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At least 145 records · Page 8

The ladder and readout cables of intermediate silicon strip detector for sPHENIX

A new silicon-strip-type detector was developed for precise charged-particle tracking in the central rapidity region of heavy ion collisions. A new detector and collaboration at the Relativistic Heavy Ion Collider at Brookhaven National Laboratory is sPHENIX, which is a major upgrade of the PHENIX detector. The intermediate tracker (INTT) is part of the advanced tracking system of the sPHENIX detector complex together with a CMOS monolithic-active-pixel-sensor based silicon-pixel vertex detector, a time-projection chamber, and a micromegas-based detector. The INTT detector is barrel shaped and comprises 56 silicon ladders. Two different types of strip sensors of 78 micron pitch and 320 micron thick are mounted on each half of a silicon ladder. Each strip sensor is segmented into 8 × 2 and 5 × 2 blocks with lengths of 16 and 20 mm. Strips are read out with a silicon strip-readout (FPHX) chip. In order to transmit massive data from the FPHX to the down stream readout electronics card (ROC), a series of long and high speed readout cables were developed. This document focuses on the silicon ladder, the readout cables, and the ROC of the INTT. The radiation hardness is studied for some parts of the INTT devices in the last part of this document, since the INTT employed some materials from the technology frontier of the industry whose radiation hardness is not necessarily well known.

43 PARTICLE ACCELERATORS↗

Performance studies of the Mu2e cosmic ray veto detector

The cosmic ray veto (CRV) detector of the Mu2e experiment consists of four layers of plastic scintillation counters that surround the detector solenoid. These counters are embedded with wavelength-shifting fibers and are read out by silicon photomultipliers (SiPMs). The performance of a subset of the CRV counters was studied in a cosmic-ray test stand. Here, using data taken over a two-year period, we report the single-layer muon detection efficiency and the rate at which the light yield degrades due to the aging of the plastic scintillation counters.

Aging↗

Evaluation of 3D pixel silicon sensors for the CMS Phase-2 Inner Tracker

The high-luminosity upgrade of the CERN LHC requires the replacement of the CMS tracking detector to cope with the increased radiation fluence while maintaining its excellent performance. An extensive R&D program, aiming at using 3D pixel silicon sensors in the innermost barrel layer of the detector, has been carried out by CMS in collaboration with the FBK (Trento, Italy) and CNM (Barcelona, Spain) foundries. The sensors will feature a pixel cell size of 25 × 100 µm 2 , with a centrally located electrode connected to the readout chip. The sensors are read out by the RD53A and CROCv1 chips, developed in 65 nm CMOS technology by the RD53 Collaboration, a joint effort between the ATLAS and CMS groups. This paper reports the results achieved in beam test experiments before and after irradiation, up to a fluence of approximately 2 . 6 × 1 0 16 n eq /cm 2 . Measurements of assemblies irradiated to a fluence of 1 × 10 16 n˙eq/cm 2 show a hit detection efficiency higher than 96% at normal incidence, with fewer than 2% of channels masked, across a bias voltage range greater than 50 V . Even after irradiation to a higher fluence of 1.6 × 10 16 n˙eq/cm 2 , similar performance is maintained over a bias voltage range of 30 V , remaining well within CMS requirements.

3D pixel↗

Pixelated plastic scintillator array manufacturing using fast-, photo-curable resin

Pixelated plastic scintillator arrays can serve as high efficiency and high resolution neutron imaging detectors. Manufacturing these arrays is intensive in both time and labor. This article presents a fabrication method based on additive manufacturing for two-dimensional plastic organic scintillator arrays using a custom-built automated assembly machine and a custom photocurable resin that has significant non-aromatic acrylate oligomer content. The process involves two main stages: fully autonomous production of one-dimensional layered arrays, followed by semi-autonomous cutting and stacking to form two-dimensional pixel arrays. One-dimensional arrays were manufactured at a rate of around 4 layers per hour with minimal defects and tight dimensional tolerances, while two-dimensional arrays up to 7 x 7 pixels and 70 mm in length were completed in approximately 3.5 hours. Final arrays exhibited dimensional deviations of less than 0.5 mm. Two-dimensional arrays read out by a multi-anode photomultiplier tube demonstrated per-pixel position resolution and pulse-shape discrimination, enabling gamma–neutron interaction separation in mixed radiation environments.

