝜇 + ⁢𝜇 − in Proton-Proton Collisions at $\sqrt{s}$ = 13.6 TeV

A search for the rare decay 𝐷 0 → 𝜇 + ⁢𝜇 − is reported using proton-proton collision events at $\sqrt{s}$ =13.6 TeV collected by the CMS detector in 2022–2023, corresponding to an integrated luminosity of 64.5 fb −1 . This is the first analysis to use a newly developed inclusive dimuon trigger, expanding the scope of the CMS flavor physics program. The search uses 𝐷 0 mesons obtained from 𝐷* + → 𝐷 0 ⁢𝜋 + decays. No significant excess is observed. A limit on the branching fraction of ℬ⁡(𝐷 0 → 𝜇 + ⁢𝜇 − ) < 2.4 × 10 −9 at 95% confidence level is set. This is the most stringent upper limit set on any flavor changing neutral current decay in the charm sector.

Charmed mesons↗

NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography

Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6–5.0× faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.

Xiao, Zhongcan [ORNL] (ORCID:0000000220761961)↗

A Survey on the Design, Detection, and Prevention of Pre-Silicon Hardware Trojans

The complexity of the semiconductor design lifecycle and globalized manufacturing process creates concern over the threat of deliberate malicious alterations, or hardware Trojans, being inserted into microelectronic designs. This has resulted in a significant corpus of hardware Trojan research including Trojan design and benchmarking efforts and development of corresponding metrics and detection and prevention techniques, over the last two decades. In this survey, we first highlight efforts in Trojan design and benchmarking, followed by a cataloging of seminal and recent works in Trojan detection and prevention and their accompanied metrics. Given the volume of literature in this field, this survey considers only pre-silicon techniques. We make this distinction between pre- and post-silicon to properly scope and provide appropriate context into the capabilities of existing hardware Trojan literature. Each major section (design, prevention, and detection) is accompanied by insights, and common pitfalls, which we highlight can be addressed by future research.

42 ENGINEERING↗

Feature Engineering and Ensemble Methods for Imbalanced ICS Intrusion Detection: Pipeline Audit and Constrained Evaluation

Industries are becoming increasingly connected and are more vulnerable to cyberattacks due to the widened attack surface. Industrial Control Systems (ICS) are among the most critical sectors that malicious actors can target, as such attacks can cause significant operational disruption and physical damage. It is imperative to detect such attacks as early as possible. This paper evaluates constraint-conditioned optimistic performance estimates for traditional ML models in ICS intrusion detection (i.e., estimates obtained under contiguous, non-shuffled temporal evaluation without test-set alteration, but with pre-split feature engineering that may introduce temporal leakage, due to dataset constraints). Our findings are threefold. First, we quantify how iterative feature engineering affects tree-based ensemble performance and examine how pipeline decisions (split strategy, sampling scope, and cleaning policy) can inflate or reduce reported IDS results under constraint-bound evaluation. Second, we compare intrinsic class-imbalance handling across ensemble models. Third, under our current pipeline constraints (including pre-split feature engineering), CatBoost achieves the best performance on Water Storage Tank (accuracy: 0.9831, class-1 F1: 0.9682), while Light- GBM achieves the best performance on Gas Pipeline (accuracy: 0.9618, class-1 F1: 0.9086).

97 MATHEMATICS AND COMPUTING↗

Integration of Electrolysis Systems Into Isolated Microgrid Systems at Extreme Cold Climates

Isolated microgrid systems are generally used to power communities in remote locations where transmission line installations are cost prohibitive. These systems are usually powered by diesel generators, delivering expensive energy with high carbon emissions. However, most of these communities have special geographic access to renewable energy. These special conditions make it interesting to investigate the deployment of renewable energies and storage solutions. Within this scope, this paper analyses the integration of water electrolysis systems into off-grid communities, simulating the electrolyzer as well as the whole electrical grid in real time.

digital real-time simulation↗

Exploring Capability of Multimodal Foundation Model for Image-based Fault Detection of Photovoltaic Modules

Multimodal Foundation Model (MFM), like ChatGPT and Gemini, have emerged as powerful tools for their exceptional natural language processing capabilities and their emerging potential in image analysis. This paper investigates the application of MFMs for photovoltaic (PV) fault detection through image analysis, focusing on ChatGPT 4.0 and Gemini 1.5 Pro. Three types of PV images and the corresponding common PV faults are detected: bird droppings using visible images, cell cracks via electroluminescence (EL) images, and hotspots using infrared (IR) images. Among the two models, Gemini 1.5 Pro demonstrated superior performance, achieving near-perfect results with an average F1 score of 0.97, consistently outperforming ChatGPT 4.0 in accuracy and reliability. Unlike traditional machine learning (ML) models, MFMs can operate in a zero shot manner that does not require additional training by the user, and the input images are not limited by size, angle, scope, or PV technology. The strong adaptability and user-friendliness make MFM a promising tool for analyzing PV images and advancing health monitoring for PV modules.

Li, Baojie↗