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At least 379 records · Page 21

Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab’-DNA ligand

Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide major histocompatibility complex (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab’-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rates of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells, which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from TCR ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.

Science & Technology - Other Topics↗

Applying simulation-based inference to spectral and spatial information from the Galactic Center gamma-ray excess

Abstract The two most favored explanations of theFermiGalactic Center gamma-ray excess (GCE) are millisecond pulsars and self annihilation of the smooth dark matter halo of the galaxy. In order to distinguish between these possibilities, we would like to optimally use all information in the available data, including photon direction and energy information.To date, analyses of the GCE have generally treated directional and energy information separately, or have ignored one or the other completely.Here, we develop a method for analyzing the GCE that relies on simulation-basedinference with neural posterior models to jointly analyze photon directional and spectral information while correctly accounting for the spatial and energy resolution of the telescope, here assumed to be theFermiLarge Area Telescope (LAT).Our results also have implications for analyses of the diffuse gamma-ray background, which we discuss.

Astronomy & Astrophysics↗

Analyzing line-of-sight selection biases in galaxy-scale strong lensing with external convergence and shear

The upcoming Vera Rubin Observatory Legacy Survey of Space and Time (LSST) will dramatically increase the number of strong gravitational lensing systems, requiring precise modeling of line-of-sight (LOS) effects to mitigate biases in lensing observations and cosmological inferences. We develop a method to construct joint distributions of external convergence (κ ext ) and shear (γ ext ) for strong lensing LOS by aggregating large-scale structure simulations with high-resolution halo renderings and non-linear correction. Our approach captures both smooth background matter and perturbations from halos, enabling accurate modeling of LOS effects. Here, we apply non-linear LOS corrections to κ ext and γ ext that address the non-additive lensing effects caused by objects along the LOS in strong lensing. We find that, with a minimum image separation of 1.0'', non-linear LOS correction due to the presence of a dominant deflector slightly increases the ratio of quadruple to double lenses; this non-linear LOS correction also introduces systematic biases of ∼ 0.1% for galaxy-AGN lens in the inferred Hubble constant (H 0 ) if not accounted for. We also observe a 0.66% bias for galaxy-galaxy lenses on H 0 , and even larger biases 1.02% for galaxy-AGN systems if LOS effects are not accounted for. These results highlight the importance of LOS for precision cosmology. The publicly available code and datasets provide tools for incorporating LOS effects in future analyses.

Hubble constant↗

Overview of the recent experimental research on the J-TEXT tokamak

The J-TEXT capability is enhanced compared to two years ago with several upgrades of its diagnostics and the increase of electron cyclotron resonance heating (ECRH) power to 1 MW. With the application of electron cyclotron wave (ECW), the ECW assisted plasma startup is achieved; the tearing mode is suppressed; the toroidal injection of 300 kW ECW drives around 24 kA current; fast electrons are generated with toroidal injected ECW and the runaway current conversion efficiency increases with ECRH power. The mode coupling between 2/1 and 3/1 modes are extensively studied. The coupled 2/1 and 3/1 modes usually lead to major disruption. Their coupling can be either suppressed or avoided by external resonant magnetic perturbation fields and hence avoids the major disruption. It is also found that the 2/1 threshold of external field is significantly reduced by a pre-excited 3/1 mode, which can be either a locked island or an external kink mode. The disruption control is studied by developing prediction methods capable of cross tokamak application and by new mitigation methods, such as the biased electrode or electromagnetic pellet injector. The high-density operation and related disruptions are studied from various aspects. Approaching the density limit, the collapse of the edge shear layer is observed and such collapse can be prevented by applying edge biasing, leading to an increased density limit. The density limit is also observed to increase, if the plasma is operated in the poloidal divertor configuration or the plasma purity is increased by increasing the pre-filled gas pressure or ECRH power during the start-up phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Accuracy versus precision in boosted top tagging with the ATLAS detector

The identification of top quark decays where the top quark has a large momentum transverse to the beam axis, known as top tagging , is a crucial component in many measurements of Standard Model processes and searches for beyond the Standard Model physics at the Large Hadron Collider. Machine learning techniques have improved the performance of top tagging algorithms, but the size of the systematic uncertainties for all proposed algorithms has not been systematically studied. This paper presents the performance of several machine learning based top tagging algorithms on a dataset constructed from simulated proton-proton collision events measured with the ATLAS detector at $\sqrt{s}$ = 13 TeV. The systematic uncertainties associated with these algorithms are estimated through an approximate procedure that is not meant to be used in a physics analysis, but is appropriate for the level of precision required for this study. The most performant algorithms are found to have the largest uncertainties, motivating the development of methods to reduce these uncertainties without compromising performance. To enable such efforts in the wider scientific community, the datasets used in this paper are made publicly available.

