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At least 1,189 records · Page 66

Adaptive two-regime method: Application to front propagation

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al., J. R. Soc., Interface 9, 859 (2012)] to multiscale problems which require a dynamic selection of regions where detailed Brownian dynamics simulation is used. Typical applications include a front propagation or spatio-temporal oscillations. In this paper, the ATRM is used for an in-depth study of front propagation in a stochastic reaction-diffusion system which has its mean-field model given in terms of the Fisher equation [R. Fisher, Ann. Eugen. 7, 355 (1937)]. It exhibits a travelling reaction front which is sensitive to stochastic fluctuations at the leading edge of the wavefront. Previous studies into stochastic effects on the Fisher wave propagation speed have focused on lattice-based models, but there has been limited progress using off-lattice (Brownian dynamics) models, which suffer due to their high computational cost, particularly at the high molecular numbers that are necessary to approach the Fisher mean-field model. By modelling only the wavefront itself with the off-lattice model, it is shown that the ATRM leads to the same Fisher wave results as purely off-lattice models, but at a fraction of the computational cost. The error analysis of the ATRM is also presented for a morphogen gradient model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative resonant soft x-ray reflectivity of ultrathin anisotropic organic layers: Simulation and experiment of PTCDA on Au

Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

STRUCTURE AND EVOLUTION OF CIRCUMBINARY DISKS AROUND SUPERMASSIVE BLACK HOLE BINARIES

We explore properties of circumbinary disks around supermassive black hole (SMBH) binaries in centers of galaxies by reformulating standard viscous disk evolution in terms of the viscous angular momentum flux F{sub J}. If the binary stops gas inflow and opens a cavity in the disk, then the inner disk evolves toward a constant-F{sub J} (rather than a constant M-dot ) state. We compute disk properties in different physical regimes relevant for SMBH binaries, focusing on the gas-assisted evolution of systems starting at separations 10{sup -4} - 10{sup -2} pc, and find the following. (1) Mass pileup at the inner disk edge caused by the tidal barrier accelerates binary inspiral. (2) Binaries can be forced to merge even by a disk with a mass below that of the secondary. (3) Torque on the binary is set non-locally, at radii far larger than the binary semi-major axis; its magnitude does not reflect disk properties in the vicinity of the binary. (4) Binary inspiral exhibits hysteresis-it depends on the past evolution of the disk. (5) The Eddington limit can be important for circumbinary disks even if they accrete at sub-Eddington rates, but only at late stages of the inspiral. (6) Gas overflow across the orbit of the secondary can be important for low secondary mass, high- M-dot systems, but mainly during the inspiral phase dominated by the gravitational wave emission. (7) Circumbinary disks emit more power and have harder spectra than constant M-dot disks; their spectra are very sensitive to the amount of overflow across the secondary orbit.

79 ASTRONOMY AND ASTROPHYSICS↗

Artificial Intelligence for a Resilient and Flexible Power Grid

Recent widespread and extreme natural disasters as well as the drive towards clean sustainable energy sources necessitate a transformational operational and technological approaches to improve power grid resilience. Convergence of artificial intelligence (AI), distributed computing, and connectivity technologies enables these new approaches to deliver a sustainable electric grid. In particular, AI-based techniques can enable proactive decision-making by processing massive amounts of data to deliver intelligence at various levels of the system, edge devices to control room. In this chapter, we will explore the potential applications AI-based technology will unlock and challenges to address to achieve a sustainable, flexible power grid.

Omitaomu, Femi↗

Graph Theory and IC Component Design Analysis

Graph analysis in large integrated circuit (IC) designs is an essential tool for verifying design logic and timing via dynamic timing analysis (DTA). IC designs resemble graphs with each logic gate as a vertex and the conductive connections between gates as edges. Using DTA digital statistical correlations, graph condensation, and graph partitioning, it is possible to identify high-entropy component centers and paths within an IC design. Identification of high-entropy component centers (HECC) enables focused DTA, effectively lowering the computational complexity of DTA on large integrated circuit graphs. In this paper, a devised methodology termed IC layout subgraph component center identification (CCI) is used to identify described. CCI lowers DTA computationally complexity by condensing IC graphs into reduced subgraphs in which dominant logic functions are verified.

