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At least 757 records · Page 42

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗

Synchro-Waveform-Based Event Identification Using Multi-Task Time-Frequency Transform Networks

Influenced by the transient dynamics and reduced inertia characteristics of high-penetration renewable energy systems, power system events frequently exhibit distinct characteristics such as high-frequency components including wide-band oscillations and hyper-harmonics. This makes standard systems face challenges including significant latency and reduced accuracy due to limited data resolution. However, current methods face significant limitations, including insufficient pattern capture ability, low noise immunity, limited feature learning, and restricted localization capabilities, thereby hindering real-time performance. To tackle this issue, this paper proposed a novel synchro-waveform-based event identification approach via a Multi-task Time-frequency Transform Network (MTTNet). Initially, a Time-frequency Transform Block (TTB) is developed to extract both local and global information. The TTB leverages both Fourier and S-transforms to derive comprehensive time-frequency information from synchro-waveforms. Subsequently, a multi-task learning strategy is employed to identify the type and distinguish localization of events. Integrating the TTB and multi-task learning, the MTTNet is designed for synchro-waveform-based event identification, incorporating an adaptive weighting strategy and simplified computation for the S-transform. Two different datasets, comprising simulated and actual synchro-waveforms, are collected from the IEEE 123 bus system and a real-world high-penetration renewable energy system using a universal grid analyzer. Extensive experiments on various conditions are carried out. In conclusion, results demonstrated that the MTTNet consistently surpasses both basic and advanced baselines, with maximum improvements of 13.24% and 9.86%, respectively, while reducing the calculation burden by 15-19 times to achieve real-time event identification.

Event identification↗

Distributed Brillouin fiber laser sensor

Brillouin fiber sensors can provide distributed strain and temperature measurements over long distances in standard off-the-shelf fiber by measuring the Brillouin frequency shift as a function of position along a fiber. The primary drawback of these systems is their limited sensitivity, which results from the challenge in identifying the Brillouin frequency shift to within a small fraction of the Brillouin linewidth. In this work, we introduce a technique that overcomes this fundamental limitation by establishing a series of lasing modes that experience Brillouin amplification at discrete spatial locations in the test fiber. The linewidth narrowing and high intensity associated with the lasing transition enable precise measurements of this lasing frequency. As an initial demonstration, we present a sensor that simultaneously excites 40 lasing modes in a 400 m fiber, providing a measurement of the strain at 40 discrete locations with a spatial resolution of 4 m. Each sensor exhibits a minimum detectable strain as low as 4 nε/Hz 1/2 with a dynamic range of >5 mε and a bandwidth of ~10 kHz. As the first demonstration that Brillouin lasing can be used for distributed fiber sensing, this work establishes an approach that could enable ultra-high strain sensitivity using off-the-shelf fiber.

47 OTHER INSTRUMENTATION↗

Current Status of Developing Ultrafast Mega-electron-volt Electron Microsope

Recent studies of ultrafast electron microscopy (UEM) techniques show the use of short bunches of relativistic electrons is promising for the development of a new instrument for imaging various materials. Compared to conventional electron microscopes, the main advantage of UEMs with the electron energy of a few MeV is the possibility to study thick samples. We will discuss the progress of UEM design to date, the principal challenges on the way to a high resolution, and possible methods for their mitigation including the design of low-aberration magnetic optics, RF and mechanical subsystems with high stability, and precise collimation of electrons scattered in the samples.

43 PARTICLE ACCELERATORS↗

Photon Doppler Velocimetry to Spatially Resolve Plasma Density in a Power Flow Gap

The understanding of power flow plasmas is important as we look towards next generation pulsed power (NGPP) as current losses could prohibit the goals of that facility. Therefore, it is important to have accurate diagnostics of the plasma parameters on the current machines, which can be used to help inform and improve simulations. Having these plasma parameters will help validate models and simulations to provide confidence when they are expanded to conditions relevant to NGPP. One important plasma parameter that can be measured is the electron density, which can be measured by photonic Doppler velocimetry (PDV). A PDV system has several key advantages over other interferometers by measuring relatively low densities (> 1 × 10 15 cm -2 ) with both spatial and temporal resolution. Experiments were performed on the Mykonos pulsed power machine, which is a 1 MA sub scale machine in which recent platforms have been developed to explore current densities relevant to the inner magnetically insulated transmission line (MITL) on the Z machine. Experiments were performed on two different platforms, the thin foil platform and the Mykonos parallel plate platform (MP3). In addition, a combination of both single-point and multi-point measurements were used. The single-point measurements proved to be very promising, providing a clear increase in density at about 70 ns into the current rise on thin foil experiments up to about 5 × 10 17 cm -3 before the probe stopped providing signal. While we did also see returns from multi-point measurements on both platforms, the signals were not as easy to interpret due to strong background effects. However, they do show initial promise for this diagnostic to measure density at several points across a 1 mm gap. These measurements provide insights in how to improve the diagnostic so that it can provide useful information on power flow relevant experiments.

