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At least 1,369 records · Page 76

Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike’s stability. Taken together, the network approach serves as a valuable tool to evaluate communication “hot-spots” in proteins to guide design of stable immunogens.

60 APPLIED LIFE SCIENCES↗

Influence of Pt-Metal Alloy Catalysts with Various Ionomers on Oxygen Reduction Reaction in Fuel Cell Application

Pt-M/C (M = Co, Ni, Mn, etc.) alloy catalysts exhibit superior oxygen reduction reaction (ORR) activity compared to pure Pt/C, leading to a high energy efficiency in hydrogen fuel cells. However, many Pt-M/C alloy catalysts were synthesized and evaluated at the lab scale in model test-bed systems like rotating disc electrodes, which don't always correlate to performance within a fuel cell system; there is a clear need to evaluate catalysts in electrodes that can be prepared at industrially relevant scales to evaluate how factors like ink formulation can greatly affect device-level of fuel cell performance. Herein, three commercial Pt-M/C alloy catalysts (two Pt-Co/C and one Pt-Ni/C) were comprehensively characterized by various techniques. The results show that the average particle sizes of the three catalysts are close to 5 nm; the atomic ratio of Pt/M is around 4; and the M was successfully embedded into Pt lattice, resulting in the positive shift of Pt 4f in XPS spectra and XRD patterns. These catalytic materials were incorporated into 9 different cathode catalyst layers (CCLs) with three kinds of ionomers (Nafion D2020, high oxygen permeability ionomer (HOPI), and Aquivion D79-25BS), and their performance in proton exchange membrane fuel cells (PEMFCs) were investigated. The results demonstrate that the Pt-Co/C catalysts possess a higher mass activity (MA) than Pt-Ni/C; the cathodes with Nafion ionomer provide the highest MA while electrodes with Aquivion ionomer showed the lowest activity, attributed to poor H+ conductivity resulting from suboptimal ionomer incorporation. Finally, these alloys were shown to exceed DOE targets for MA and H2/Air performance reported in the recent publications at beginning of life and after 90k cycle catalyst AST protocol. This study provides valuable performance benchmarks for these materials guiding future Pt-M/C catalyst design and material integration for heavy duty PEMFC applications.

08 HYDROGEN↗

Analysis of attenuation data from the decommissioned ZIon unit 1 reactor pressure vessel beltline weld

In order to examine the attenuation of radiation damage through the thickness of an irradiated reactor pressure vessel (RPV), four segments were acquired from the Zion Unit 1 power plant RPV after the plant was decommissioned. The Zion Unit 1 RPV Beltline Weld Segment 1 was cut into seven blocks, consisting of five base metal and two beltline welds from the high fluence region of the segment. Through-wall test specimens were machined and tested. Specimens included those used for Charpy impact, Master Curve fracture toughness testing, and chemical analysis. The observed through-thickness ductile-to-brittle transition temperatures in the beltline weld deviated significantly from the expected behavior based on the attenuation of fast fluence as a function of depth into the RPV. Beginning at the inside surface, the 41-J Charpy transition temperature was either flat or slightly increasing until the ¾ -T location. The results of a simple, model-based analysis of the Zion beltline weld material that included the irradiation conditions and material chemistry were generally consistent with industry trend curves and the standard attenuation model, rather than the observed data. Although there was no archive material from the RPV available to permit measurement of the unirradiated properties, fracture toughness specimens fabricated from archive surveillance weld were used to obtain an estimate of the initial through-thickness values of the Charpy transition temperature. The Charpy shifts obtained using this approach were similarly in disagreement with the predictions of the US NRC Regulatory Guide 1.99, Rev. 2. However, testing of irradiated Charpy specimens taken from the RPV following post-irradiation annealing (10 hr. at 500 °C) provided a quite different estimate of the unirradiated properties which improved the agreement between the inferred through-thickness Charpy shifts and exponential attenuation model included in Regulatory Guide 1.99/2. In conclusion, the analysis of the Zion data and data obtained in previous post-mortem examinations of decommissioned RPVs indicates that more work is needed to understand the through-thickness properties of RPV materials in order to properly assess through-wall damage attenuation.

