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At least 685 records · Page 38

In Situ Analysis and Visualization of Fusion Simulations: Lessons Learned

The trends in high performance computing, where far more data can be computed that can ever be stored, have made in situ techniques an important area of research and development. Simulation campaigns, where domain scientists work with computer scientists to run a simulation and perform in situ analysis and visualization are important, and complex undertakings. In this paper we report our experiences performing in situ analysis and visualization on two campaigns. The two campaigns were related, but had important differences in terms of the codes that were used, the types of analysis and visualization required, and the visualization tools used. Further, we report the lessons learned from each campaign.

Kim, Mark B.↗

Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform

Abstract Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae . We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.

09 BIOMASS FUELS↗

Reinforcement learning for block decomposition of planar CAD models

Abstract The problem of hexahedral mesh generation of general CAD models has vexed researchers for over 3 decades and analysts often spend more than 50% of the design-analysis cycle time decomposing complex models into simpler blocks meshable by existing techniques. The decomposed blocks are required for generating good quality meshes (tilings of quadrilaterals or hexahedra) suitable for numerical simulations of physical systems governed by conservation laws. We present a novel AI-assisted method for decomposing (segmenting) planar CAD (computer-aided design) models into well shaped rectangular blocks. Even though the simple examples presented here can also be meshed using many conventional methods, we believe this work is proof-of-principle of a AI-based decomposition method that can eventually be generalized to complex 2D and 3D CAD models. Our method uses reinforcement learning to train an agent to perform a series of optimal cuts on the CAD model that result in a good quality block decomposition. We show that the agent quickly learns an effective strategy for picking the location and direction of the cuts and maximizing its rewards. This paper is the first successful demonstration of an agent autonomously learning how to perform this block decomposition task effectively, thereby holding the promise of a viable method to automate this challenging process for more complex cases.

97 MATHEMATICS AND COMPUTING↗

A Regularized Variance-Reduced Modified Extragradient Method for Stochastic Hierarchical Games

We consider an N -player hierarchical game in which the i th player’s objective comprises of an expectation-valued term, parametrized by rival decisions, and a hierarchical term. Such a framework allows for capturing a broad range of stochastic hierarchical optimization problems, Stackelberg equilibrium problems, and leader-follower games. We develop an iteratively regularized and smoothed variance-reduced modified extragradient framework for iteratively approaching hierarchical equilibria in a stochastic setting. We equip our analysis with rate statements, complexity guarantees, and almost-sure convergence results. We then extend these statements to settings where the lower-level problem is solved inexactly and provide the corresponding rate and complexity statements. Our model framework encompasses many game theoretic equilibrium problems studied in the context of power markets. We present a realistic application to the study of virtual power plants, emphasizing the role of hierarchical decision making and regularization. Preliminary numerics suggest that empirical behavior compares well with theoretical guarantees.

Tikhonov regularization↗

Radiochronometric discordance in cast uranium metal: a multi-laboratory intercomparison exercise

Here, the model age of a nuclear material is crucial in nuclear forensic analysis. Uranium metals with complex production histories often exhibit discordant model ages from the 230 Th– 234 U and 231 Pa– 235 U chronometers. Recent studies involving targeted uranium metal castings have enhanced our understanding of decay product behavior during casting, aiding nuclear forensic interpretation. Building on this prior work, forensics laboratories at Atomic Weapons Establishment (AWE), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL) conducted an interlaboratory comparison to investigate spatial heterogeneity in uranium metal cast under controlled conditions. Each laboratory measured samples of a mixed feedstock and its corresponding cast product. This work furthers our understanding of discordant model ages and the use of discordance as a signature to enhance confidence in interpretations of radiochronometric data for nuclear forensics.

