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At least 847 records · Page 47

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How Topological Polymer Loops on the Nanoparticle Surface Control the Mechanical Properties of Nanocomposites

Carbon black (CB) and silica (SiO 2 ) filled elastomers are known to be the most successful polymer nanocomposites (PNCs) in industry, where “bound rubber (BR)” (i.e., polymer chains that are physically or chemically adsorbed on the nanofiller surface) plays a critical role in their reinforcement. Here, we report a molecular-scale mechanism underlying the “BR-induced reinforcement” by integrating neutron scattering experiments and molecular dynamics simulations. Simplified non-cross-linked SiO 2 -filled polybutadiene (PB) and CB-filled PB reveal the critical role of topological polymer loops in the BR for the enhanced mechanical performance. The average loop size on the SiO 2 surface modified with a silane coupling agent is much smaller than that on the CB surface and the loops on the SiO 2 surface are densely formed, preventing interdigitation with the matrix chains. On the other hand, the larger, uncrowded loops formed on the CB surface facilitate the interdigitation with the matrix polymer chains even near the filler surface. In this way, a strong connectivity is established between a matrix and a nanofiller, resulting in an adhesive filler–polymer interface. Furthermore, our findings shed light on rich and complex physics and materials design problems in PNCs, where the topological polymer structure on the nanofiller surface directly controls the macroscopic mechanical properties.

36 MATERIALS SCIENCE↗

Intrinsic Kinetics of Polyethylene Terephthalate Pyrolysis via Micropyrolysis and Multivariate Chromatographic Analysis

This study provides an in-depth investigation of the primary decomposition of polyethylene terephthalate (PET) via pyrolysis, employing an experimental-analytic workflow that integrates design of experiments (DoE), micropyrolysis coupled with comprehensive two-dimensional gas chromatography (GC×GC), and multivariate data analysis to verify intrinsic kinetic conditions and elucidate evolving product distributions for mapping key reaction pathways. Peaks that could not be identified using commercial spectral libraries were assigned using Mass Frontier simulations, enabling the identification of divinyl terephthalate, ethyl vinyl terephthalate, and 2-(benzoyloxy)ethyl vinyl terephthalate. A polar×polar (non-orthogonal) column set tailored for the detection of carboxylic acids enhanced the quantification of benzoic acid, 4-vinylbenzoic acid, 4-ethylbenzoic acid, and methylbenzoic acid by up to 6-fold relative to an orthogonal column combination (non-polar×mid-polar). Moreover, pyrolysis variables were systematically evaluated using a Box- Behnken design (BBD), encompassing pyrolysis temperature (500−600 °C), sample weight (50−150 μg), and carrier gas flow rate (100−300 mL min −1 ). Among these, pyrolysis temperature was the only statistically significant factor influencing product yields, ranging from 58.78 to 84.26 wt %. In contrast, neither the sample weight nor the carrier gas flow rate had a significant effect on product yields within the evaluated experimental space. At 600 °C, the major pyrolysis products were benzoic acid (up to 20.20 ± 1.46 wt %) and CO 2 (up to 21.28 ± 1.46 wt %), which can be produced through decarboxylation reactions. These findings underscore the critical importance of selecting appropriate analytical columns for the accurate quantification of heteroatomcontaining products such as carboxylic acids, which may otherwise be underestimated or undetected due to their reactivity with the stationary phase of non-polar and mid-polar columns, as well as other GC components. They also highlight the importance of selecting pyrolysis conditions for investigating the primary decomposition of PET under an isothermal kinetically limited regime.

aromatic compounds↗

Climate Drives Modeled Forest Carbon Cycling Resistance and Resilience in the Upper Great Lakes Region, USA

Forests dominate the global terrestrial carbon budget, but their ability to continue doing so in the face of a changing climate is uncertain. A key uncertainty is how forests will respond (resistance) and recover from (resilience) to rising levels of disturbance of varying intensities. This knowledge gap can optimally be addressed by integrating manipulative field experiments with ecophysiological modeling. We used the ED-2.2 model to project carbon fluxes for a northern temperate deciduous forest subjected to a real-world disturbance severity manipulation experiment. ED-2.2 was run for 150 years, starting from near bare ground in 1900, and subjected to three disturbance treatments under an ensemble of climate conditions. Both disturbance severity and climate strongly affected carbon fluxes, and interacted with one another. We then calculated metrics of functional ecosystem stability. Modeled gross primary production exhibited a mean resistance of -0.13, -0.23, and -0.42 (unitless) in response to increasing disturbance severity of 45%, 65%, and 85% mortality, respectively; and resilience of 0.002, 0.004, 0.008 (yr-1) respectively. This pattern held true for other carbon fluxes, meaning that in general simulated GPP declined more initially but recovered more quickly from higher mortality. Notably, however, heterotrophic respiration responded more slowly to disturbance, and its highly variable response was affected by different drivers. This work provides insight into how future conditions might affect the functional stability of mature forests in this region under ongoing climate change and changing disturbance regimes.