Charpy impact↗

Machine learning with knowledge constraints for process optimization of open-air perovskite solar cell manufacturing

Perovskite photovoltaics (PV) have achieved rapid development in the past decade in terms of power conversion efficiency of small-area lab-scale devices; however, successful commercialization still requires further development of low-cost, scalable, and high-throughput manufacturing techniques. One of the critical challenges of developing a new fabrication technique is the high-dimensional parameter space for optimization, but machine learning (ML) can readily be used to accelerate perovskite PV scaling. Herein, we present an ML-guided framework of sequential learning for manufacturing process optimization. We apply our methodology to the Rapid Spray Plasma Processing (RSPP) technique for perovskite thin films in ambient conditions. With a limited experimental budget of screening 100 process conditions, we demonstrated an efficiency improvement to 18.5% as the best-in-our-lab device fabricated by RSPP, and we also experimentally found 10 unique process conditions to produce the top-performing devices of more than 17% efficiency, which is 5 times higher rate of success than the control experiments with pseudo-random Latin hypercube sampling. Our model is enabled by three innovations: (a) flexible knowledge transfer between experimental processes by incorporating data from prior experimental data as a probabilistic constraint; (b) incorporation of both subjective human observations and ML insights when selecting next experiments; (c) adaptive strategy of locating the region of interest using Bayesian optimization first, and then conducting local exploration for high-efficiency devices. Furthermore, in virtual benchmarking, our framework achieves faster improvements with limited experimental budgets than traditional design-of-experiments methods (e.g., one-variable-at-a-time sampling). This framework shows the capability of incorporating researchers’ domain knowledge into the ML-guided optimization loop; therefore, it has the potential to facilitate the wider adoption of ML in scaling to perovskite PV manufacturing.

14 SOLAR ENERGY↗

Non-bonding interaction of dual atom catalysts for enhanced oxygen reduction reaction

Here, we demonstrate the design of graphene-supported dual atom catalysts (DACs) for the four-electron oxygen reduction reaction (ORR), by utilizing the non-bonding interaction of counterpart metals (M) that synergistically tune the electronic properties and catalytic activity of the Fe active site in FeMN 6 -DAC and FeMN 8 -DAC systems, where M stands for Fe, Co, Ni, Cu, and Zn. More specifically, for Fe-M distances below 15Å, the non-bonding interaction is significant, making the system act as the DAC. We predicted that FeNiN 6 -DAC and FeNiN 8 -DAC exhibit a low ORR overpotential (η ORR ) of 0.28 V and 0.47 V, respectively, which are at the summits of volcano plots. This low η ORR originates from the high Bader charge transfer coupled with high spin density at the Fe site in both the FeNiN 6 -DAC and FeNiN 8 -DAC systems, which weakens the adsorption of OH* intermediate while enhancing its desorption to H 2 O. Guided by these density functional theory (DFT) computational results, we synthesized FeCoN 8 -DAC and FeNiN 8 -DAC along with N-doped graphene and confirmed their structures with scanning transmission electron microscopy (STEM), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and electron spin resonance (ESR). We verify experimentally the catalytic activities and find that FeNiN 8 -DAC has the low experimental overpotential of 0.39 V with a Tafel slope of 47 mVdec -1 . Based on these results, we propose a DFT-guided strategy to tune the charge transfer and spin population of the active site toward designing DACs for electrochemical ORR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimization of neutron chopper and optics for CENTAUR, the SANS/WANS diffractometer at the spallation neutron source second target station

Herein this report presents the physics design and optimization of the neutron chopper and optics systems for the CENTAUR instrument, a multifunctional small-angle and wide-angle neutron scattering diffractometer for the Spallation Neutron Source Second Target Station. This instrument will offer a wide range of capabilities, including small-angle neutron scattering with wide Q coverage (e.g., 0.001–20 Å –1 ), providing a tool to investigate structures from atomic to mesoscopic scales simultaneously. To efficiently transport desired neutrons from the compact high-brightness cold source, several innovative designs are utilized: a time-zero chopper with a straight guide system for short-wavelength neutrons, octagonal guides for higher flux, and a correlation chopper to reduce inelastic scattering. The optimization process considers factors such as useable time-integrated flux, instrument resolution, brilliance transfer, divergence, and acceptance diagram uniformity. The overall design prioritizes flexibility to accommodate diverse user requirements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Incident beamline design for a modern cold triple axis spectrometer at the High Flux Isotope Reactor

A modern cold triple axis spectrometer is being planned for the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Here, we describe the design of an incident beamline that will put a flux of ~ 10 8 $\frac {n}{cm^{2}s}$ on a sample with an area of 2 cm X 2 cm. It takes current physical constraints at HFIR into account and it can accommodate both single and multiplexed analyzer-detector secondary spectrometers and large superconducting magnets. The proposed incident beamline includes a multi-channel guide with horizontal focusing, a neutron velocity selector, components to facilitate an incident beam polarization option, and a double-focusing pyrolytic graphite monochromator. Here, this work describes the process of optimizing the guide system and monochromator and summarizes the expected performance of the incident beamline for non-polarized operation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Numerical modeling of impurity powder injection in W7-X