42 ENGINEERING↗

Computationally predicted energies and properties of defects in GaN

Recent developments in theoretical techniques have significantly improved the predictive power of density-functional-based calculations. In this article, we discuss how such advancements have enabled improved understanding of native point defects in GaN. We review the methodologies for the calculation of point defects, and discuss how techniques for overcoming the band-gap problem of density functional theory affect native defect calculations. In particular, we examine to what extent calculations performed with semilocal functionals (such as the generalized gradient approximation), combined with correction schemes, can produce accurate results. The properties of vacancy, interstitial, and antisite defects in GaN are described, as well as their interaction with common impurities. We also connect the first-principles results to experimental observations, and discuss how native defects and their complexes impact the performance of nitride devices. Overall, we find that lower-cost functionals, such as the generalized gradient approximation, combined with band-edge correction schemes can produce results that are qualitatively correct. However, important physics may be missed in some important cases, particularly for optical transitions and when carrier localization occurs.

36 MATERIALS SCIENCE↗

High-performance finite-difference time-domain simulations of C-Mod and ITER RF antennas

Finite-difference time-domain methods have, in recent years, developed powerful capabilities for modeling realistic ICRF behavior in fusion plasmas [1, 2, 3, 4]. When coupled with the power of modern high-performance computing platforms, such techniques allow the behavior of antenna near and far fields, and the flow of RF power, to be studied in realistic experimental scenarios at previously inaccessible levels of resolution. In this talk, we present results and 3D animations from high-performance FDTD simulations on the Titan Cray XK7 supercomputer, modeling both Alcator C-Mod’s field-aligned ICRF antenna and the ITER antenna module. Much of this work focuses on scans over edge density, and tailored edge density profiles, to study dispersion and the physics of slow wave excitation in the immediate vicinity of the antenna hardware and SOL. An understanding of the role of the lower-hybrid resonance in low-density scenarios is emerging, and possible implications of this for the NSTX launcher and power balance are also discussed. In addition, we discuss ongoing work centered on using these simulations to estimate sputtering and impurity production, as driven by the self-consistent sheath potentials at antenna surfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A study of defects in iron-based binary alloys by the Mössbauer and positron annihilation spectroscopies

The room temperature positron annihilation lifetime spectra and {sup 57}Fe Mössbauer spectra were measured for pure Fe as well as for iron-based Fe{sub 1−x}Re{sub x}, Fe{sub 1−x}Os{sub x}, Fe{sub 1−x}Mo{sub x}, and Fe{sub 1−x}Cr{sub x} solid solutions, where x is in the range between 0.01 and 0.05. The measurements were performed in order to check if the known from the literature, theoretical calculations on the interactions between vacancies and solute atoms in iron can be supported by the experimental data. The vacancies were created during formation and further mechanical processing of the iron systems under consideration so the spectra mentioned above were collected at least twice for each studied sample synthesized in an arc furnace— after cold rolling to the thickness of about 40 μm as well as after subsequent annealing at 1270 K for 2 h. It was found that only in Fe and the Fe-Cr system the isolated vacancies thermally generated at high temperatures are not observed at the room temperature and cold rolling of the materials leads to creation of another type of vacancies which were associated with edge dislocations. In the case of other cold-rolled systems, positrons detect vacancies of two types mentioned above and Mössbauer nuclei “see” the vacancies mainly in the vicinity of non-iron atoms. This speaks in favour of the suggestion that in iron matrix the solute atoms of Os, Re, and Mo interact attractively with vacancies as it is predicted by theoretical computations and the energy of the interaction is large enough for existing the pairs vacancy-solute atom at the room temperature. On the other hand, the corresponding interaction for Cr atoms is either repulsive or attractive but smaller than that for Os, Re, and Mo atoms. The latter is in agreement with the theoretical calculations.