47 OTHER INSTRUMENTATION↗

Optimizing cloud motion estimation on the edge with phase correlation and optical flow

Abstract. Phase correlation (PC) is a well-known method for estimating cloud motion vectors (CMVs) from infrared and visible spectrum images. Commonly, phase shift is computed in the small blocks of the images using the fast Fourier transform. In this study, we investigate the performance and the stability of the blockwise PC method by changing the block size, the frame interval, and combinations of red, green, and blue (RGB) channels from the total sky imager (TSI) at the United States Atmospheric Radiation Measurement user facility's Southern Great Plains site. We find that shorter frame intervals, followed by larger block sizes, are responsible for stable estimates of the CMV, as suggested by the higher autocorrelations. The choice of RGB channels has a limited effect on the quality of CMVs, and the red and the grayscale images are marginally more reliable than the other combinations during rapidly evolving low-level clouds. The stability of CMVs was tested at different image resolutions with an implementation of the optimized algorithm on the Sage cyberinfrastructure test bed. We find that doubling the frame rate outperforms quadrupling the image resolution in achieving CMV stability. The correlations of CMVs with the wind data are significant in the range of 0.38–0.59 with a 95 % confidence interval, despite the uncertainties and limitations of both datasets. A comparison of the PC method with constructed data and the optical flow method suggests that the post-processing of the vector field has a significant effect on the quality of the CMV. The raindrop-contaminated images can be identified by the rotation of the TSI mirror in the motion field. The results of this study are critical to optimizing algorithms for edge-computing sensor systems.

54 ENVIRONMENTAL SCIENCES↗

Spin Squeezing as a Probe of Emergent Quantum Orders

Nuclear magnetic resonance (NMR) experiments can reveal local properties in materials, but are often limited by the low signal-to-noise ratio. Spin squeezed states have an improved resolution below the Heisenberg limit in one of the spin components, and have been extensively used to improve the sensitivity of atomic clocks, for example [1]. Interacting and entangled spin ensembles with non-linear coupling are a natural candidate for implementing squeezing. Furthermore, we propose measurement of the spin-squeezing parameter that itself can act as a local probe of emergent orders in quantum materials. In particular, we demonstrate how to investigate an anisotropic electric field gradient via its coupling to the nuclear quadrupole moment. While squeezed spin states are pure, the squeezing parameter can be estimated for both pure and mixed states. We evaluate the range of fields and temperatures for which a thermal-equilibrium state is sufficient to improve the resolution in an NMR experiment and probe relevant parameters of the quadrupole Hamiltonian, including its anisotropy.

36 MATERIALS SCIENCE↗

Infrared photon-number-resolving imager using a Skipper-CCD

Imaging in a broad light-intensity regime with a high signal-to-noise ratio is a key capability in fields as diverse as Quantum Metrology and Astronomy. Achieving high signal-to-noise ratios in quantum imaging leads to surpassing the classical limit in parameter estimation. In astronomical detection, the search for habitable exoplanets demands imaging in the infrared its atmospheres looking for biosignatures. These optical applications are hampered by detection noise, which critically limits their potential, and thus demands photon-number and spatial resolution detectors. Here we report an imaging device in the infrared wavelength range able to arbitrarily reduce the readout noise. We built a Measured Exposure Skipper-CCD Sensor Instrument equipped with a thick back-illuminated sensor, with photon-number-resolving capability in a wide dynamic range, spatial resolution, high quantum efficiency in the near-infrared and ultra-low dark counts. This device allows us to image objects in a broad range of intensities within the same frame and, by reducing the readout noise to less than 0.2e$^-$, to distinguish even those shapes with less than two photons per pixel, unveiling what was previously hidden in the noise. These results pave the way for building high-standard infrared imagers based on Skipper-CCDs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The putative center in NGC 1052