54 ENVIRONMENTAL SCIENCES↗

A multi-chord, two-color interferometer using Hilbert transform phase detection for measuring electron density in spheromak plasmas

A new, four-chord, CO 2 /He–Ne heterodyne interferometer has been designed and built for measuring line-averaged plasma density in the HIT-SI3 and subsequent HIT-SIU sustained spheromak devices. The two-color system successfully eliminates vibration-induced errors caused by mirrors that are secured to the vacuum chamber and is able to resolve electron densities ne in the full operating range of 10 18 –10 20 m –3 in both experiments with an integrated error of 4.7 × 10 17 m –2 . Here, data are presented from high toroidal current plasma discharges, showing the time evolution of electron densities n e and j Φ /n e along multiple chords.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Model-independent measurement of 𝐷 0 −$\overline{D}$ 0 mixing parameters in 𝐷 0 → 𝐾$^{0}_{𝑆}$⁢𝜋 + ⁢𝜋 − decays at Belle and Belle II

We perform a model-independent measurement of the 𝐷 0 −$\overline{D}$ 0 mixing parameters using samples of 𝑒 + ⁢𝑒 − -collision data collected by the Belle and Belle II experiments that have integrated luminosities of 951 fb −1 and 408 fb −1 , respectively. Approximately 2.05 × 10 6 neutral 𝐷 mesons are reconstructed in the 𝐷 0 → 𝐾$^{0}_{S}$⁢𝜋 + ⁢𝜋 − channel, with the neutral 𝐷 flavor tagged by the charge of the pion in the 𝐷* + → 𝐷 0⁢ 𝜋 + decay. Assuming charge-parity symmetry, the mixing parameters are measured to be 𝑥 = (4.0 ±1.7 ±0.4) × 10 −3 and 𝑦 = (2.9 ±1.4 ±0.3) × 10 −3 , where the first uncertainties are statistical and the second systematic. The results are consistent with previous determinations.

Charmed mesons↗

Superconducting Qubits above 20 GHz Operating over 200 mK

Current state-of-the-art superconducting microwave qubits are cooled to extremely low temperatures to avoid sources of decoherence. Higher qubit operating temperatures would significantly increase the cooling power available, which is desirable for scaling up the number of qubits in quantum computing architectures and integrating qubits in experiments requiring increased heat dissipation. To operate superconducting qubits at higher temperatures, it is necessary to address both quasiparticle decoherence (which becomes significant for aluminum junctions above 160 mK) and dephasing from thermal microwave photons (which are problematic above 50 mK). Using low-loss niobium-trilayer junctions, which have reduced sensitivity to quasiparticles due to the higher superconducting transition temperature of niobium, we fabricate transmons with higher frequencies than previously studied, up to 24 GHz. We measure decoherence and dephasing times of about 1 μs, corresponding to average qubit quality factors of approximately 10 5 , and find that decoherence is unaffected by quasiparticles up to 1 K. Without relaxation from quasiparticles, we are able to explore dephasing from purely thermal sources, finding that our qubits can operate up to approximately 250 mK while maintaining similar performance. The thermal resilience of these qubits creates new options for scaling up quantum processors, enables hybrid quantum experiments with high heat-dissipation budgets, and introduces a material platform for even-higher-frequency qubits.

Josephson junctions↗

Enhancing synchrotron radiation micro-CT images using deep learning: an application of Noise2Inverse on bone imaging

In bone-imaging research, in situ synchrotron radiation micro-computed tomography (SRµCT) mechanical tests are used to investigate the mechanical properties of bone in relation to its microstructure. Low-dose computed tomography (CT) is used to preserve bone's mechanical properties from radiation damage, though it increases noise. To reduce this noise, the self-supervised deep learning method Noise2Inverse was used on low-dose SRµCT images where segmentation using traditional thresholding techniques was not possible. Simulated-dose datasets were created by sampling projection data at full, one-half, one-third, one-fourth and one-sixth frequencies of an in situ SRµCT mechanical test. After convolutional neural networks were trained, Noise2Inverse performance on all dose simulations was assessed visually and by analyzing bone microstructural features. Visually, high image quality was recovered for each simulated dose. Lacunae volume, lacunae aspect ratio and mineralization distributions shifted slightly in full, one-half and one-third dose network results, but were distorted in one-fourth and one-sixth dose network results. Following this, new models were trained using a larger dataset to determine differences between full dose and one-third dose simulations. Significant changes were found for all parameters of bone microstructure, indicating that a separate validation scan may be necessary to apply this technique for microstructure quantification. Noise present during data acquisition from the testing setup was determined to be the primary source of concern for Noise2Inverse viability. While these limitations exist, incorporating dose calculations and optimal imaging parameters enables self-supervised deep learning methods such as Noise2Inverse to be integrated into existing experiments to decrease radiation dose.