36 MATERIALS SCIENCE↗

Results of the AGR-5/6/7 UCO TRISO fuel irradiation test in the Advanced Test Reactor

AGR-5/6/7 was the last in a series of irradiation experiments sponsored by the U.S. Department of Energy in support of the development and qualification of TRISO coated particle fuel for use in a high-temperature gas-cooled reactor. This experiment was conducted to verify the performance of the reference-design TRISO-coated low-enriched UCO fuel for modular high-temperature gas-cooled reactor normal operating conditions and to explore fuel performance at temperatures substantially beyond those typical of normal operation. A total of 194 UCO fuel compacts in five capsules were irradiated in the Advanced Test Reactor for 360.9 effective full-power days, achieving final burnup ranging from 5.66% to 15.26% fissions per initial heavy metal atom and fast neutron fluence ranging from 1.62 × 10 25 to 5.55 × 10 25 n/m 2 (E > 0.18 MeV). Calculated time-averaged fuel temperatures ranged from 467 °C to 1432 °C, with a peak fuel temperature of 1536 °C. During the first five irradiation cycles (∼180 effective full-power days), 85m Kr fission gas release-rate-to-birth-rate ratios were 10 −7 –10 −6 , indicating no particle failures. Near the end of the sixth cycle, a substantial number of in-pile particle failures occurred in Capsule 1. The fission gas release from this capsule impacted the readings from the other four capsules and led to unreliable fission gas release measurements for all capsules during the last four cycles. A preliminary post-irradiation examination of Capsule 1 fuel and internal components revealed the in-pile particle failures resulted from operational issues with the capsule, not subpar performance of the fuel particles.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The anomalous magnetic moment of the muon in the Standard Model: an update

We present the current Standard Model (SM) prediction for the muon anomalous magnetic moment, a μ , updating the first White Paper (WP20) [1]. The pure QED and electroweak contributions have been further consolidated, while hadronic contributions continue to be responsible for the bulk of the uncertainty of the SM prediction. Significant progress has been achieved in the hadronic light-by-light scattering contribution using both the data-driven dispersive approach as well as lattice-QCD calculations, leading to a reduction of the uncertainty by almost a factor of two. The most important development since WP20 is the change in the estimate of the leading-order hadronic-vacuum-polarization (LO HVP) contribution. A new measurement of the e + e - → π + π - cross section by CMD-3 has increased the tensions among data-driven dispersive evaluations of the LO HVP contribution to a level that makes it impossible to combine the results in a meaningful way. At the same time, the attainable precision of lattice-QCD calculations has increased substantially and allows for a consolidated lattice-QCD average of the LO HVP contribution with a precision of about 0.9%. Adopting the latter in this update has resulted in a major upward shift of the total SM prediction, which now reads $a^{SM}_{μ}$ = 116 592 033 (62) x $10^{-11}$ (530 ppb). When compared against the current experimental average based on the E821 experiment and runs 1–6 of E989 at Fermilab, one finds $a^{exp}_{μ} -a^{SM}_{μ}= 38 (63)$ x $10^{-11}$, which implies that there is no tension between the SM and experiment at the current level of precision. The final precision of E989 (127 ppb) is the target of future efforts by the Theory Initiative. The resolution of the tensions among data-driven dispersive evaluations of the LO HVP contribution will be a key element in this endeavor.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Comment on “Deep Proteogenomics of a Photosynthetic Cyanobacterium”

Proteomic researchers strive to achieve complete annotation of protein-coding DNA sequences to provide a foundational context for their relevant biological data. A recent deep proteogenomic study using a photosynthetic cyanobacterium Synechocystis sp. PCC 6803 by Spät et al. proposed 64 refined open reading frames (ORFs). By searching LC-MS/MS data from affinity chromatography-isolated protein complexes, our laboratory identified that six of these high-abundance ORFs possess Nterminal initiation start sites that differ than those proposed in the alternative models. Our findings are supported by highly confident MS2 data, phylogenetic analysis, chemical labeling, and established data from two independent research groups. Based on these highquality experimental identifications, we subsequently propose a standardized strategy and set of criteria for future deep proteogenomic efforts to ensure accurate and stringent proteogenomic annotation.