In this work, we present numerical simulation results of powder injection in W7-X using the EMC3-EIRENE and DIS codes. First, we model powder injection experiments performed in W7-X with the Probe Mounted Powder Injector. The simulation results qualitatively agree with visible imaging measurements. Secondly, we perform predictive simulations to guide the installation of an Impurity Powder Dropper in W7-X, allowing to choose in between several available non-vertical ports to maximize the amount of powder penetrating into the plasma, as well as the verticality of the port, to minimize sticking of the powders in the in-vessel stainless steel guiding tube. Port AEM41 is selected as the best candidate for IPD installation. The robustness of the simulation results has been verified for different plasma densities, powder materials and sizes, powder friction coefficient and changes in the plasma flow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Debunking common myths in coastal circulation modeling

Despite tremendous progress in algorithm development, computational efficiency and transition into operations over the past two decades, coastal modeling still lacks scientific rigor due to proliferation of many ‘gray’ areas related to various modeling choices made by modelers. Here, in this paper, we propose some guiding principles for the modeling community to improve performance, and we also debunk commonly held myths that make the coastal modeling lack rigor. Using our own experience in developing seamless cross-scale unstructured-grid based models for the past two decades, we describe in unprecedented detail the end-to-end modeling process (i.e., from digital elevation models (DEMs) to mesh generation to post analysis), and demonstrate that defensible modeling is within reach for any end user by following three guiding principles: (1) Bathymetry is a first order forcing in coastal domains and thus should be respected in all aspects of modeling; (2) Oceanographic processes are driven across multiple spatial scales and so models should enable appropriate resolution as needed; and (3) Model assessment should focus on physical processes. Through qualitative and quantitative model assessments, we demonstrate the fundamental role played by bathymetry/topography as embedded in DEMs in making the results defensible, which is unfortunately glossed over in many modeling studies. Focusing on process-based assessment simplifies the calibration process. A major conclusion of this work is that model developers and operators should maximize the scientific rigor for in silico oceanography by avoiding some common pitfalls that rely on error compensation at the expense of representation of physical system processes. We present some best practice procedures for defensive and trustworthy numerical modeling.

54 ENVIRONMENTAL SCIENCES↗

A Bayesian Framework for Milling Stability Prediction and Reverse Parameter Identification

This paper describes a physics-guided Bayesian framework for identifying the milling stability boundary and system parameters through iterative testing. Prior uncertainties for the parameters are identified through physical simulation and literature reviews, without physical testing of the actual milling system. Those uncertainties are then propagated to the stability map using a physics-based stability model, which is used to suggest a test point. The uncertainties are updated based on the new information acquired from the cutting test to form a new probability distribution, called the posterior. Finally, the posterior are compared to measured values for the stability boundary and system parameters to evaluate the approach. Based on experimental observations, the advantages and disadvantages of using a physics-guided model are discussed.

Cornelius, Aaron↗

An ecologically-constrained deep learning model for tropical leaf phenology monitoring using PlanetScope satellites

In tropical forests, leaf phenology signals leaf-on/off status and exhibits considerable variability across scales from a single tree-crown to the entire forest ecosystem. Such phenology signals importantly regulate large-scale biogeochemical cycles and regional climate. PlanetScope CubeSats data with a 3-m resolution and near-daily global coverage provide an unprecedented opportunity to monitor both fine- and ecosystem-scale phenology variability along large environmental gradients. However, a scalable method that accurately characterizes leaf phenology from PlanetScope with biophysically meaningful metrics remains lacking. Here we developed an index-guided, ecologically constrained autoencoder (IG-ECAE) method to automatically derive a deciduousness metric (i.e. percentage of tree canopies with leaf-off status within an image pixel) from PlanetScope. The IG-ECAE first estimated the reflectance spectra of leafy/leafless canopies based on their spectral indices characteristics, then used the derived reflectance spectra to guide an autoencoder deep learning method with additional ecological constraints to refine the reflectance spectra, and finally used linear spectral unmixing to estimate the relative abundance of leafless canopies (or deciduousness) per PlanetScope image pixel. We tested the IG-ECAE method at 16 tropical forest sites spanning multiple continents and a large precipitation gradient (1470-2819 mm year -1 ). Among these sites, we evaluated the PlanetScope-derived deciduousness with corresponding measures derived from WorldView-2 (n=9 sites) and local phenocams (n=9 sites). Our results show that PlanetScope-derived deciduousness agrees: 1) with that derived from WorldView-2 at the patch level (90m×90m) with r 2 =0.89 across all sites; and 2) with that derived from phenocams to quantify ecosystem-scale seasonality with r 2 ranging from 0.62-0.96. These results demonstrate the effectiveness and scalability of IG-ECAE in characterizing the wide variability in deciduousness across scales from pixels to forest ecosystems, and from a single date to the full annual cycle, indicating the potential for using high-resolution satellites to track the large-scale phenological patterns and response of tropical forests to climate change.