Obata, Yoshihiro (ORCID:0000000303659129)↗

Commissioning of the large-scale lead tungstate scintillating calorimeter

Here, we report on the installation and initial commissioning of a large-scale lead tungstate (PbWO4) scintillating crystal calorimeter developed for high-rate photon detection and precise energy measurement. The calorimeter comprises 1596 high-granularity, high-resolution scintillating crystals optimized for electromagnetic-shower detection over a wide energy range. Scintillation light from each crystal is read out by Hamamatsu R4125 photomultiplier tubes equipped with a custom voltage divider and front-end amplifier to ensure stable gain at high rates. All calorimeter modules were fabricated and characterized using a light-emitting diode–based optical test system prior to installation to verify uniformity and photodetector performance. After installation, the electromagnetic calorimeter was fully integrated into the experiment data acquisition and energy-based trigger systems. The optical response of the modules was equalized using the light-monitoring system, cosmic-ray muons, and photons from Compton-scattering events. Commissioning results demonstrate a reliably calibrated optical response and stable detector performance during the first run. These results validate the calorimeter design and commissioning methodology for large-scale scintillator-based photonic instrumentation.

Analog to digital converters↗

Streaming Data from Experimental Facilities to Supercomputers for Real-Time Data Processing

In this paper we demonstrate direct data streaming from instruments and detectors at a large-scale experimental facility to a supercomputer for real-time data processing and feedback. Streaming data to supercomputers introduces the potential for novel scientific applications and workflow models, including the ability to provide real-time feedback from very large datasets during an experiment and the integration of real-time ML training and inference at scale. We discuss a successful demonstration for real-time processing of data from the Advanced Photon Source (APS) on the Polaris supercomputer using an EPICS-based streaming framework. We describe the capabilities of the streaming framework itself, and outline the architecture that allows us to process experimentally derived data on a supercomputer without file-based data transfers. We present throughput measurements that are indicative of system performance capable of sustaining the expected data production rates of the facility, as well as discuss some outstanding challenges and our future directions.

real-time processing↗

PNNL-m-q/lipidimea

Lipidomics Integrated Multi-Experiment Analysis tool

Jacobson, Jeremy [Pacific Northwest National Labor↗

Transverse Beam Emittance Measurement by Undulator Radiation Power Noise

Generally, turn-to-turn power fluctuations of incoherent spontaneous synchrotron radiation in a storage ring depend on the 6D phase-space distribution of the electron bunch. In some cases, if only one parameter of the distribution is unknown, this parameter can be determined from the measured magnitude of these power fluctuations. In this contribution, we report the results of our experiment at the Integrable Optics Test Accelerator (IOTA) storage ring, where we carried out an absolute measurement (no free parameters or calibration) of a small vertical emittance (5–15 nm rms) of a flat beam by this new method, under conditions, when the small vertical emittance is unresolvable by a conventional synchrotron light beam size monitor.

43 PARTICLE ACCELERATORS↗

PIP-II 800 MeV Proton Linac Beam Pattern Generator

The PIP2 IT Beam Pattern Generator is the system that synchronizes beam injection and the RF systems between the PIP2 LINAC to the Booster. The RF frequencies of these two accelerator systems are not harmonically related. Synchronization is accomplished by controlling two MEBT Beam Choppers, which select 162.5MHz beam bunches from the LEBT and RFQ to produce an appropriate reduced beam bunch pattern that enables bucket-to-bucket transfer to the Booster RF at 46.46MHz (84th harmonic). This chopping pattern also reduces the beam current to an average of 2mA over the Booster injection, matching the Linac nominal beam current. The BPG also generates the RF frequency/phase reference which the Booster will phase lock to during injection. The BPG is fully programmable, allowing for arbitrary beam patterns with adjustable timing parameters, having a fine adjustment resolution of 38ps. The latter is accomplished using digital signal processing techniques. This paper discusses the design of the BPG, its construction, test results, and operational experience after being integrated into the PIP2 IT test accelerator and concludes with a discussion of the system’s performance and future plans.