cyanobacteria↗

Tuning Exciton Emission via Ferroelectric Polarization at a Heterogeneous Interface between a Monolayer Transition Metal Dichalcogenide and a Perovskite Oxide Membrane

Here we demonstrate the integration of a thin BaTiO 3 (BTO) membrane with monolayer MoSe 2 in a dual gate device that enables in-situ manipulation of the BTO ferroelectric polarization with a voltage pulse. While two-dimensional (2D) transition metal dichalcogenides (TMDs) offer remarkable adaptability, their hybrid integration with other families of functional materials beyond the realm of 2D materials has been challenging. Released functional oxide membranes offer a solution for 2D/3D integration via stacking. 2D TMD excitons can serve as a local probe of the ferroelectric polarization in BTO at a heterogeneous interface. Using photoluminescence (PL) of MoSe 2 excitons to optically readout the doping level, we find that the relative population of charge carriers in MoSe 2 depends sensitively on the ferroelectric polarization. This finding points to a promising avenue for future-generations versatile sensing devices with high sensitivity, fast read-out, and diverse applicability for advanced signal processing.

42 ENGINEERING↗

In Situ Atmospheric Plume Thermometry via Carbon Monoxide Spectral Profile: Laboratory and Field Validation

For small molecules with large rotational constants, knowing the relative intensities of the ro-vibrational transitions can be used to determine the temperature within a gas plume. We demonstrate the use of carbon monoxide (CO) as an in situ spectroscopic probe of gas plume temperature by application of both laboratory and standoff Fourier transform infrared spectroscopy to monitor the CO spectral response at different temperatures. Here, the measured CO rotational contours were analyzed using a simple Boltzmann model to deduce the population distribution of the J-levels, from which the in-plume temperature is deduced. The method was vetted by comparing deduced temperatures in both static laboratory measurements of known temperatures, as well as field measurements using a simulated smokestack release. For the smokestack experiments, spectroscopically deduced temperatures were compared to readings from a series of thermocouples placed at strategically sampled distances along the plume trajectory. Both the spectroscopically-derived and thermocouple-measured temperatures revealed an expansion-induced (mixing) rapid cooling of the plume, with the infrared thermometry values displaying greater temperature values which are believed to better represent the actual plume temperatures.

Analysis of rotational structure↗

Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra

Identifying molecular structure based on spectroscopic readings is a key task in a variety of chemical and biological applications. Common spectroscopy techniques, such as Infrared (IR) Spectroscopy and Mass Spectrometry (MS), provide detailed information on the structure of molecular compounds but nonetheless require expert-level knowledge to decode. Machine learning has emerged as a potential solution for automating structure prediction from chemical spectra; however, current approaches generally focus on single sensor modalities, neglecting to leverage the complementary information contained within differing spectra. In this paper, we introduce Peak2Patch, a novel approach to fusion-enhanced prediction of functional groups from IR and mass spectra. First, we perform a detailed comparison of backbone networks for encoding both sparse mass spectra and dense IR spectra and demonstrate the superior performance of transformer neural networks over current state-of-the-art convolutional neural networks. Second, we evaluate three broad categories of fusion: early (raw feature), middle (deep feature), and late (decision) fusion, demonstrating the potential of a deep feature fusion-based approach. Lastly, we present Peak2Patch, our attention-based fusion scheme, which leverages cross-attention to mix features between encoded tokens of the two modalities. We validate our approach on a publicly available multimodal spectroscopic data set of 790k simulated molecules, demonstrating a large improvement in functional group prediction over both the previous state-of-the-art and our own strong single-modal baselines.