230Th/234U↗

Effect of Tool Offset and Rotational Speed in Dissimilar Friction Stir Welding of AISI 304 Stainless Steel and Mild Steel

In the present study, dissimilar friction stir welding was carried out between stainless steel (UNS S30400) and mild steel (UNS G10080) plates of 4 mm thickness using a tungsten carbide tool. The influence of tool rotational speeds (600, 875 rpm) and tool offsets (0.6, 1.2 mm) on mechanical properties, i.e., hardness, tensile strength, and impact toughness of welded joints was investigated. Maximum tensile strength of the joint was about 107.6% of the mild steel under rotational speed of 875 rpm and tool offset of 1.2 mm. The maximum hardness reached in the stir zone was about 281 HV{sub 0.5} due to the phase transformations and grain refinement. Charpy’s notch toughness of the welded joints was observed lower than the base materials. The microstructural characterizations were carried by using an optical microscope, and FESEM–EDS analysis which revealed the complex material mixing and material movement during the welding. Tungsten-rich bands were observed in the weld micrograph especially toward the advancing side. During this study, various wear mechanisms like oxidation wear, abrasive wear, and adhesion wear were responsible for the degradation of tungsten carbide tool.

36 MATERIALS SCIENCE↗

IDEAL: Images Across Domains, Experiments, Algorithms and Learning

Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this article, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

97 MATHEMATICS AND COMPUTING↗

Differential Mobility Spectrometry for Improved Selectivity in Hydrophilic Interaction Liquid Chromatography-Tandem Mass Spectrometry Analysis of Paralytic Shellfish Toxins

Paralytic shellfish toxins (PSTs) are neurotoxins produced by dinoflagellates and cyanobacteria that cause paralytic shellfish poisoning in humans. PST quantitation by LC-MS is challenging because of their high polarity, lability as gas-phase ions, and large number of potentially interfering analogues. Differential mobility spectrometry (DMS) has the potential to improve the performance of LC-MS methods for PSTs in terms of selectivity and limits of detection. This work describes a comprehensive investigation of the separation of 16 regulated PSTs by DMS and the development of highly selective LC-DMS-MS methods for PST quantitation. The effects of all DMS parameters on the separation of PSTs from one another were first investigated in detail. The labile nature of 11α-gonyautoxin epimers gave unique insight into fragmentation of labile analytes before, during, and after the DMS analyzer. Two sets of DMS parameters were identified that either optimized the resolution of PSTs from one another or transmitted them at a limited number of compensation voltage (CV) values corresponding to structural subclasses. These were used to develop multidimensional LC-DMS-MS/MS methods using existing HILIC-MS/MS parameters. In both cases, improved selectivity was observed when using DMS, and the quantitative capabilities of a rapid UPLC-DMS-MS/MS method were evaluated. Limits of detection of the developed method were similar to those without DMS, and differences were highly analyte-dependant. Analysis of shellfish matrix reference materials showed good agreement with established methods. The developed methods will be useful in cases where specific matrix interferences are encountered in the LC-MS/MS analysis of PSTs in complex biological samples. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

In-service corrosion and grain boundary oxidation in neutron-irradiated 316 stainless steel baffle-former bolts

Reactor core internal components such as baffle-former bolts (BFBs) are subjected to significant mechanical stress, corrosive environment, and neutron irradiation from the reactor core during the plant operation. Over the long operation period, these conditions lead to potential degradation and of the bolts. In this work, characterization was performed on the oxidized surface of stainless steel BFBs harvested from a commercial pressurized water reactor (PWR) after 40 years of operation. The analysis shows that a complex multilayered surface oxide with six identified layers formed that is different from 2-layer structure commonly observed in model experiments. The oxide varies by composition – predominantly Fe, Cr, and Ni, grain size, and phase, and has features resembling both unirradiated and radiation/ corrosion experiments likely due to the low radiation flux compared to ion-irradiation or the test reactor radiation. In addition, grain boundary oxidative attack featured a pathway for Fe and other elements to move from the metal matrix to the outermost oxide. In conclusion, the results help assess PWR lifetime extension, put into context previous experimental studies, and provide input for designing experiments combining radiation and corrosion effects.

