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At least 1,153 records · Page 64

Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ~120 kDa, called Legobody, does not perturb the nanobody–target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of the marker distribution in gyrokinetic $δf$ particle-in-cell simulations

The evolution of the particle weight in a δf particle-in-cell simulation depends on the marker distribution that can evolve in a turbulent field due to turbulent diffusion. When Monte Carlo methods are used to implement the test particle collision operator, or when the particle motion is not strictly Hamiltonian in a collisionless simulation, the marker distribution will evolve along the particle trajectory and, in general, cannot be known exactly. A two-dimensional numerical marker distribution is proposed as an approximation. It is shown to be advantageous over other common methods for evaluating the marker distribution in long-time turbulence simulations. A generalized two-weight δf-method is proposed to mitigate the marker evolution problem.

, Monte Carlo methods↗

High energy particle astronomy.

Discussion of techniques currently used in high energy particle astronomy for measuring charged and neutral cosmic rays and their isotope and momentum distribution. Derived from methods developed for accelerator experiments in particle physics, these techniques help perform important particle astronomy experiments pertaining to nuclear cosmic ray and gamma ray research, electron and position probes, and antimatter searches.

Buffington, A.↗

The ATLAS experiment at the CERN Large Hadron Collider: a description of the detector configuration for Run 3

The ATLAS detector is installed in its experimental cavern at Point 1 of the CERN Large Hadron Collider. During Run 2 of the LHC, a luminosity of ℒ = 2 × 10 34 cm -2 s -1 was routinely achieved at the start of fills, twice the design luminosity. For Run 3, accelerator improvements, notably luminosity levelling, allow sustained running at an instantaneous luminosity of ℒ = 2 × 10 34 cm -2 s -1 , with an average of up to 60 interactions per bunch crossing. The ATLAS detector has been upgraded to recover Run 1 single-lepton trigger thresholds while operating comfortably under Run 3 sustained pileup conditions. A fourth pixel layer 3.3 cm from the beam axis was added before Run 2 to improve vertex reconstruction and b-tagging performance. New Liquid Argon Calorimeter digital trigger electronics, with corresponding upgrades to the Trigger and Data Acquisition system, take advantage of a factor of 10 finer granularity to improve triggering on electrons, photons, taus, and hadronic signatures through increased pileup rejection. The inner muon endcap wheels were replaced by New Small Wheels with Micromegas and small-strip Thin Gap Chamber detectors, providing both precision tracking and Level-1 Muon trigger functionality. Trigger coverage of the inner barrel muon layer near one endcap region was augmented with modules integrating new thin-gap resistive plate chambers and smaller-diameter drift-tube chambers. Tile Calorimeter scintillation counters were added to improve electron energy resolution and background rejection. Upgrades to Minimum Bias Trigger Scintillators and Forward Detectors improve luminosity monitoring and enable total proton-proton cross section, diffractive physics, and heavy ion measurements. These upgrades are all compatible with operation in the much harsher environment anticipated after the High-Luminosity upgrade of the LHC and are the first steps towards preparing ATLAS for the High-Luminosity upgrade of the LHC. This paper describes the Run 3 configuration of the ATLAS detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Deep learning-based spatiotemporal multi-event reconstruction for delay line detectors

Abstract Accurate observation of two or more particles within a very narrow time window has always been a challenge in modern physics. It creates the possibility of correlation experiments, such as the ground-breaking Hanbury Brown–Twiss experiment, leading to new physical insights. For low-energy electrons, one possibility is to use a Microchannel plate with subsequent delay lines for the readout of the incident particle hits, a setup called a Delay Line Detector. The spatial and temporal coordinates of more than one particle can be fully reconstructed outside a region called the dead radius. For interesting events, where two electrons are close in space and time, the determination of the individual positions of the electrons requires elaborate peak finding algorithms. While classical methods work well with single particle hits, they fail to identify and reconstruct events caused by multiple nearby particles. To address this challenge, we present a new spatiotemporal machine learning model to identify and reconstruct the position and time of such multi-hit particle signals. This model achieves a much better resolution for nearby particle hits compared to the classical approach, removing some of the artifacts and reducing the dead radius a factor of eight. We show that machine learning models can be effective in improving the spatiotemporal performance of delay line detectors.