47 OTHER INSTRUMENTATION↗

Towards revealing intrinsic vortex-core states in Fe-based superconductors through statistical discovery

Abstract In type-II superconductors, electronic states within magnetic vortices hold crucial information about the paring mechanism and can reveal non-trivial topology. While scanning tunneling microscopy/spectroscopy (STM/S) is a powerful tool for imaging superconducting vortices, it is challenging to isolate the intrinsic electronic properties from extrinsic effects like subsurface defects and disorders. Here we combine STM/STS with basic machine learning to develop a method for screening out the vortices pinned by embedded disorder in iron-based superconductors. Through a principal component analysis of large STS data within vortices, we find that the vortex-core states in Ba(Fe 0.96 Ni 0.04 ) 2 As 2 start to split into two categories at certain magnetic field strengths, reflecting vortices with and without pinning by subsurface defects or disorders. Our machine-learning analysis provides an unbiased approach to reveal intrinsic vortex-core states in novel superconductors and shed light on ongoing puzzles in the possible emergence of a Majorana zero mode.

Guo, Yueming↗

An atomic cluster expansion potential for twisted multilayer graphene

Twisted multilayer graphene, characterized by its moiré patterns arising from inter-layer rotational misalignment, serves as a rich platform for exploring quantum phenomena. Machine learning interatomic potentials (MLIPs) are a promising approach to model such systems. Our work develops a method to generate training and test datasets for fitting MLIPs that capture all possible misalignments but remain small-scale to facilitate efficient data generation and parameter estimation. To achieve this, we generate configurations with periodic boundary conditions suitable for density functional theory calculations, and then introduce an internal twist and shift within those supercell structures. Using this technique, supplemented with an active learning workflow, we fit an Atomic Cluster Expansion potential for simulating twisted multilayer graphene and test it for accuracy and robustness on a range of simulation tasks.

2D materials↗

Few-mode and anisotropic quantum transport in InSb nanoribbons using an all-van der Waals material-based gate

High-quality electrostatic gating is a fundamental ingredient for successful semiconducting device physics, and a key element of realizing clean quantum transport. Inspired by the widespread improvement of transport quality when two-dimensional van der Waals (vdW) materials are gated exclusively by other vdW materials, we have developed a method for gating non-vdW materials with an all-vdW gate stack, consisting of a hexagonal boron nitride dielectric layer and a few-layer graphite gate electrode. We demonstrate this gating approach on MOVPE-grown InSb nanoribbons (NRs), a novel variant of the InSb nanowire, with a flattened cross-section. In our all-vdW gated NR devices we observe conductance features that are reproducible and have low- to near-zero gate hysteresis. We also report quantized conductance, which persists to lower magnetic fields and longer channel lengths than typical InSb nanowire devices reported to date. Additionally, we observe level splitting that is highly anisotropic in an applied magnetic field, which we attribute to the ribbon cross-section. The performance of our devices is consistent with the reduced disorder expected from the all-vdW gating scheme, and marks the first report of ballistic, few-modes quantum transport in a non-vdW material with an all-vdW gate. Our results establish all-vdW gating as a promising approach for high-quality gating of non-vdW materials for quantum transport, which is in principle applicable generically, beyond InSb systems. In addition, the work showcases the specific potential of all-vdW gate/InSb NR devices for enabling clean quantum devices that may be relevant for spintronics and topological superconductivity studies.

InSb↗

MINE: maximally informative next experiment—toward a new GWAS experimental design and methodology

Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.

Genetics & Heredity↗

The structure and interaction of polymers affects secondary cell wall banding patterns in Arabidopsis

Abstract Xylem tracheary elements (TEs) synthesize patterned secondary cell walls (SCWs) to reinforce against the negative pressure of water transport. VASCULAR-RELATED NAC-DOMAIN 7 (VND7) induces differentiation, accompanied by cellulose, xylan, and lignin deposition into banded domains. To investigate the effect of polymer biosynthesis mutations on SCW patterning, we developed a method to induce tracheary element transdifferentiation of isolated protoplasts, by transient transformation with VND7. Our data showed that proper xylan elongation is necessary for distinct cellulose bands, cellulose–xylan interactions are essential for coincident polymer patterns, and cellulose deposition is needed to override the intracellular organization that yields unique xylan patterns. These data indicate that a properly assembled cell wall network acts as a scaffold to direct polymer deposition into distinctly banded domains. We describe the transdifferentiation of protoplasts into TEs, providing an avenue to study patterned SCW biosynthesis in a tissue-free environment and in various mutant backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗

Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing bypasses embryo lethality

Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate crosslinking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect crosslinking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here we developed a method to generate viable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in callus tissue via CRISPR/Cas9-mediated gene editing. We combined this with a candidate gene approach to characterize the male gametophyte defective 2 (MPG2) gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We showed that in the callus mutant cell walls, RG-II does not crosslink normally because it lacks 3-deoxy-D-manno-octulosonic acid (Kdo) and thus cannot form the α-L-Rhap-(1→5)-α-D-kdop-(1→ sidechain. We suggest that MGP2 encodes an inverting RG-II CMP-β-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization. Our method also provides a viable strategy for further identifying proteins involved in the biosynthesis of RG-II.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement of the branching ratio of 16 N , 15 C , 12 B , and 13 B isotopes through the nuclear muon capture reaction in the Super-Kamiokande detector

The Super-Kamiokande detector has measured solar neutrinos for more than 25 years. The sensitivity for solar neutrino measurement is limited by the uncertainties of energy scale and background modeling. Decays of unstable isotopes with relatively long half-lives through nuclear muon capture, such as 16 N, 15 C, 12 B, and 13 B, are detected as background events for solar neutrino observations. Here, in this study, we developed a method to form a pair of stopping muon and decay candidate events and evaluated the production rates of such unstable isotopes. We then measured their branching ratios considering both their production rates and the estimated number of nuclear muon capture processes as Br⁡( 16 N) = (9.0 ± 0.1)%, Br⁡( 15 C) = (0.6 ± 0.1)%, Br⁡( 12 B) = (0.98 ± 0.18)%, Br⁡( 13 B) = (0.14 ± 0.12)%, respectively. The result for 16 N has world-leading precision at present and the results for 15 C, 12 B, and 13 B are the first branching ratio measurements for those isotopes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Theory of quantum circuits with Abelian symmetries

Quantum circuits with gates (local unitaries) respecting a global symmetry have broad applications in quantum information science and related fields, such as condensed-matter theory and quantum thermodynamics. However, despite their widespread use, fundamental properties of such circuits are not well understood. Recently, it was found that generic unitaries respecting a global symmetry cannot be realized, even approximately, using gates that respect the same symmetry. This observation raises important open questions: What unitary transformations can be realized with k -local gates that respect a global symmetry? In other words, in the presence of a global symmetry, how does the locality of interactions constrain the possible time evolution of a composite system? In this work, we address these questions for the case of Abelian (commutative) symmetries and develop constructive methods for synthesizing circuits with such symmetries. Remarkably, as a corollary, we find that, while the locality of interactions still imposes additional constraints on realizable unitaries, certain restrictions observed in the case of non-Abelian symmetries do not apply to circuits with Abelian symmetries. For instance, in circuits with a general non-Abelian symmetry such as SU ( d ) , the unitary realized in a subspace with one irreducible representation (charge) of the symmetry dictates the realized unitaries in multiple other sectors with inequivalent representations of the symmetry. Furthermore, in certain sectors, rather than all unitaries respecting the symmetry, the realizable unitaries are the symplectic or orthogonal subgroups of this group. We prove that none of these restrictions appears in the case of Abelian symmetries. This result suggests that global non-Abelian symmetries may affect the thermalization of quantum systems in ways not possible under Abelian symmetries. Published by the American Physical Society 2024

Marvian, Iman↗

Theory for Equivariant Quantum Neural Networks

Quantum neural network architectures that have little to no inductive biases are known to face trainability and generalization issues. Inspired by a similar problem, recent breakthroughs in machine learning address this challenge by creating models encoding the symmetries of the learning task. This is materialized through the usage of equivariant neural networks the action of which commutes with that of the symmetry. In this work, we import these ideas to the quantum realm by presenting a comprehensive theoretical framework to design equivariant quantum neural networks (EQNNs) for essentially any relevant symmetry group. We develop multiple methods to construct equivariant layers for EQNNs and analyze their advantages and drawbacks. Our methods can find unitary or general equivariant quantum channels efficiently even when the symmetry group is exponentially large or continuous. As a special implementation, we show how standard quantum convolutional neural networks (QCNNs) can be generalized to group-equivariant QCNNs where both the convolution and pooling layers are equivariant to the symmetry group. We then numerically demonstrate the effectiveness of a S U ( 2 ) -equivariant QCNN over symmetry-agnostic QCNN on a classification task of phases of matter in the bond-alternating Heisenberg model. Our framework can be readily applied to virtually all areas of quantum machine learning. Lastly, we discuss about how symmetry-informed models such as EQNNs provide hopes to alleviate central challenges such as barren plateaus, poor local minima, and sample complexity. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Pentaquarks made of light quarks and their admixture to baryons