36 MATERIALS SCIENCE↗

Partnership for Edge Physics Simulation

A major goal of our participation in the Edge Physics Simulation project has been to contribute to the understanding of the self-organization of tokamak turbulence fluctuations resulting in the formation of a staircase structure in the ion temperature. A second important goal is to demonstrate how small scale turbulence in plasmas self-organizes with dynamically driven quasi-stationary flow shear. These goals have been accomplished through the analyses of the statistical properties of XGC1 flux driven Gyrokinetic electrostatic ion temperature gradient (ITG) turbulence simulation data in which neutrals are included. The ITG turbulence data, and in particular fluctuation data, were obtained from a massively parallel flux-driven gyrokinetic full-f particle-in-cell simulation of a DIII-D like equilibrium. Below some the findings are summarized. It was observed that the emergence of staircase structure is related to the variations in the normalized temperature gradient length (R/LT) and the poloidal flow shear. Average turbulence intensity is found to be large in the vicinity of minima in R/LTi, where ITG growth is expected to be lower. The distributions of the occurrences of potential fluctuation are found to be Gaussian away from the staircase-step locations, but they are found to be non-Gaussian in the vicinity of staircase-step locations. The results of analytically derived expressions for the distribution of the occurrences of turbulence intensity and intensity flux were compared with the corresponding quantities computed using XGC1 simulation data and good agreement is found. The derived expressions predicts inward and outward propagation of turbulence intensity flux in an intermittent fashion. The outward propagation of turbulence intensity flux occurs at staircase-step locations and is related to the change in poloidal flow velocity shear and to the change in the ion temperature gradient. The standard deviation, skewness and kurtosis for turbulence quantities were computed and found to be large in the vicinity of the staircase-step structures. Large values of skewness and kurtosis can be explained by a temporary opening and closing of the structure which allows turbulence intensity events to propagate. The staircase patterns may reduce the ion heat transport and a manipulation of these patterns may be used to optimize heat transport in tokamaks. An additional objective of the research in support of the Edge Physics Simulation initiative has been to improve the understanding of scrape-off layer thermal transport. In planning experiments and designing future tokamaks, it is important to understand the physical effects that contribute to divertor heat-load fluxes. The research accomplished will contribute to developing new models for the scrape-off layer region. The XGC0 code was used to compute the heat fluxes and the heat-load width in the outer divertor plates of C-Mod and DIII-D tokamaks. It was observed that the width of the XGC0 neoclassical heat-load was approximately inversely proportional to the total plasma current. Anomalous transport in the H-mode pedestal region of five Alcator C-Mod discharges, representing a collisionality scan, was analyzed. The understanding of anomalous transport in the pedestal region is important for the development of a comprehensive model for the H-mode pedestal slope. It was found that the electron thermal anomalous diffusivities at the pedestal top increase with the electron collisionality. This dependence can point to the DRIBM as the modes that drive the anomalous transport in the plasma edge of highly collisional discharges. The effects of plasma shaping on the H-mode pedestal structure was also investigated. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities were discussed. For the discharges with higher elongation, it was found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continued to evolve to higher pedestal pressures and bootstrap currents until the peeling ballooning stability conditions were satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes were triggered at earlier times. The plasma elongation was found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency was large, and the H-mode pedestal evolves rapidly. It was found that the temperature of neutrals in the scrape-off-layer region can affect the dynamics of the H-mode pedestal buildup. However, the final pedestal profiles were nearly independent of the neutral temperature. The elongation and triangularity affected the pedestal widths of plasma density and electron temperature profiles differently. This study illustrated a new mechanism for controlling the pedestal bootstrap current and the pedestal stability.

97 MATHEMATICS AND COMPUTING↗

Feature Selection and Inferential Procedures for Video Data [Slides]

With the rise of electronic and high-dimensional data, new and innovative feature detection and statistical methods are required to perform accurate and meaningful statistical analysis of these datasets that provide unique statistical challenges. In the area of feature detection, much of the recent feature detection research in the computer vision community has focused on deep learning methods, which require large amounts of labeled training data. However, in many application areas, training data is very limited and often difficult to obtain. We develop methods for fast, unsupervised, precise feature detection for video data based on optical flows, edge detection, and clustering methods. We also use pretrained neural networks and interpretable linear models to extract features using very limited training data. In the area of statistics, while high-dimensional data analysis has been a main focus of recent statistical methodological research, much focus has been on populations of high-dimensional vectors, rather than populations of high-dimensional tensors, which are three-dimensional arrays that can be used to model dependent images, such as images taken of the same person or ripped video frames. Our feature detection method is a non-model-based method that fusses information from dense optical flow, raw image pixels, and frame differences to generate detections. Our hypothesis testing methods are based on the assumption that dependent images are concatenated into a tensor that follows a tensor normal distribution, and from this assumption, we derive likelihood-ratio, score, and regression-based tests for one- and multiple-sample testing problems. Our methods will be illustrated on simulated and real datasets. We conclude this report with comments on the relationship between feature detection and hypothesis testing methods.

