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At least 361 records · Page 20

Quantitative proton radiography and shadowgraphy for arbitrary intensities

Charged-particle radiography and shadowgraphy data can be directly inverted to obtain a line-integrated transverse Lorentz force or a line-integrated transverse refractive index gradient if intensity modulations due to scattering and absorption are negligible, and angular deflections are small. We develop a new direct-inversion algorithm based on plasma physics and compare it to a new Monge–Ampère code and an existing power diagram code. The measured or source intensity is represented by electrons subject to drag, and the other intensity by fixed ions. The decrease in kinetic plus electrostatic energy determines convergence. The displacement of the electrons from their initial to their equilibrium positions determines the line-integrated force or refractive index gradient. We have implemented two approaches: PIC (particle in cell) and Lagrangian fluid, in 1-D and 2-D. The PIC code works for arbitrary intensities, can work efficiently in parallel, and can make use of existing codes. The Lagrangian code requires less memory and is faster than the PIC code without massively parallel processing, but fails in 2-D for large intensity modulations. The Monge–Ampère code is by far the fastest in 2-D, without massively parallel processing, but fails for intensities with large voids, high contrast ratios and large deflections across the boundaries, and could not obtain the degree of convergence possible with the PIC code. As a result, the power diagram code was by far the slowest and most memory intensive, and failed for large peaks in the measured intensity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Particle control via cryopumping and its impact on the edge plasma profiles of Alcator C-Mod

At the high n e proposed for high-field fusion reactors, it is uncertain whether ionization, as opposed to plasma transport, will be most influential in determining n e at the pedestal and separatrix. A database of Alcator C-Mod discharges is analyzed to evaluate the impact of source modification via cryopumping. The database contains similarly-shaped H-modes at fixed I P = 0.8 MA and B t = 5.4 T, spanning a large range in P net and ionization. Measurements from an edge Thomson scattering system are combined with those from a midplane-viewing Ly α camera to evaluate changes to n e and T e in response to changes in ionization rates, S ion ∙ $n^{sep}_e$ and $T^{ped}_e$ are found to be most sensitive to changes to $S^{sep}_{ion}$, as opposed to $n^{ped}_e$ and $T^{sep}_e$. Dimensionless quantities, namely α MHD and v*, are found to regulate attainable pedestal values. Select discharges at different values of P net and in different pumping configurations are analyzed further using SOLPS-ITER. It is determined that changes to plasma transport coefficients are required to self-consistently model both plasma and neutral edge dynamics. Pumping is found to modify the poloidal distribution of atomic neutral density, n 0 , along the separatrix, increasing n 0 at the active X-point. Opaqueness to neutrals from high n e in the divertor is found to play a role in mediating neutral penetration lengths and hence, the poloidal distribution of neutrals along the separatrix. Pumped discharges thus require a larger particle diffusion coefficient than that inferred purely from 1D experimental profiles at the outer midplane.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Effects of low-frequency voltage on nonlinear standing wave excitation, plasma uniformity, and ion dynamics in dual-frequency asymmetric capacitive discharges

Abstract It is known that in very-high-frequency (VHF) capacitively coupled plasmas, the higher harmonics generated by nonlinear sheath motion can enhance the standing wave effect (SWE), which can lead to center-peaked plasma density profiles. In this work, an improved nonlinear electromagnetic model incorporating a transmission line model, an electron momentum balance model, a bulk plasma model, a collisionless nonlinear numerical sheath model, and an ion Monte-Carlo collision (MCC) model is developed to study the effects of low-frequency (LF) voltage V L on the nonlinear standing wave excitation, plasma uniformity, and ion energy and angular distribution functions (IEDFs and IADFs) in dual-frequency (DF) asymmetric capacitive argon discharges at relatively low pressure of 3 Pa. The plasma diffusion in the radial direction and ion dynamics within the LF oscillating sheath are self-consistently considered. The LF voltage V L at 2 MHz varies from 0 to 700 V while the HF voltage V H at 60 MHz is fixed at 100 V. Simulation results indicate that without the addition of an LF source (i.e. V L = 0 V), there are a considerable number of high-order harmonics with short wavelengths, leading to significant SWE and central peak in the radial plasma density profile. Nevertheless, the high-order harmonic excitations tend to be weakened and merely occur around the phase of the full LF sheath collapse due to a shorter characteristic damping time of the surface waves as V L increases. This, combined with increased surface wavelengths of both the driving frequency and the higher harmonics at a higher V L , leads to suppressed standing waves and improved plasma uniformity. Meanwhile, the simulations show that both the low and the high energy peaks of IEDF move towards higher energies, and the energy peak separation width ΔEbecomes wider with the increase of V L . The IEDF at the radial center of the powered electrode exhibits a broader ΔEthan that at the edge. For the IADF, an increased V L results in more ions incident on the electrode with a smaller deflection angle. Because of a thinner sheath and a higher sheath voltage at the electrode center, the peak value of IADF at the electrode center is greater than that at the edge.