Computer Science↗

Ion composition and temperature in the topside ionosphere.

Particle and energy continuity equations derived and solved by computer method ion composition and plasma temperature measured by Explorer XXII PARTICLE and energy continuity equations derived and solved by computer method for ion composition and plasma temperature measured by Explorer XXII

IONOSPHERIC ION DENSITY↗

Energy-preserving coupling of explicit particle-in-cell with Monte Carlo collisions

The particle-in-cell (PIC) and Monte Carlo collisions (MCC) methods are workhorses of many numerical simulations of physical systems. Recently, it was pointed out that, while the two methods can be exactly—or nearly—energy-conserving independently, combining the two leads to anomalous numerical heating. This paper reviews the standard explicit PIC-MCC algorithm, elucidates the origins of the anomalous numerical heating, and explains how to couple the two methods such that the anomalous numerical heating is avoided.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Numerical Investigation of Slag Behavior for RSRM

It is known that the flow field of the redesigned solid rocket motor (RSRM) is very complicated due to the complex characteristics of turbulent multi-phase flow, chemical reaction, particle combustion, evaporation, breakup and agglomeration etc. It requires multi-phase calculations, chemical reaction simulation, and particle combustion, evaporation, and breakup models to obtain a better understanding of thermophysics for the RSRM design using numerical methods. Also, the slag buildup due to the molten particles is another factor affecting the performance of the RSRM. To achieve this goal, the volume of fluid (VOF) method is used to capture the free surface motion so as to simulate the accumulation of the molten particles (slag) of the RSRM. A finite rate chemistry model is used to simulate the chemical reaction effects. For multi-phase calculations, the Hermsen combustion model is used for the aluminum particle combustion analysis and the Taylor Analogy Breakup (TAB) model is used for the particle breakup analysis. An interphase mas-exchange model introduced by Spalding is used for the evaporation calculation. The particle trajectories are calculated using a one-step implicit method for several groups of particle sizes by which the drag forces and heat fluxes are then coupled with the gas phase equations. The preliminary results predicted a reasonable physical simulation of the particle effects using a simple two dimensional solid rocket motor configuration. It shows that the AL/AL2O3 particle sizes are reduced due to the combustion, evaporation, and breakup. The flow field is disturbed by the particles. Mach number distributions in the nozzle are deformed due to the effect of particle concentrations away from the center line.

Liaw, P.↗

Quantifying particle-scale 3D granular dynamics during rapid compaction from time-resolved in situ 2D x-ray images

Understanding the particle-scale dynamics of granular materials during rapid compaction and flow is of fundamental importance for manufacturing, planetary science, geology, and defense applications. Time-resolved 2D radiography and static 3D x-ray tomography are powerful in situ tools for studying particle-scale dynamics but provide detail only in 2D or with significant time-scale limitations, respectively. Here, we introduce a new method that uses 2D in situ x-ray imaging for determining time-resolved 3D particle-scale dynamics in rapidly compressed granular materials. The method employs initial particle packing structures obtained from x-ray tomography, a 2D x-ray image generation algorithm, and an optimization algorithm. We first describe and validate the method using finite element simulations. Furthermore, we then apply the technique to x-ray phase-contrast images obtained during rapid compaction of granular materials with varying particle morphology and sample thickness. The depth-resolved particle-scale dynamics reveal complex velocity and porosity fields evolving heterogeneously along and perpendicular to the compaction direction. We characterize these features, their fluctuations near the compaction front, and the compaction front thickness. Our technique can be applied to understanding granular dynamics during rapid compaction events, and rearrangements during slower, but non-quasi-static, flows.