97 MATHEMATICS AND COMPUTING↗

Empirical Refinement of the GADRAS Detector Response Function

The Gamma Detector Response and Analysis Software (GADRAS) was augmented to enable empirical refinement of the Detector Response Function (DRF) for gamma-ray detectors. This capability is included in GADRAS starting with Version 18.8.2, which was released in February 2019 Empirical refinement enables improved computational accuracy for gamma-ray spectra when detectors exhibit characteristics that are essentially unique to a particular sensor. This report discusses how to perform the empirical refinement, and examples are presented for the following scenarios where empirical refinement is appropriate: Large plastic scintillators, which are generally composed of polyvinyl toluene (PVT), often exhibit low-energy peaks that are not associated with incident gamma rays. Regardless of whether they are artifacts produced by poor light collection or pulse processing methods, accurate spectral synthesis requires replication of these features; Some detectors, particularly those using Silicon Photomultipliers (SiPM), exhibit energy shifts of Compton edges and escape peaks relative to the same scintillator material attached to a photomultiplier tube. Empirical refinement compensates for these effects, which derive from nonlinearities in the detector response; The change in the DRF as a function of displacement of the source relative to the detector axis cannot always be replicated adequately using only the few shielding parameters that are used by the response function. Empirical refinement enables improved accuracy for computation of spectra during linear transits or when the detector is close to a large radiation source. This is a particularly important consideration for collimated detectors; and, Gamma-ray imagers exhibit complex relationships between spectral response and spatial locations. Empirical refinement enables substantial improvement of the DRF accuracy for imagers.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example

Although the critical role of allostery in controlling enzymatic processes is well appreciated, there is a current dearth in our understanding of its underlying mechanisms, including communication between binding sites. One potential key aspect of inter-site communication is the mechanical coupling between residues in a protein. Here, we introduce a graph-based computational approach to investigate the mechanical coupling between distant parts of a protein, highlighting effective pathways via which protein motion can transfer energy between sites. In this method, each residue is treated as a node on a weighted, undirected graph, where the edges are defined by locally correlated motions of those residues and weighted by the strength of the correlation. The method was validated against experimental data on allosteric regulation in the human liver pyruvate kinase as obtained from full-protein alanine-scanning mutagenesis (systematic mutation) studies. The method provides semi-quantitative information on the regulatory importance of specific structural elements. It is shown that these elements are key for the mechanical coupling between distant parts of the protein by providing effective pathway for energy transfer. It is also shown that, while there are a multitude of energy transfer pathways between distant parts of a protein, these pathways share a few common nodes that represent effective “chokepoints.”

Johnson, Lewis E.↗

Mapping Metals Incorporation of a Whole Single Catalyst Particle Using Element Specific X-ray Nanotomography

Full-field transmission X-ray microscopy has been used to determine the 3D structure of a whole individual fluid catalytic cracking (FCC) particle at high spatial resolution and in a fast, noninvasive manner, maintaining the full integrity of the particle. Using X-ray absorption mosaic imaging to combine multiple fields of view, computed tomography was performed to visualize the macropore structure of the catalyst and its availability for mass transport. We mapped the relative spatial distributions of Ni and Fe using multiple-energy tomography at the respective X-ray absorption K-edges and correlated these distributions with porosity and permeability of an equilibrated catalyst (E-cat) particle. Both metals were found to accumulate in outer layers of the particle, effectively decreasing porosity by clogging of pores and eventually restricting access into the FCC particle.