43 PARTICLE ACCELERATORS↗

Proposal for a proton-bunch compression experiment at IOTA in the strong space-charge regime

The longitudinal compression of intense proton bunches with strong space-charge force is an essential component of a proton-based muon source for a muon collider. This paper discusses a proton-bunch compression experiment at the Integrable Optics Test Accelerator (IOTA) storage ring at Fermilab to explore optimal radio frequency (RF) cavity and lattice configurations. IOTA is a compact fixed-energy storage ring that can circulate a 2.5-MeV proton beam with varying beam parameters and lattice configurations. The study will aim to demonstrate a bunch-compression factor of at least 2 in the IOTA ring while examining the impact of intense space-charge effects on the compression process.

43 PARTICLE ACCELERATORS↗

IOTA experiment for proton pulse compression at extreme space-charge

The longitudinal compression of intense proton bunches with strong space-charge force is an essential component of a proton driver for a muon collider. We propose a proton bunch compression experiment at the Integrable Optics Test Accelerator (IOTA) storage ring at Fermilab to explore optimal radio frequency (RF) cavity and lattice configurations. IOTA is a compact fixed-energy storage ring dedicated to beam physics R&D that can circulate a 2.5-MeV proton beam with extreme space-charge. Using ImpactX and its 3D space-charge solver, simulations indicate that bunch length can be rapidly reduced by a factor of at least two, without appreciable degradation in transverse beam quality, even under strong space-charge conditions. However, longitudinal defocusing presents a large effect in short-pulsed proton beams, and the optimization of bunch compression under such conditions is discussed.

Simons, Benjamin [Northern Illinois U.; Fermilab]↗

Turbulent Transport Studies at ASDEX Upgrade Enabled by Correlation Electron Cyclotron Emission and nT-phase Diagnostic. Final report

Work performed on project titled, "Turbulent Transport Studies at ASDEX Upgrade Enabled by Correlation Electron Cyclotron Emission and nT-phase Diagnostic". We conducted an integrated project of experiment and model validation at ASDEX Upgrade (AUG) to expand knowledge of the underlying physics of high-performance, ELM-free regimes suitable for long pulse operation. Both the I-mode and QH-mode high-confinement regimes have potential as operating scenarios in a future reactor. Additional fluctuation measurements provided critical constraints on transport models, and elucidate the transport mechanisms associated with benevolent quasi-coherent modes in the edge and pedestal region of QH-mode and I-mode. This research expanded knowledge of turbulent-transport in tokamaks in support of ITER and other burning plasma experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development of Temperature Compensation Tools for SPNDs Operating in High Temperature Environments

Two rhodium-based self-powered neutron detectors (Rh-SPNDs) were irradiated at the Massachusetts Institute of Technology Reactor as a follow-on experiment to the heated irradiation previously conducted at the Neutron Radiography facility at Idaho National Laboratory. The experiment was conducted over the temperature ranges of 600-850°C to further examine the effects of temperature on the Rh-SPNDs. Four tests of varying temperature and power were performed. The tests identified two types of temperature effects consistent with historical evaluations. One effect is a prompt proportionality to temperature at steady-state reactor power due to the decrease in Rh-SPND insulation resistance. The other effect is a delayed effect generated from displacement currents generated by changing the space charge within the insulator as a function of temperature. The result of this experiment demonstrates a characterizable responses to temperature that is feasible for developing a temperature compensation tool for SPND operating in high temperatures. The characteristics identified in this experiment will be integrated within the delayed-response compensation techniques for FY23 evaluation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

FAST-1.0: A Computer Code for Thermal-Mechanical Nuclear Fuel Analysis under Steady-state and Transients: Developed under NQA-1-2017

Fuel Analysis under Steady-state and Transients (FAST) is the US Nuclear Regulatory Commission (NRC)’s computer code that calculates the steady-state and transient response of nuclear reactor fuel rods during long-term in-reactor burnup, anticipated operational occurrences (AOOs), design basis accidents (DBAs), and dry storage conditions. The code calculates the temperature, pressure, and deformation of a fuel rod as functions of time-dependent fuel rod power and coolant boundary conditions. The phenomena modeled by the code include: heat conduction through the fuel and other materials, heat transfer from the cladding-to-coolant, cladding elastic and plastic deformation, including creep, fuel-cladding mechanical interaction, fission gas release from the fuel, rod internal pressure and void volume, and cladding oxidation. The code contains necessary material and coolant properties, as well as clad-to-coolant heattransfer correlations, for normal operation through postulated accidents for today’s US-based light water reactor (LWR) fuel designs. FAST-1.0 also contains preliminary materials and models for new LWR fuel concepts, such as accident tolerant fuel (ATF), and non-LWR fuel concepts such as metallic fuels for sodium fast reactors (SFRs). FAST has been developed for use on Windows and Linux operating systems. This document describes FAST-1.0, which is the first official version of this code. This document is one of a series of documents on FAST; the other documents detail the material properties used by FAST as well as its integral assessment to experiments and commercial data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