36 MATERIALS SCIENCE↗

Decomposition of multi-particle azimuthal correlations in Q-cumulant analysis*

Abstract The method of Q -cumulants is a powerful tool for studying the fine details of azimuthal anisotropies in high energy nuclear collisions. This paper presents a new method, based on mathematical induction, to evaluate the analytical form of high-order Q -cumulants. The capability of this method is demonstrated via a toy model that uses the elliptic power distribution to simulate the anisotropic emission of particles, quantified in terms of Fourier flow harmonics . The method can help in studying the large amount of event statistics that can be collected in the future and allow measurements of the very high central moments of the distribution. This can, in turn, facilitate progress in understanding the initial geometry, the input to the hydrodynamic calculations of medium expansion in high energy nuclear collisions, and the constraints on it.

Physics↗

Online-compatible unsupervised nonresonant anomaly detection

There is a growing need for anomaly detection methods that can broaden the search for new particles in a model-agnostic manner. Most proposals for new methods focus exclusively on signal sensitivity. However, it is not enough to select anomalous events—there must also be a strategy to provide context to the selected events. In this work, we propose the first complete strategy for unsupervised detection of nonresonant anomalies that includes both signal sensitivity and a data-driven method for background estimation. Our technique is built out of two simultaneously trained autoencoders that are forced to be decorrelated from each other. This method can be deployed off-line for nonresonant anomaly detection and is also the first complete on-line-compatible anomaly detection strategy. We show that our method achieves excellent performance on a variety of signals prepared for the ADC2021 data challenge.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

PUMIPic: A mesh-based approach to unstructured mesh Particle-In-Cell on GPUs

Unstructured mesh particle-in-cell, PIC, simulations executing on the current and next generation of massively parallel systems require new methods for both the mesh and particles to achieve performance and scalability on GPUs. The traditional approach to implementing PIC simulations defines data structures and algorithms in terms of particles with a full copy of the unstructured mesh on every process. To effectively scale the unstructured mesh and particles, mesh-based PIC uses the unstructured mesh as the predominant data structure with the particles stored in terms of the mesh entities. Here, this paper details the PUMIPic library, a framework for developing efficient and performance-portable mesh-based PIC simulations on GPU systems. A pseudo physics simulation based on a five-dimensional gyro-kinetic code for modeling plasma physics is used to examine the performance of PUMIPic. Scaling studies of the unstructured mesh partition and number of particles are performed up to 4096 nodes of the Summit system at Oak Ridge National Laboratory. The studies show that mesh-based PIC can utilize a partitioned mesh and maintain scaling up to system limitations.

97 MATHEMATICS AND COMPUTING↗

Laser-driven ionization mechanisms of aluminum for single particle aerosol mass spectrometry

Single particle aerosol mass spectrometry (SPAMS), an analytical technique for measuring the size and composition of individual micron-scale particles, is capable of analyzing atmospheric pollutants and bioaerosols much more efficiently and with more detail than conventional methods which require the collection of particles onto filters for analysis in the laboratory. Despite SPAMS’ demonstrated capabilities, the primary mechanisms of ionization are not fully understood, which creates challenges in optimizing and interpreting SPAMS signals. In this paper, we present a well-stirred reactor model for the reactions involved with the laser-induced vaporization and ionization of an individual particle. The SPAMS conditions modeled in this paper include a 248 nm laser which is pulsed for 8 ns to vaporize and ionize each particle in vacuum. The ionization of 1 μm, spherical Al particles was studied by approximating them with a 0-dimensional plasma chemistry model. The primary mechanism of absorption of the 248 nm photons was pressure-broadened direct photoexcitation to Al(y 2 D). Atoms in this highly excited state then undergo superelastic collisions with electrons, heating the electrons and populating the lower energy excited states. We found that the primary ionization mechanism is electron impact ionization of various excited state Al atoms, especially Al(y 2 D). Because the gas expands rapidly into vacuum, its temperature decreases rapidly. The rate of three-body recombination (e - + e - + Al + → Al + e - ) increases at low temperature, and most of the electrons and ions produced recombine within several μs of the laser pulse. The importance of the direct photoexcitation indicates that the relative peak heights of different elements in SPAMS mass spectra may be sensitive to the available photoexcitation transitions. We also discuss the effects of laser intensity, particle diameter, and expansion dynamics.