02 PETROLEUM↗

Manufacture of gradient micro-structures of magnesium alloys using two stage extrusion dies

This paper aims to manufacture magnesium alloy metals with gradient micro-structures using hot extrusion process. The extrusion die was designed to have a straight channel part combined with a conical part. Materials pushed through this specially-designed die generate a non-uniform velocity distribution at cross sections inside the die and result in different strain and strain rate distributions. Accordingly, a gradient microstructure product can be obtained. Using the finite element analysis, the forming temperature, effective strain, and effective strain rate distributions at the die exit were firstly discussed for various inclination angles in the conical die. Then, hot extrusion experiments with a two stage die were conducted to obtain magnesium alloy products with gradient micro-structures. The effects of the inclination angle on the grain size distribution at cross sections of the products were also discussed. Using a die of an inclination angle of 15°, gradient micro-structures of the grain size decreasing gradually from 17 μm at the center to 4 μm at the edge of product were achieved.

36 MATERIALS SCIENCE↗

Modeling of convective cells, turbulence, and transport induced by a radio-frequency antenna in the tokamak boundary plasma

The edge turbulence model Hermes (Dudson et al 2017 Plasma Phys. Control. Fusion 59 05401) is set up for plasma boundary simulations with an radiofrequency (RF) antenna, using parameters characteristic of a tokamak edge. Cartesian slab geometry is used with thin plate limiters representing the ion cyclotron range of frequency (ICRF) antenna side-wall limiters. Ad-hoc DC electric biasing of the limiters, motivated by calculations with VSim (Nieter et al 2004 J. Comput. Phys. 196 448), represents an induced RF sheath rectified potential in the plasma turbulence model. Flux-driven turbulence simulations demonstrate a realistic distribution of plasma profiles and fluctuations. There is a clear effect of the antenna sheath voltage leading to formation of convective cells; bias-induced convective transport flattens the scrape-off layer density profile and fluctuations penetrate into the shadow region of the limiters as the bias voltage increases. Turbulent transport for impurity ions is inferred by following ion trajectories in the simulated plasma turbulence fields, showing Bohm-like effective diffusion rates. All in all, the model elucidates the key physical phenomena governing the effects of ICRF-induced antenna biasing on the tokamak boundary plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

First-principles simulations of 2-D semiconductor devices: Mobility, I-V characteristics, and contact resistance

We report in this paper ab-initio quantum transport simulations of different types of single-layer 2-D semiconductors: transition metal and group IV dichalcogenides in the 2H or 1T phase as well as black phosphorus. The electron and hole phonon-limited mobilities of eight selected 2-D crystals are first analyzed before using these materials as n- or p-type channels of ultra-scaled single-gate transistors, computing their I-V characteristics in the presence of electron-phonon scattering, and comparing them to each other. Finally, the properties of metal-MoS 2 contacts are investigated. It is revealed that the current tends to flow at the edge of the metal layer before entering the semiconductor, thus limiting the injection efficiency.

Luisier, M.↗

Framework Application for Core Edge Transport Simulations (FACETS) Performance Analysis (Final Report)

The goal of the FACETS project (Framework Application for Core-Edge Transport Simulations) was to provide a multiphysics, parallel framework application (FACETS) that will enable whole-device modeling for the U.S. fusion program, to provide the modeling infrastructure needed for ITER, the next step fusion confinement device. Through use of modern computational methods, including component technology and object oriented design, FACETS is able to switch from one model to another for a given aspect of the physics in a flexible manner. This enables use of simplified models for rapid turnaround or high-fidelity models that can take advantage of the largest supercomputer hardware. FACETS does so in a heterogeneous parallel context, where different parts of the application execute in parallel by utilizing task farming, domain decomposition, and/or pipelining as needed and applicable. ParaTools, Inc. was tasked with supporting the performance analysis and tuning of the FACETS components and framework in order to achieve the parallel scaling goals of the project. The TAU Performance System® was used for instrumentation, measurement, archiving, and profile / tracing analysis. ParaTools, Inc. also assisted in FACETS performance engineering efforts. Through the use of the TAU Performance System, ParaTools provided instrumentation, measurement, analysis and archival support for the FACETS project. Performance optimization of key components has yielded significant performance speedups. TAU was integrated into the FACETS build for both the full coupled application and the UEDGE component. The performance database provided archival storage of the performance regression testing data generated by the project, and helped to track improvements in the software development.

97 MATHEMATICS AND COMPUTING↗