Context. Many active galaxies harbor powerful relativistic jets, however, the detailed mechanisms of their formation and acceleration remain poorly understood.Aims. To investigate the area of jet acceleration and collimation with the highest available angular resolution, we study the innermost region of the bipolar jet in the nearby low-ionization nuclear emission-line region (LINER) galaxy NGC 1052.Methods. We combined observations of NGC 1052 taken with VLBA, GMVA, and EHT over one week in the spring of 2017. Our study is focused on the size and continuum spectrum of the innermost region containing the central engine and the footpoints of both jets. We employed a synchrotron-self absorption model to fit the continuum radio spectrum and we combined the size measurements from close to the central engine out to ∼1 pc to study the jet collimation.Results. For the first time, NGC 1052 was detected with the EHT, providing a size of the central region in-between both jet bases of 43 μas perpendicular to the jet axes, corresponding to just around 250 RS (Schwarzschild radii). This size estimate supports previous studies of the jets expansion profile which suggest two breaks of the profile at around 3 × 103 RS and 1 × 104 RS distances to the core. Furthermore, we estimated the magnetic field to be 1.25 Gauss at a distance of 22 μas from the central engine by fitting a synchrotron-self absorption spectrum to the innermost emission feature, which shows a spectral turn-over at ∼130 GHz. Assuming a purely poloidal magnetic field, this implies an upper limit on the magnetic field strength at the event horizon of 2.6 × 104 Gauss, which is consistent with previous measurements.Conclusions. The complex, low-brightness, double-sided jet structure in NGC 1052 makes it a challenge to detect the source at millimeter (mm) wavelengths. However, our first EHT observations have demonstrated that detection is possible up to at least 230 GHz. This study offers a glimpse through the dense surrounding torus and into the innermost central region, where the jets are formed. This has enabled us to finally resolve this region and provide improved constraints on its expansion and magnetic field strength.Key words: methods: observational / techniques: high angular resolution / techniques: interferometric / galaxies: active / galaxies: jets / galaxies: Seyfert⋆⋆ NASA Hubble Fellowship Program, Einstein Fellow.

79 ASTRONOMY AND ASTROPHYSICS↗

Jet energy scale and resolution measured in proton–proton collisions at $\sqrt{s}=13$ TeV with the ATLAS detector

Jet energy scale and resolution measurements with their associated uncertainties are reported for jets using 36–81 fb -1 of proton–proton collision data with a centre-of-mass energy of √s=13 TeV collected by the ATLAS detector at the LHC. Jets are reconstructed using two different input types: topo-clusters formed from energy deposits in calorimeter cells, as well as an algorithmic combination of charged-particle tracks with those topo-clusters, referred to as the ATLAS particle-flow reconstruction method. The anti-k t jet algorithm with radius parameter R=0.4 is the primary jet definition used for both jet types. This result presents new jet energy scale and resolution measurements in the high pile-up conditions of late LHC Run 2 as well as a full calibration of particle-flow jets in ATLAS. Jets are initially calibrated using a sequence of simulation-based corrections. Next, several in situ techniques are employed to correct for differences between data and simulation and to measure the resolution of jets. The systematic uncertainties in the jet energy scale for central jets (|η|<1.2) vary from 1% for a wide range of high-p T jets (250 T <2000 GeV), to 5% at very low p T (20 GeV) and 3.5% at very high p T (>2.5 TeV). The relative jet energy resolution is measured and ranges from (24±1.5)% at 20 GeV to (6±0.5)% at 300 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Low-threshold sapphire detector for rare event searches

Low mass nuclear recoil dark matter and coherent-elastic-neutrino-nucleus-scattering (CE$v$NS) searches confront similar challenges in choosing ultra-low threshold and large-mass detectors. Here, we report experimental results from a 100 g single-crystal sapphire detector design with a diameter of 76 mm and thickness of 4 mm instrumented with transition edge sensors (TES). Sapphire is a crystal of aluminum oxide (Al 2 O) and has been found to be a good candidate for light mass dark matter search experiments due to its lower atomic mass compared to other detector materials such as germanium and silicon. This new phonon-assisted sapphire detector was characterized to yield a baseline recoil energy resolution of 28.4 ± 0.4 eV. The detector is designed to be sensitive to low-energy rare interactions with an intention to investigate the low-mass region of dark matter phase-space and search for CE$v$NS at the reactor site.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electrochemically modulated single-molecule localization microscopy for in vitro imaging cytoskeletal protein structures

A new concept of electrochemically modulated single-molecule localization super-resolution imaging is developed. Applications of single-molecule localization super-resolution microscopy have been limited due to insufficient availability of qualified fluorophores with favorable low duty cycles. The key for the new concept is that the “On” state of a redox-active fluorophore with unfavorable high duty cycle could be driven to “Off” state by electrochemical potential modulation and thus become available for single-molecule localization imaging. The new concept was carried out using redox-active cresyl violet with unfavorable high duty cycle as a model fluorophore by synchronizing electrochemical potential scanning with a single-molecule localization microscope. The two cytoskeletal protein structures, the microtubules from porcine brain and the actins from rabbit muscle, were selected as the model target structures for the conceptual imaging in vitro. The super-resolution images of microtubules and actins were obtained from precise single-molecule localizations determined by modulating the On/Off states of single fluorophore molecules on the cytoskeletal proteins via electrochemical potential scanning. Importantly, this method could allow more fluorophores even with unfavorable photophysical properties to become available for a wider and more extensive application of single-molecule localization microscopy.