Physics↗

Multi-task graph neural networks for simultaneous prediction of global and atomic properties in ferromagnetic systems *

Abstract We introduce a multi-tasking graph convolutional neural network, HydraGNN, to simultaneously predict both global and atomic physical properties and demonstrate with ferromagnetic materials. We train HydraGNN on an open-source ab initio density functional theory (DFT) dataset for iron-platinum with a fixed body centered tetragonal lattice structure and fixed volume to simultaneously predict the mixing enthalpy (a global feature of the system), the atomic charge transfer, and the atomic magnetic moment across configurations that span the entire compositional range. By taking advantage of underlying physical correlations between material properties, multi-task learning (MTL) with HydraGNN provides effective training even with modest amounts of data. Moreover, this is achieved with just one architecture instead of three, as required by single-task learning (STL). The first convolutional layers of the HydraGNN architecture are shared by all learning tasks and extract features common to all material properties. The following layers discriminate the features of the different properties, the results of which are fed to the separate heads of the final layer to produce predictions. Numerical results show that HydraGNN effectively captures the relation between the configurational entropy and the material properties over the entire compositional range. Overall, the accuracy of simultaneous MTL predictions is comparable to the accuracy of the STL predictions. In addition, the computational cost of training HydraGNN for MTL is much lower than the original DFT calculations and also lower than training separate STL models for each property.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗

DEEPEN 3D PFA Favorability Models and 2D Favorability Maps at Newberry Volcano

DEEPEN stands for DE-risking Exploration of geothermal Plays in magmatic ENvironments. Part of the DEEPEN project involved developing and testing a methodology for a 3D play fairway analysis (PFA) for multiple play types (conventional hydrothermal, superhot EGS, and supercritical). This was tested using new and existing geoscientific exploration datasets at Newberry Volcano. This GDR submission includes images, data, and models related to the 3D favorability and uncertainty models and the 2D favorability and uncertainty maps. The DEEPEN PFA Methodology is based on the method proposed by Poux et al. (2020), which uses the Leapfrog Geothermal software with the Edge extension to conduct PFA in 3D. This method uses all available data to build a 3D geodata model which can be broken down into smaller blocks and analyzed with advanced geostatistical methods. Each data set is imported into a 3D model in Leapfrog and divided into smaller blocks. Conditional queries can then be used to assign each block an index value which conditionally ranks each block's favorability, from 0-5 with 5 being most favorable, for each model (e.g., lithologic, seismic, magnetic, structural). The values between 0-5 assigned to each block are referred to as index values. The final step of the process is to combine all the index models to create a favorability index. This involves multiplying each index model by a given weight and then summing the resulting values. The DEEPEN PFA Methodology follows this approach, but split up by the specific geologic components of each play type. These components are defined as follows for each magmatic play type: 1. Conventional hydrothermal plays in magmatic environments: Heat, fluid, and permeability 2. Superhot EGS plays: Heat, thermal insulation, and producibility (the ability to create and sustain fractures suitable for and EGS reservoir) 3. Supercritical plays: Heat, supercritical fluid, pressure seal, and producibility (the proper permeability and pressure conditions to allow production of supercritical fluid) More information on these components and their development can be found in Kolker et al., 2022. For the purposes of subsurface imaging, it is easier to detect a permeable fluid-filled reservoir than it is to detect separate fluid and permeability components. Therefore, in this analysis, we combine fluid and permeability for conventional hydrothermal plays, and supercritical fluid and producibility for supercritical plays. More information on this process is described in the following sections. We also project the 3D favorability volumes onto 2D surfaces for simplified joint interpretation, and we incorporate an uncertainty component. Uncertainty was modeled using the best approach for the dataset in question, for the datasets where we had enough information to do so. Identifying which subsurface parameters are the least resolved can help qualify current PFA results and focus future efforts in data collection. Where possible, the resulting uncertainty models/indices were weighted using the same weights applied to the respective datasets, and summed, following the PFA methodology above, but for uncertainty. There are two different versions of the Leapfrog model and associated favorability models: - v1.0: The first release in June 2023 - v2.1: The second release, with improvements made to the earthquake catalog (included additional identified events, removed duplicate events), to the temperature model (fixed a deep BHT), and to the index models (updated the seismicity-heat source index models for supercritical and EGS, and the resistivity-insulation index models for all three play types). Also uses the jet color map rather than the magma color map for improved interpretability. - v2.1.1: Updated to include v2.0 uncertainty results (see below for uncertainty model versions) There are two different versions of the associated uncertainty models: - v1.0: The first release in June 2023 - v2.0: The se...