47 OTHER INSTRUMENTATION↗

Testing strong-field QED with the avalanche precursor

A two-beam high-power laser facility is essential for the study of one of the most captivating phenomena predicted by strong-field quantum electrodynamics (QED) and yet unobserved experimentally: the avalanche-type cascade. In such a cascade, the energy of intense laser light can be efficiently transformed into high-energy radiation and electron–positron pairs. The future 50-petawatt-scale laser facility NSF OPAL will provide unique opportunities for studying such strong-field QED effects, as it is designed to deliver two ultra-intense, tightly focused laser pulses onto the interaction point. In this work, we investigate the potential of such a facility for studying elementary particle and plasma dynamics deeply in the quantum radiation-dominated (RD) regime, and the generation of QED avalanches. With three-dimensional particle-in-cell simulations, we demonstrate that QED avalanche precursors can be reliably triggered under realistic laser parameters and layout (namely, focusing f/2, tilted optical axes, and non-ideal co-pointing) with the anticipated capabilities of NSF OPAL. We demonstrate that seed electrons can be efficiently injected into the laser focus by using targets of three types: a gas of heavy atoms, an overcritical plasma, and a thin foil. A strong positron and high-energy photon signal is generated in all cases. The cascade properties can be identified from the final particle distributions, which have a clear directional pattern. At increasing laser field intensity, such distributions provide signatures of the transition, first, to the RD interaction regime, and then to a QED avalanche. Our findings can also be used for designing related future experiments.

Lasers↗

Calibration sources for the LEGEND-200 experiment

In the search for a monochromatic peak as the signature of neutrinoless double beta decay an excellent energy resolution and an ultra-low background around the Q-value of the decay are essential. The LEGEND-200 experiment performs such a search with high-purity germanium detectors enriched in 76 Ge immersed in liquid argon. To determine and monitor the stability of the energy scale and resolution of the germanium diodes, custom-made, low-neutron emission 228 Th sources are regularly deployed in the vicinity of the crystals. Here we describe the production process of the 17 sources available for installation in the experiment, the measurements of their alpha- and gamma- activities, as well as the determination of the neutron emission rates with a low-background LiI(Eu) detector operated deep underground. With a flux of ( 4.27 ± 0.60 stat ± 0.92 syst ) × 10 -4 n / (kBq·s), approximately one order of magnitude below that of commercial sources, the neutron-induced background rate, mainly from the activation of 76 Ge, is negligible compared to other background sources in LEGEND-200.

47 OTHER INSTRUMENTATION↗

Fabrication, Modeling, and Testing of a Prototype Thermal Energy Storage Containment

Increasing penetration of variable renewable energy resources requires the deployment of energy storage at a range of durations. Long-duration energy storage (LDES) technologies will fulfill the need to firm variable renewable energy resource output year round; lithium-ion batteries are uneconomical at these durations. Thermal energy storage (TES) is one promising technology for LDES applications because of its siting flexibility and ease of scaling. Particle-based TES systems use low-cost solid particles that have higher temperature limits than the molten salts used in traditional concentrated solar power systems. A key component in particle-based TES systems is the containment silo for the high-temperature (>1100 degrees C) particles. This study combined experimental testing and computational modeling methods to design and characterize the performance of a particle containment silo for LDES applications. A laboratory-scale silo prototype was built and validated the congruent transient finite element analysis (FEA) model. The performance of a commercial-scale silo was then characterized using the validated model. The commercial-scale model predicted a storage efficiency above 95% after 5 days of storage with a design storage temperature of 1200 degrees C. Insulation material and concrete temperature limits were considered as well. The validation of the methodology means the FEA model can simulate a range of scenarios for future applications. This work supports the development of a promising LDES technology with implications for grid-scale electrical energy storage, but also for thermal energy storage for industrial process heating applications.

clean energy↗

Fabrication, Modeling, and Testing of a Prototype for Particle Thermal Energy Storage Containment