Baffle-former bolt↗

Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex

CD27 is a tumor necrosis factor (TNF) receptor, which stimulates lymphocytes and promotes their differentiation upon activation by TNF ligand CD70. Activation of the CD27 receptor provides a costimulatory signal to promote T cell, B cell, and NK cell activity to facilitate antitumor and anti-infection immunity. Aberrant increased and focused expression of CD70 on many tumor cells renders CD70 an attractive therapeutic target for direct tumor killing. However, despite their use as drug targets to treat cancers, the molecular basis and atomic details of CD27 and CD70 interaction remain elusive. Here we report the crystal structure of human CD27 in complex with human CD70. Analysis of our structure shows that CD70 adopts a classical TNF ligand homotrimeric assembly to engage CD27 receptors in a 3:3 stoichiometry. By combining structural and rational mutagenesis data with reported disease-correlated mutations, we identified the key amino acid residues of CD27 and CD70 that control this interaction. We also report increased potency for plate-bound CD70 constructs compared with solution-phase ligand in a functional activity to stimulate T-cells in vitro. These findings offer new mechanistic insight into this critical costimulatory interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reduced-order modeling on a near-term quantum computer

Quantum computing is an advancing area of research in which computer hardware and algorithms are developed to take advantage of quantum mechanical phenomena. In recent studies, quantum algorithms have shown promise in solving linear systems of equations as well as systems of linear ordinary differential equations (ODEs) and partial differential equations (PDEs). Reducedorder modeling (ROM) algorithms for studying fluid dynamics have shown success in identifying linear operators that can describe flowfields, where dynamic mode decomposition (DMD) is a particularly useful method in which a linear operator is identified from data. In this work, DMD is reformulated as an optimization problem to propagate the state of the linearized dynamical system on a quantum computer. This reformulation was chosen as a means of facilitating implementation on a near-term quantum computer. Quadratic unconstrained binary optimization (QUBO), a technique for optimizing quadratic polynomials in binary variables, allows for quantum annealing algorithms to be applied. A quantum circuit model (quantum approximation optimization algorithm, QAOA) is utilized to obtain predictions of the state trajectories. Results are shown for the quantum-ROM predictions for flow over a 2D cylinder at Re = 220 and flow over a NACA0009 airfoil at Re = 500 and α = 15°. The quantum-ROM predictions are found to depend on the number of bits utilized for a fixed point representation and the truncation level of the DMD model. Comparisons with DMD predictions from a classical computer algorithm are made, as well as an analysis of the computational complexity and prospects for future, more fault-tolerant quantum computers.

97 MATHEMATICS AND COMPUTING↗

Homochiral coordination polymers with helixes and metal clusters based on lactate derivatives

Utilizing the lactic acid derivatives (R)-4-(1-carboxyethoxy)benzoic acid (denoted: (R)-H{sub 2}CBA) and (S)-4-(1-carboxyethoxy)benzoic acid (denoted: (S)-H{sub 2}CBA)as chiral linkers to self-assemble with 4, 4′-bipyridine (denoted: BIP) and Cd(II) ions, a couple of three-dimensional homochiral coordination polymers, namely [Cd{sub 3}((R)-CBA){sub 3} (BIP){sub 2}(H{sub 2}O)]·xGuest (1-D) and [Cd{sub 3}((S)-CBA){sub 3}(BIP){sub 2}(H{sub 2}O)]·xGuest (1-L), have been synthesized under solvothermal reaction condition. Single crystal X-ray diffraction analysis reveals the two complexes contain single helical chains based on enantiopure ligands and cadmium clusters. Moreover, some physical characteristics such as PXRD, thermal stability, solid-state circular dichroism (CD) and luminescent were also investigated. - Graphical abstract: Utilizing enantiomeric lactic acid derivatives (R)-H{sub 2}CBA and (S)-H{sub 2}CBA to assemble with Cd{sup 2+} ions and ancillary BIP ligands, a couple of 3D homochiral coordination polymers with metal clusters and helical chains have been prepared by hydrothermal reaction. - Highlights: • Chiral lactic acid derivative. • Enantiomeric coordination polymer. • Helical chain. • Trinuclear cadmium cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide

The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. Here we investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH2, motivated by prior studies that demonstrated that this amphipathic beta strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five beta sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel beta sheets, while the outer walls are antiparallel beta sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectrally-dependent positive and negative photo-plastic effects in CdZnTe and CdZnTeSe

We studied the Vickers microhardness HV0.025 of CdZnTe and CdZnTeSe samples upon illumination with quasi-monochromatic light with wavelengths ranging between 750 and 1540 nm. We observed that light with a wavelength close to or above the bandgap of the samples results in a positive photo-plastic effect (hardening), and light in the spectral range well below the band gap can lead both to positive or negative effects depending on the parameters of deep levels in the bandgap. We performed measurements of spectrally dependent photoconductivity and compared them with HV0.025. Based on the analysis, we propose a complex qualitative model explaining the spectral dependence of HV0.025 by the charging and neutralization of deep levels by optical transitions between the valence and conduction bands and between the bands and deep levels in the band gap. Tuning of parameters of deep levels could be used to control the sign and magnitude of the photo-plastic effect.

36 MATERIALS SCIENCE↗

Numerical analysis and wave tank validation on the optimal design of a two-body wave energy converter

To improve the performance of a ‘point absorber’ type wave energy converter (WEC), an additional submerged body can be deployed. The submerged body can be used to increase the equivalent excitation force on the WEC, as well as provide resonance tuning. This paper presents numerical analysis and experimental validation of a two-body point absorber type WEC using a mechanical motion rectifier (MMR) based power takeoff. The two-body point absorber consists of a floating buoy connected to a neutrally buoyant submerged body via the power-takeoff. The mechanical motion rectifier and a ball screw translate the relative heave motion of the two bodies into unidirectional rotation, which in turn spins a generator. Frequency domain analysis suggests there is an optimal submerged body mass for maximum WEC power absorption. Regular wave simulations in the time domain are compared to the results obtained in the frequency domain. While the time domain and frequency domain results predict the same optimal mass ratio, time domain analysis provides a more complex and accurate power result. To validate the time domain model, experimental wave tank testing is conducted using a 1:30 scale model WEC. The experiment shows the two-body WEC can produce twice the amount of power as the single-body WEC with same floating buoy and can be further increased by PTO design and power electronics optimization. Furthermore, wave tank testing shows the two-body WEC has a capture width ratio up to 58% at 59 kW/m and 51% at 36 kW/m.

16 TIDAL AND WAVE POWER↗

Modeling the direct sun component in buildings using matrix algebraic approaches: Methods and validation

Simulation tools that enable annual energy performance analysis of optically-complex fenestration systems have been widely adopted by the building industry for use in building design, code development, and the development of rating and certification programs for commercially-available shading and daylighting products. The tools rely on a three-phase matrix operation to compute solar heat gains, using as input low-resolution bidirectional scattering distribution function (BSDF) data (10–15° angular resolution; BSDF data define the angle-dependent behavior of light-scattering materials and systems). Measurement standards and product libraries for BSDF data are undergoing development to support solar heat gain calculations. Simulation of other metrics such as discomfort glare, annual solar exposure, and potentially thermal discomfort, however, require algorithms and BSDF input data that more accurately model the spatial distribution of transmitted and reflected irradiance or illuminance from the sun (0.5° resolution). This study describes such algorithms and input data, then validates the tools (i.e., an interpolation tool for measured BSDF data and the five-phase method) through comparisons with ray-tracing simulations and field monitored data from a full-scale testbed. Simulations of daylight-redirecting films, a micro-louvered screen, and venetian blinds using variable resolution, tensor tree BSDF input data derived from interpolated scanning goniophotometer measurements were shown to agree with field monitored data to within 20% for greater than 75% of the measurement period for illuminance-based performance parameters. The three-phase method delivered significantly less accurate results. We discuss the ramifications of these findings on industry and provide recommendations to increase end user awareness of the current limitations of existing software tools and BSDF product libraries.

14 SOLAR ENERGY↗