15 GEOTHERMAL ENERGY↗

Angular distribution of photoelectrons at 584A using polarized radiation

Photoelectron angular distributions for Ar, Xe, N2, O2, CO, CO2, and NH3 were obtained at 584 A by observing the photoelectrons at a fixed angle and simply rotating the plane of polarization of a highly polarized photon source. The radiation from a helium dc glow discharge source was polarized (84%) using a reflection type polarizer.

Hancock, W. H.↗

Angular distribution of photoelectrons at 584 A using polarized radiation

Photoelectron angular distributions for Ar, Xe, N2, O2, CO, CO2, and NH3 have been obtained at 584 A by observing the photoelectrons at a fixed angle and simply rotating the plane of polarization of a highly polarized photon source. The radiation from a helium dc glow discharge source was polarized (84%) using a reflection type polarizer

Hancock, W. H.↗

Centrifugal Generator of Filled Spherical Shells

Centrifugal apparatus produces filled spherical shells for wide range of industrial and scientific applications. Rotating container has radially extending nozzle in which centrifugal force draws liquid shell material from container. Liquid shell material fed from outside container and automatically maintained at fixed level. Along axis of nozzle is tube that connects through rotating seal to source of gas or other filler material. Material-flow and rotation rates adjusted to change bubble size.

Wang, T. G.↗

The origin of the diffuse X-ray background

The Einstein Deep Survey fields are used to reexamine the problem of the origin of the extragalactic diffuse X-ray background. An approach based on fluctuation analysis is adopted, and a sophisticated Monte Carlo scheme is used to compare the X-ray images with a variety of models representing point and diffuse source contributions. Results are presented for two classes of models: those which determine the flux cutoff beyond which pointlike sources fail to contribute significantly if the log N-log S slope is fixed at the measured value of -1.5, and those which set limits on the slope of the log N-log S relation below its last measured point at the Deep Survey threshold. In both cases, it is found that the known population of X-ray-emitting quasars and any reasonable extrapolations therefrom do not comprise the entire X-ray background.

Hamilton, T. T.↗

Halotolerant and Resistant to High pH Hydrogenase from Haloalkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans

Hydrogenase is the key enzyme of energetic metabolism in cells, it catalyzing the converse reaction of hydrogen oxidation and responsible for consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins containing either Nickel and Iron, or the only Iron in theirs active center. Hydrogenases have been found in many microorganisms, such as Methanogenic, acetogenic, nitrogen-fixing, photosynthetic and sulfate-reducing bacteria that could utilize the hydrogen as energy source or use it as electron sink. Hydrogenases are subject for wide physiological, biochemical, physicochemical and genetic studies due to theirs abilities produce the molecular hydrogen as alternative source of pure energy. Notwithstanding on enough large quantity of works that deal with intracellular and extrasellular enzymes of halophilic bacteria, the data about hydrogenases and theirs functions of salts practically are absent. The study of hydrogenase in cell-free extracts of extremely halophilic eubacterium Acetohalobium mabaticum showed dramatic increasing activity of the enzyme at high concentrations of NaCl and KCI (close to saturated solution). Here we present the data of free-cells extracted hydrogenase from new haloalkaliphilic sulfate-reducing bacterium Desulfonatronum thiodismutans, which grow on highly miniralized carbonate-bicarbonate medium in salinity range 1 to 7 % and at pH 7.8 - 10.5. Studied enzyme was active in Concentration range from 0 to 4.3 M NaCl with optimum at 1.0 M NaCl. At 1.0 M NaCl the enzyme activity was increased on 20 %, but with changing concentration from 2.1 M to 3.4 M the activity decreased and was kept on constant level. NaHCO3 inhibited hydrogenase activity on more then 30 %. The maximum of enzyme activity was observed at pH 9.5 with limits 7.5 and 11.5 that practically equal to pH optimum of bacterial growth. Therefore the hydrogenase of Desulfanatronum thiodismutans is tolerant to high concentrations of sodium salts and it also resistant to high pH that make it the unique subject for different biochemical research and detects the possibility for biotechnological application.