54 ENVIRONMENTAL SCIENCES↗

Controlling the corrosion resistance of multi-principal element alloys

Multi-principal element alloys (MPEAs) offer the possibility of many degrees of freedom in the choice of alloying elements to produce either single phase solid solutions or more complex multiphase microstructures. Large ranges of material properties have been observed for MPEAs and mastery of the selection of elements and their compositions can enable novel combinations of properties not possible in traditional alloys. From the aqueous corrosion perspective, optimization of phase stability, control of heterogeneities, passive film identity and its protectiveness, as well as substrate properties such as metal-metal bond strength and activation energy associated with dissolution, can all be controlling factors governed by alloy composition and structure. These factors can mediate the electrochemical reactions controlling spontaneous corrosion. The quest for superior properties based on well-informed element choice is suggested as a path forward guiding MPEA formulations for corrosion performance. However, gaps in fundamental knowledge exist regarding (a) the specific functions of each element, (b) the behavior of elements in unusual combinations, and (c) the formation of complex protective oxides. These issues currently hold back progress in optimization of corrosion properties.

Scully, John R.↗

Microbial inoculants and invasions: a call to action

Microbial inoculants are increasingly used for beneficial purposes in agriculture, bioremediation, and medicine, but they can carry risks of generating invasive microbes. Here, we present a roadmap for guarding against these invasions, proposing developing (i) coherent mechanistic understandings of how microbial inoculants can effect invasions, (ii) predictive models forecasting microbial invasion risks, and (iii) effective management strategies. To guide mechanistic understandings, we distill 17 guiding hypotheses. For predictive modeling, we highlight data collection needs and qualitative approaches. For management strategies, we stress the importance of accurately weighing the risks against benefits. The unified approach presented here provides a route toward an effective research and management infrastructure for microbial inoculants in order to avoid potentially catastrophic microbial invasions.

invasive species↗

Noninvasive liquid level sensing with laser generated ultrasonic waves

This article proposes a noninvasive liquid level sensing technique using laser-generated ultrasound waves for nuclear power plant applications. Liquid level sensors play an important role of managing the coolant system safely and stably in the plant structure. Current sensing techniques are mostly intrusive, performing inside the fluidic structure, which is disadvantageous in terms of the regular maintenance of the plant system. Furthermore, typical intrusive sensors do not perform stably under varying environmental conditions such as temperature and radiation. In this study, sensing units are attached to the outer surface of a liquid vessel to capture guided ultrasound waves in a nonintrusive manner. The signal intensity of the guided wave dissipates when the signal interacts with the internal liquid media. The sensing mechanism is mathematically expressed as an index value to correlate the liquid level with the sensor signal. For the acoustic wave generation, laser-generated ultrasound was adopted instead of using typical contact type transducers. Following the simulation validation of the proposed concept, the performance of the developed sensor was confirmed through experimental results under elevated liquid temperature conditions. Finally, the nonlinear multivariable regression exhibited the best-fit to the datasets measured under the variable liquid level and temperature conditions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Reconnection and particle acceleration in three-dimensional current sheet evolution in moderately magnetized astrophysical pair plasma

Magnetic reconnection, a plasma process converting magnetic energy to particle kinetic energy, is often invoked to explain magnetic energy releases powering high-energy flares in astrophysical sources including pulsar wind nebulae and black hole jets. Reconnection is usually seen as the (essentially two-dimensional) nonlinear evolution of the tearing instability disrupting a thin current sheet. To test how this process operates in three dimensions, we conduct a comprehensive particle-in-cell simulation study comparing two- and three-dimensional evolution of long, thin current sheets in moderately magnetized, collisionless, relativistically hot electron–positron plasma, and find dramatic differences. We first systematically characterize this process in two dimensions, where classic, hierarchical plasmoid-chain reconnection determines energy release, and explore a wide range of initial configurations, guide magnetic field strengths and system sizes. We then show that three-dimensional (3-D) simulations of similar configurations exhibit a diversity of behaviours, including some where energy release is determined by the nonlinear relativistic drift-kink instability. Thus, 3-D current sheet evolution is not always fundamentally classical reconnection with perturbing 3-D effects but, rather, a complex interplay of multiple linear and nonlinear instabilities whose relative importance depends sensitively on the ambient plasma, minor configuration details and even stochastic events. It often yields slower but longer-lasting and ultimately greater magnetic energy release than in two dimensions. Intriguingly, non-thermal particle acceleration is astonishingly robust, depending on the upstream magnetization and guide field, but otherwise yielding similar particle energy spectra in two and three dimensions. Although the variety of underlying current sheet behaviours is interesting, the similarities in overall energy release and particle spectra may be more remarkable.