This paper is a continuation of our studies of multiquark hadrons. The antisymmetrization of their wave functions required by Fermi statistics is nontrivial, as it mixes orbital, color, spin, and flavor structures. In our previous papers we developed a method to find them based on the representations of the permutation group, and derived the explicit wave functions for baryons excited to the first and second shells (L = 1, 2), tetraquarks $qq$$\overline{q}$$\overline{q}$ and hexaquarks (6q). Now we apply it to light pentaquarks ($qqq$$\overline{q}$), in the S- and P-shells (L = 0, 1). Using Jacobi coordinates, one can use the hyperdistance approximation in 12-dimensional space. We further address the issue of “unquenching” of baryons, by considering their mixing with pentaquarks, via two channels, through the addition of σ-like or π-like $\overline{q}$$q$ pairs. This mixing is central for understanding of the observed flavor asymmetry of the antiquark sea, the amount of orbital motion issue as well as other nucleon properties.

Baryons↗

SNNPG: Using Spiking Neural Networks to Detect Attacks in the Power Grid

We explore the potential of Spiking Neural Networks (SNN) to enhance the security of power grid operations by detecting False Data Injection (FDI) attacks. These attacks manipulate PMU readings, leading to erroneous control decisions and grid disruptions. We develop a method to convert Phase Measurement Unit (PMU) data into spike trains, capturing both temporal and spatial dimensions. Using an SNN model, we conduct evaluations with simulated power grid data, showcasing accuracy in detecting FDI attacks. SNN models rapidly identify anomalies in real-time PMU data, safeguarding grid operations by alerting operators to irregular readings and preventing incorrect decisions.

artificial intelligence↗

Rolling Root Mean Square Based Multimodal Anomaly Detection for Real Time Monitoring of Smart Grid

Reliable real-time monitoring is valuable for maintaining the operational integrity of modern electrical smart grids. Deployment of heterogeneous sensing technologies in substations has enabled high-resolution, multichannel waveform monitoring, but also introduces challenges for anomaly detection due to noise, baseline drift, and modality-dependent signal characteristics. In this work, we present a computationally efficient unsupervised method for multimodal event detection based on Rolling Root Mean Square based Event Detection (RRMSED). The method is developed using in-house, field deployed sensors collecting data at a utility substation. The sensing system comprises voltage and current sensors, triaxial accelerometers, and magnetometers, collectively capturing electrical, vibrational, and magnetic waveform measurements at high temporal resolution. RRMSED operates by extracting rolling RMS energy features and their first-order temporal differences from consecutive waveform segments for each channel and then applying channel-specific statistical thresholds learned from historical data. A persistence-based exceedance logic is employed to robustly identify transient events while suppressing impulsive noise, and to provide precise temporal localization with high resolution. The framework is designed for continuous server-side operation and can be deployed in real time without requiring complex models. Experiments on simulated waveform data with known ground truth demonstrate low false positive (FP) and false negative (FN) rates. Application to real substation data shows RRMSED to identify events that are not captured by conventional monitoring indicators including fast transient detection algorithm currently deployed in the system. These results indicate that rolling RMS based features provide an effective and practical basis for real-time multimodal event detection in smart-grid substations.

Mukherjee, Subrata [ORNL] (ORCID:0000000309930338)↗

Thermal Stability of the Dot-in-Well Gain Medium for Photonic Crystal Surface Emitting Lasers

Self-assembled quantum dots (QDs) embedded in InGaAs quantum wells (QWs) are used as active regions for photonic-crystal surface-emitting lasers (PCSELs). An epitaxial regrowth method is developed to fabricate the dot-in-well (DWELL) PCSELs. Here, the epitaxial regrowth starts with the growth of a partial laser structure containing bottom cladding, waveguide, active region, and the photonic crystal (PC) layer. The PC layer is patterned to realize the cavity. Subsequently a top cladding layer is regrown to complete the laser structure. During the regrowth of the top cladding layer, the partial laser structure is subjected to high growth temperatures in excess of 600 °C resulting in an unintentional annealing of the active region. This annealing of the active region can alter the QDs by changing their size resulting in a blue shift in photoluminescence (PL) and narrowing PL emission. This effect results in the misaligning of the gain peak and the cavity resonance, resulting in sub-optimal lasing performance. DWELL active regions are known to have better thermal stability compared to both QDs and QWs and could be an ideal candidate for regrown PCSELs. We successfully demonstrate an optically-pumped epitaxially-regrown DWELL PCSEL with an emission wavelength of 1230 nm operating at room temperature. Furthermore, the DWELL active region shows excellent emission wavelength stability and intensity despite the high temperature regrowth process.

77 NANOSCIENCE AND NANOTECHNOLOGY↗