Detkova, Ekaterina N.↗

Pressure stability in explicitly coupled simulations of poromechanics with application to CO 2 sequestration

We study in detail the pressure stabilizing effects of the non-iterated fixed-stress splitting in poromechanical problems which are nearly undrained and incompressible. When applied in conjunction with a spatial discretization which does not satisfy the discrete inf–sup condition, namely a mixed piecewise linear–piecewise constant spatial discretization, the explicit fixed-stress scheme can have a pressure stabilizing effect in transient problems. This effect disappears, however, upon time step refinement or the attainment of steady state. The interpretation of the scheme as an Augmented Lagrangian method similar to Uzawa iteration for incompressible flow helps explain these results. Moreover, due to the slowly evolving solution within undrained seal regions, we show that the explicit fixed-stress scheme requires very large time steps to reveal its pressure stabilizing effect in examples of geologic CO 2 sequestration. We note that large time steps can result in large errors in drained regions, such as the aquifer or reservoir regions of these examples, and can prevent convergence of nonlinear solvers in the case of multiphase flows, which can make the explicit scheme an unreliable source of pressure stabilization. We conclude by demonstrating that pressure jump stabilization is as effective in the explicit fixed-stress setting as in the fully implicit setting for undrained problems, while maintaining the stability and convergence of the fixed-stress split for drained problems.

58 GEOSCIENCES↗

Design optimization of integrated cooling inserts in modular Fischer-Tropsch reactors

Sustainable production of liquid fuels and feedstocks from atmospheric CO 2 through carbon recycling technologies is necessary to broaden decarbonization efforts and further reduce global emissions. Fischer–Tropsch (FT) reactors can address this challenge by providing storable, high-value liquid hydrocarbon fuels and feedstocks from syngas generated through reductive CO 2 utilization. FT technology, however, is most cost effective at large-scale, fixed-site plants and does not effectively address the smaller, globally distributed CO 2 point sources. Alternatively, smaller, modular reactors can be composed together to the specific scale of the emission source, yielding a flexible solution that enables more widespread deployment. In these modular reactors, thermal management using a finned cooling insert embedded within the catalyst matrix is critical to maintaining the performance and viability. Thus, in this work, topology optimization is used to determine the cooling insert geometry that maximizes reactor productivity while preventing auto-thermal runaway. Optimal designs are generated for varying number of constituent fins and over a range of maximum operating temperatures. Constraints including minimum feature length-scales and prescribed cooling insert material are imposed on the designs to enhance manufacturability. The impact of design features such as insert tapering and increased length scale hierarchy is automatically revealed by the systematic design framework employed. Here, this approach thus generates novel optimal geometries while automating, accelerating, and enhancing the design process compared to traditional heuristic approaches for cooling insert design in modular FT reactors.

30 DIRECT ENERGY CONVERSION↗

Controlled Shifts of X-ray Emission Lines Measured with Transition Edge Sensors at the Advanced Photon Source

The measurement of shifts in the energy of X-ray emission lines is important for understanding the electronic structure and physical properties of materials. In this study, we demonstrate a method using a synchrotron source to introduce controlled eV-scale shifts of a narrow line in between fixed-energy fluorescence lines. We use this to characterize the ability of a hard X-ray superconducting Transition Edge Sensor (TES) array to measure line shifts. Fixed fluorescence lines excited by higher harmonics of the monochromatic X-ray beam are used for online energy calibration, while elastic scattering from the primary harmonic acts as the variable energy emission line under study. We use this method to demonstrate the ability to track shifts in the energy of the elastic scattering line of magnitude smaller than the TES energy resolution, and find we are ultimately limited by our calibration procedure. The method can be applied over a wide X-ray energy range and provides a robust approach for the characterization of the ability of high-resolution detectors to detect X-ray emission line shifts, and the quantitative comparison of energy calibration procedures.

Guruswamy, Tejas (ORCID:0000000241656765)↗

NEMA-Phase Compliant Traffic Signal Controller Module in SUMO

The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp

Wang, Qichao↗

Radio interferometry for international study of the earthquake mechanism

Consideration of the possibility of developing an improved technique for measuring crustal deformations over distances of hundreds to thousands of kilometers to even intercontinental distances. Attention is focused on the uses of very long baseline interferometry in the structuring of a transportable radio interferometer system capable of high-accuracy three-dimensional earth surveying. In particular, the essential elements of a system called astronomical radio interferometric earth surveying are described. This system involves the use of a pair of antennas, one fixed and one portable, which simultaneously receive random radio signals emitted from an extragalactic radio source. A combination of a readily transportable small-diameter dish for use during a limited period at a remote site with a larger-diameter antenna with a better receiver is recommended.

Macdoran, P. F.↗

Static diffusion cloud chambers

The chamber geometry and optical arrangement are described. The supersaturation range is given and consists of readings taken at five fixed points: 0.25%, 0.5%, 0.75%, 1.0%, and 1.25%. The detection system is described including light source, cameras, and photocell detectors. The temperature control and the calibration of the chamber are discussed.

Ayers, G.↗