Physics↗

Evolution of an arched magnetized laboratory plasma in a sheared magnetic field

Arched magnetized structures are a common occurrence in space and laboratory plasmas. Results from a laboratory experiment on spatio-temporal evolution of an arched magnetized plasma ( $\beta \approx 10^{-3}$ , Lundquist number $\approx 10^{4}$ , plasma radius/ion gyroradius $\approx 20$ ) in a sheared magnetic configuration are presented. The experiment is designed to model conditions relevant to the formation and destabilization of similar structures in the solar atmosphere. The magnitude of a nearly horizontal overlying magnetic field was varied to study its effects on the writhe and twist of the arched plasma. In addition, the direction of the guiding magnetic field along the arch was varied to investigate its role in the formation of either forward- or reverse-S shaped plasma structures. The electrical current in the arched plasma was well below the current required to make it kink unstable. A significant increase in the writhe of the arched plasma was observed with larger magnitudes of overlying magnetic field. A forward-S shaped arched plasma was observed for a guiding magnetic field oriented nearly antiparallel to the initial arched plasma current, while the parallel orientation yielded the reverse-S shaped arched plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development of compact tokamak fusion reactor use cases to inform future transport studies

The OMFIT STEP (Meneghini et al. , Nucl. Fusion , vol. 10, 2020, p. 1088) workflow has been used to develop inductive and steady-state H-mode core plasma scenario use cases for a $B_0 = 8 \, {\rm T}$ , $R_0 = 4 \, {\rm m}$ machine to help guide and inform future higher-fidelity studies of core transport and confinement in compact tokamak reactors. Both use cases are designed to produce 200 MW or more of net electric power in an up-down symmetric plasma with minor radius $a = 1.4 \, {\rm m}$ , elongation $\kappa = 2.0$ , triangularity $\delta = 0.5$ and effective charge $Z_{{\rm eff}} \simeq 2$ . Additional considerations based on the need for compatibility of the core with reactor-relevant power exhaust solutions and external actuators were used to guide and constrain the use case development. An extensive characterization of core transport in both scenarios is presented, the most important feature of which is the extreme sensitivity of the results to the quantitative stiffness level of the transport model used as well as the predicted critical gradients. This sensitivity is shown to arise from different levels of transport stiffness exhibited by the models, combined with the gyroBohm-normalized fluxes of the predictions being an order of magnitude larger than other H-mode plasmas. Additionally, it is shown that although heating in both plasmas is predominantly to the electrons and collisionality is low, the plasmas remain sufficiently well coupled for the ions to carry a significant fraction of the thermal transport. As neoclassical transport is negligible in these conditions, this situation inherently requires long-wavelength ion gyroradius-scale turbulence to be the dominant transport mechanism in both plasmas. These results are combined with other basic considerations to propose a simple heuristic model of transport in reactor-relevant plasmas, along with simple metrics to quantify coupling and core transport properties across burning and non-burning plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fast-ion transport in quasisymmetric equilibria in the presence of a resonant Alfvénic perturbation

Significant progress has been made in designing magnetic fields that provide excellent confinement of the guiding-centre trajectories of alpha particles using quasisymmetry (QS). Given the reduction in this transport channel, we assess the impact of resonant Alfvén eigenmodes (AEs) on the guiding-centre motion. The AE amplitudes are chosen to be consistent with experimental measurements and large-scale simulations. We evaluate the drift resonance condition, phase-space island width and island overlap criterion for quasisymmetric configurations. Kinetic Poincaré plots elucidate features of the transport, including stiff transport above a critical perturbation amplitude. Our analysis highlights key departures from the AE-driven transport in tokamaks, such as the avoidance of phase-space island overlap in quasihelical configurations and the enhanced transport due to wide phase-space islands in low magnetic shear configurations. In configurations that are closer to QS, with QS deviations $\delta B/B_0 \lesssim 10^{-3}$ , the transport is primarily driven by the AE, while configurations that are further from QS, $\delta B/B_0 \sim 10^{-2}$ , experience significant transport due to the QS-breaking fields in addition to the AE.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