Increasing penetration of variable renewable energy resources requires the deployment of energy storage at a range of durations. Long-duration energy storage (LDES) technologies will fulfill the need to firm variable renewable energy resource output throughout the year. Conventional electrochemical batteries (e.g., lithium-ion) are uneconomical in this role due to high energy capacity costs. Thermal energy storage (TES) is one promising technology for LDES applications because of its siting flexibility and ease of scaling. Particle-based TES systems use low-cost solid particles that have higher temperature limits than the molten salts used in traditional concentrated solar power systems. A key component in particle-based TES systems is the containment silo for the high-temperature (> 1100 degrees C) particles. This study combined experimental testing and computational modeling methods to design and characterize the performance of a particle containment silo for LDES applications. A containment silo prototype was built at a laboratory scale and used to validate a congruent transient finite element analysis (FEA) model. The validation compared the actual and predicted temperature profile through the prototype over six days as the particles cooled from their initial temperature. The performance of a commercial scale (> 5 GWhth) was then characterized using the validated model. The transient FEA model was subject to several charge-discharge cycles to mimic a possible operating schedule. The commercial-scale model predicted a storage efficiency in excess of 95% after five days of storage with a design storage temperature of 1200 degrees C. Insulation material and concrete temperature limits were considered as well. The validation of the methodology means the FEA model can simulate a range of scenarios for future applications. This work supports the development of a promising LDES technology with implications for grid-scale electrical energy storage, but also for thermal energy storage for industrial process heating applications.

ENERGY STORAGE↗

Investigation of Coincidence Counting for Improving Minimal Detectable Activity of 110m Ag in Single Particle Gamma Analysis

Post-irradiation examination (PIE) of fuel particles from the fourth Advanced Gas Reactor Fuel Development and Qualification (AGR) Program irradiation (AGR-5/6/7) is being performed at Oak Ridge National Laboratory (ORNL). Tristructural isotropic (TRISO)-coated particles and associated compacts for the AGR-5/6/7 experiment fabricated by BWX Technologies Nuclear Operations Group were formed into a graphite matrix compact and irradiated at the Advanced Test Reactor at Idaho National Laboratory. At ORNL, particles are deconsolidated from the graphite matrix compact and individually scanned for emitted gamma rays with the Irradiated Microsphere Gamma Analyzer (IMGA). The IMGA system comprises a single high purity germanium (HPGe) detector, an automated particle handling vacuum system, and an ORTEC DSPEC-50 digital spectrometer for gamma ray analysis. IMGA quantifies gamma ray-emitting fission product inventories of individual TRISO particles, and these inventories can be compared with the measured average inventories per particle and radionuclide inventories predicted by AGR-5/6/7 physics calculations to determine if a particle experienced radionuclide release. Details on IMGA data collection methods can be found in the literature. The TRISO particle’s SiC layer provides structural support, as well as a barrier for fission product release during irradiation or subsequent safety testing. A weakened or compromised SiC layer can be identified by the release of radionuclides, such as 137 Cs, which is detected by IMGA. However, select radionuclides, such as 90 Sr, 110 mAg, and 154 Eu have been shown to migrate through an intact SiC layer. Measurement of the radionuclide 110 mAg is significant as its release has been shown to be particularly sensitive to in-reactor conditions (e.g., temperature) with broad variable particle to-particle release behaviors observed within a single compact. As such, 110 mAg activity is often used for particle selection for comprehensive PIE as bounding 110 mAg retention particles are hypothesized to represent limits in particle behaviors within a compact. As TRISO particle fuel PIE activities continue over time, IMGA measurements of the 110 mAg inventory are eventually hindered because of its relatively short half-life (~250 days). As the fuel ages from its end of irradiation (EOI) date, the measurement uncertainty and minimum detectable activity (MDA) of 110m Ag increase because the detector background continuum begins to dominate. For particles from the second AGR irradiation experiment (AGR-2), the 110m Ag MDA was above 20% of the calculated average particle inventory after approximately five half-lives, and 110m Ag activity was no longer measurable with IMGA after approximately seven half-lives. Therefore, coincidence counting approaches have been explored to determine feasibility of leveraging new approaches to overcome limitations associated with increasing MDA over time.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