electrochemical modulation↗

High-count-rate effects in event processing for the XRISM/Resolve X-ray microcalorimeter. II. Energy scale and resolution in orbit

The Resolve instrument on the X-ray Imaging and Spectroscopy Mission (XRISM) uses a 36 pixel microcalorimeter designed to deliver high-resolution, non-dispersive X-ray spectroscopy. Although it is optimized for extended sources with low count rates, Resolve observations of bright point sources are still able to provide unique insights into the physics of these objects, as long as high-count-rate effects are addressed in the analysis. These effects include the loss of exposure time for each pixel, changes in the energy scale, and changes in the energy resolution. To investigate these effects under realistic observational conditions, we observed the bright X-ray source, the Crab Nebula, with XRISM at several offset positions with respect to the Resolve field of view and with continuous illumination from 55 Fe sources on the filter wheel. For the spectral analysis, we excluded data where exposure-time loss was too significant to ensure reliable spectral statistics. The energy scale at 6 keV shows a slight negative shift in the high-count-rate regime. The energy resolution at 6 keV worsens as the count rate in electrically neighboring pixels increases, but can be restored by applying a nearest-neighbor coincidence cut (“cross-talk cut”). We examined how these effects influence the observation of bright point sources, using GX 13+1 as a test case, and identified an eV-scale energy offset at 6 keV between the inner (brighter) and outer (fainter) pixels. Users who seek to analyze velocity structures on the order of tens of km s–1 should account for such high-count-rate effects. These findings will aid in the interpretation of Resolve data from bright sources and provide valuable considerations for designing and planning for future microcalorimeter missions.

X-rays: general↗

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗

The KIPM Detector Consortium

Kinetic Inductance Phonon-Mediated (KIPM) Detectors, microcalorimeters that leverage kinetic inductance detectors (KIDs) to read out phonon signals from the device substrate, are an attractive architecture for low-threshold rare-event searches due to their large response to small changes in quasiparticle density and native multiplexability, enabling scalability. We have established a consortium comprising university and national lab groups dedicated to advancing the state-of-the-art in these detectors, with the ultimate goal of designing a detector with a kg-scale target mass and sub-eV threshold on energy deposited in the substrate, enabling searches for both light dark matter and low-energy neutrino interactions. This consortium brings together experts in KID design, phonon and quasiparticle dynamics, and noise modeling, along with specialized fabrication facilities, test platforms, and unique calibration capabilities. Recently, our consortium has demonstrated a sensor resolution (i.e., resolution in the quasiparticle channel) of 2.1 eV, the current record for such devices. The current focus of the consortium is modeling and improving the phonon collection efficiency and implementing low-Tc superconductors, both of which serve to improve the overall energy resolution and threshold of the detectors. In this talk, I will provide an overview of the consortium and its capabilities, highlight some recent results from its member groups, and discuss near term plans toward reaching the ultimate goal.

Temples, Dylan J. [Fermilab]↗

Infrared nanoimaging and nanospectroscopy of electrochemical energy storage materials and interfaces

Electrochemical interfaces are central to the function and performance of energy storage devices. Thus, the development of new methods to characterize these interfaces, in conjunction with electrochemical performance, is essential for bridging the existing knowledge gaps and accelerating the development of energy storage technologies. Of particular need is the ability to characterize surfaces or interfaces in a non-destructive way with adequate resolution to discern individual structural and chemical building blocks. To this end, sub-diffraction-limit low-energy infrared optical probes that exploit near-field interactions within atomic force microscopy platforms, such as pseudoheterodyne nanoimaging, photothermal nanoimaging and nanospectroscopy, and nanoscale Fourier transform infrared spectroscopy, are all powerful emerging techniques. These are capable of non-destructive surface probing and imaging at nanometer resolution. This review outlines recent efforts to characterize ex situ, in situ, and operando electrode materials and electrochemical interfaces in rechargeable batteries with these advanced infrared near-field probes.

25 ENERGY STORAGE↗

Vector elastic deconvolution migration with dual wavefield decomposition

Here, we report elastic-wave imaging using multicomponent data can provide more useful subsurface information than acoustic-wave imaging, but it is usually algorithmically challenging. We have developed a vector elastic deconvolution migration method for high-resolution imaging of subsurface structures in isotropic and anisotropic elastic media. Our new method uses a vector deconvolution imaging condition based on dual wavefield decomposition, including an explicit directional wavefield separation using the Hilbert transform and a P/S vector wavefield decomposition using the low-rank decomposition method. Using three elastic models, we numerically determine that our new method produces notably higher resolution and more amplitude-balanced elastic images compared with a crosscorrelation-based vector elastic reverse time migration method.

58 GEOSCIENCES↗