Jacobson, Philip [Sandia National Laboratories (SN↗

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Coherent Control over Nuclear Hyperpolarization Using an Optically Initializable Chromophore-Radical System

Chromophore radicals (CR) are emerging as important components for molecular quantum information science (QIS), especially in the context of quantum sensing. Here, we demonstrate that the optically hyperpolarized electrons in a 1,6,7,12-tetrakis(4-tert-butylphenoxy)-perylene-3,4,9,10-bis(dicarboximide) (tpPDI) covalently linked to a partially deuterated 1,3-bis(diphenylene)-d 16 -2-phenylallyl radical (BDPA-d 16 ) can be coherently manipulated via pulsed dynamic nuclear polarization (DNP) methods to transfer polarization to nuclear spins and back. Under light illumination at 85 K, electron hyperpolarization in BDPA is enhanced 2.1- to 2.4-fold over thermal polarization and lasts for more than 100 ms. By applying nuclear orientation via electron spin-locking (NOVEL) DNP, this optically amplified electron hyperpolarization was successfully transferred to a 1 H nuclear spin within the CR system and efficiently returned to the electron spin for readout via reverse-NOVEL. The NOVEL transfer efficiency of 65% amounts to a 688-fold nuclear spin hyperpolarization of the target nuclear spin, considering the 2.1-fold electron spin hyperpolarization. This reversible coherent manipulation of hyperpolarization transfer highlights the utility of CR systems to initialize and read out nuclear spin states in a disordered matrix at moderate cryogenic temperatures. Coupled with CRs’ environmental compatibility, tunability, and precise state initialization, these results highlight the promising role of nuclear spins in CRs for QIS applications, including quantum sensing and memory.

charge transfer↗

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive gene loss in the common bean pan-genome during range expansion and domestication

The common bean ( Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring error rates of mid-circuit measurements

High-fidelity mid-circuit measurements, which read out the state of specific qubits in a multiqubit processor without destroying them or disrupting their neighbors, are a critical component for useful quantum computing. They enable fault-tolerant quantum error correction, dynamic circuits, and other paths to solving classically intractable problems. But there are few methods to assess their performance comprehensively. In this work, we address this gap by introducing the first randomized benchmarking protocol that measures the rate at which mid-circuit measurements induce errors in many-qubit circuits. Using this protocol, we detect and eliminate previously undetected measurement-induced crosstalk in a 20-qubit trapped-ion quantum computer. Then, we use the same protocol to measure the rate of measurement-induced crosstalk error on a 27-qubit IBM Q processor, and quantify how much of that error is eliminated by dynamical decoupling.

Hothem, Daniel [Sandia National Laboratories (SNL-↗

Probing boron vacancy defects in hBN via single spin relaxometry

Spin defects in solids offer promising platforms for quantum sensing and memory due to their long coherence times and optical addressability. Here, we integrate a single nitrogen-vacancy (NV) center in diamond with scanning probe microscopy to detect, read out, and spatially map spin-based quantum sensors at the nanoscale. Using the boron vacancy ($V$$^{–}_{B}$) center in hexagonal boron nitride—an emerging two-dimensional spin system—as a model, we detect its electron spin resonance indirectly via changes in the spin relaxation time (T 1 ) of a nearby NV center, eliminating the need for optical excitation or fluorescence detection of the $V$$^{–}_{B}$. Cross-relaxation between NV and $V$$^{–}_{B}$ ensembles significantly reduces NV T1, enabling quantitative nanoscale mapping of defect densities beyond the optical diffraction limit and clear resolution of hyperfine splitting in isotopically enriched h 10 B 15 N. Our method demonstrates interactions between spin sensors in 3D and 2D materials, establishing NV centers as versatile probes for characterizing otherwise inaccessible spin defects.

Quantum metrology↗

Signatures of nonthermal carriers in nonlinear photoluminescence

Ultrafast light emission from plasmonic nanostructures provides a sensitive probe of the energetic electrons generated by intense optical excitation. The way this emission scales with excitation intensity has long been read through the lens of heated electron populations at an elevated temperature, yet this picture cannot reconcile the variety of behaviors seen across different materials and experiments. We argue that transient nonthermal electrons play a far larger role than has been appreciated. We present a unified description that reproduces emission behavior across diverse systems and outline experiments needed to resolve their signatures.

nanoscale materials↗