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At least 937 records · Page 52

Chiral Thirring–Wess model with Faddeevian regularization

Replacing vector type of interaction of the Thirring–Wess model by the chiral type a new model is presented which is termed here as chiral Thirring–Wess model. Ambiguity parameters of regularization are so chosen that the model falls into the Faddeevian class. The resulting Faddeevian class of model in general does not possess Lorentz invariance. However we can exploit the arbitrariness admissible in the ambiguity parameters to relate the quantum mechanically generated ambiguity parameters with the classical parameter involved in the masslike term of the gauge field which helps to maintain physical Lorentz invariance instead of the absence of manifestly Lorentz covariance of the model. The phase space structure and the theoretical spectrum of this class of model have been determined through Dirac’s method of quantization of constraint system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Optimizing Space Data-Communications Scheduling Method and Algorithm with Interference Mitigation, Generalized for a Broad Class of Optimization Problems

NASA's space data-communications infrastructure-the Space Network and the Ground Network-provide scheduled (as well as some limited types of unscheduled) data-communications services to user spacecraft. The Space Network operates several orbiting geostationary platforms (the Tracking and Data Relay Satellite System (TDRSS)), each with its own servicedelivery antennas onboard. The Ground Network operates service-delivery antennas at ground stations located around the world. Together, these networks enable data transfer between user spacecraft and their mission control centers on Earth. Scheduling data-communications events for spacecraft that use the NASA communications infrastructure-the relay satellites and the ground stations-can be accomplished today with software having an operational heritage dating from the 1980s or earlier. An implementation of the scheduling methods and algorithms disclosed and formally specified herein will produce globally optimized schedules with not only optimized service delivery by the space data-communications infrastructure but also optimized satisfaction of all user requirements and prescribed constraints, including radio frequency interference (RFI) constraints. Evolutionary algorithms, a class of probabilistic strategies for searching large solution spaces, is the essential technology invoked and exploited in this disclosure. Also disclosed are secondary methods and algorithms for optimizing the execution efficiency of the schedule-generation algorithms themselves. The scheduling methods and algorithms as presented are adaptable to accommodate the complexity of scheduling the civilian and/or military data-communications infrastructure within the expected range of future users and space- or ground-based service-delivery assets. Finally, the problem itself, and the methods and algorithms, are generalized and specified formally. The generalized methods and algorithms are applicable to a very broad class of combinatorial-optimization problems that encompasses, among many others, the problem of generating optimal space-data communications schedules.

ground stations↗

Surface representations of two- and three-dimensional fluid flow topology

We discuss our work using critical point analysis to generate representations of the vector field topology of numerical flow data sets. Critical points are located and characterized in a two-dimensional domain, which may be either a two-dimensional flow field or the tangential velocity field near a three-dimensional body. Tangent curves are then integrated out along the principal directions of certain classes of critical points. The points and curves are linked to form a skeleton representing the two-dimensional vector field topology. When generated from the tangential velocity field near a body in a three-dimensional flow, the skeleton includes the critical points and curves which provide a basis for analyzing the three-dimensional structure of the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations to generate surfaces representing the topology of the associated flow separations.

Helman, James L.↗

Structure of BTK kinase domain with the second-generation inhibitors acalabrutinib and tirabrutinib

Bruton’s tyrosine kinase (BTK) is the target of the therapeutic agent, Ibrutinib, that treats chronic lymphocyte leukemia (CLL), mantle cell lymphoma (MCL) and other B cell malignancies. Ibrutinib is a first in class, covalent BTK inhibitor that limits B-cell survival and proliferation. Designing new inhibitors of BTK has been an important objective for advancing development of improved therapeutic agents against cancer and autoimmune disorders. Based on the success of Ibrutinib, several second-generation irreversible BTK inhibitors have been developed that exhibit fewer off-target effects. However, the binding-mode and their interaction with Btk have not been experimentally determined and evaluated at atomic resolution. Here we determined the first crystal structure of the BTK kinase domain in complex with acalabrutinib. In addition, we report a structure of the BTK/tirabrutinib complex and compare these structures with previously solved structures. The structures provide insight in the superior selectivity reported for acalabrutinb and guide future BTK inhibitor development.

60 APPLIED LIFE SCIENCES↗

A Model Tree Generator (MTG) Framework for Simulating Hydrologic Systems: Application to Reservoir Routing

Data-driven algorithms have been widely used as effective tools to mimic hydrologic systems. Unlike black-box models, decision tree algorithms offer transparent representations of systems and reveal useful information about the underlying process. A popular class of decision tree models is model tree (MT), which is designed for predicting continuous variables. Most MT algorithms employ an exhaustive search mechanism and a pre-defined splitting criterion to generate a piecewise linear model. However, this approach is computationally intensive, and the selection of the splitting criterion can significantly affect the performance of the generated model. These drawbacks can limit the application of MTs to large datasets. To overcome these shortcomings, a new flexible Model Tree Generator (MTG) framework is introduced here. MTG is equipped with several modules to provide a flexible, efficient, and effective tool for generating MTs. The application of the algorithm is demonstrated through simulation of controlled discharge from several reservoirs across the Contiguous United States (CONUS).

54 ENVIRONMENTAL SCIENCES↗

Progress Toward Generation of a Navier-Stokes Database for a Harrier in Ground Effect

The Harrier YAV-8B aircraft is capable of vertical and short-field take-off and landing (V/STOL) by directing its four exhaust nozzles toward the ground, or conventional flight by rotating its nozzles into a horizontal position. The British Royal Air Force and the United States Marine Corps have used this aircraft for more than 30 years to provide a quick reaction time for troop support, and reduce the need for long runways. The success of this powered-lift (PL) vehicle has also prompted the more recent design of the Joint Strike Fighter (JSF). However there are significant safety issues that must be addressed when operating a PL vehicle in close proximity to the ground. Hot Gas Ingestion (HGI) by the inlets can result in a rapid loss of powered lift; and high-speed jet flows along the ground plane can induce low pressures underneath the vehicle, causing a 'suck-down' effect. Under these conditions, departure from controlled flight may occur. Moreover, unsteady ground vortices and jet fountains can affect the aircraft,s controllability and its proximity to ground troops. The viscous, time-dependent flow fields of PL vehicles are difficult to accurately and efficiently predict using Computational Fluid Dynamics (CFD). A number of researchers have used the time-dependent Reynolds-averaged Navier-Stokes (RANS) equations to compute flows for single and multiple jets in a cross-flow. A few have added some geometric complexity to the problem by computing flows for jet-augmented delta wings near a ground plane. Smith et.al. computed for the first time a single RANS solution about a simplified Harrier. This geometry included a fuselage, wing, leading edge root extension (LERX), inlets, and exhaust nozzles. All of these investigations cite two practical problems with computing these flows: 1) the need for improved solution accuracy; and, 2) the need for faster solution methods. We view the need for faster solution methods as key to improving the solution accuracy and making this class of computation more routine. One can hardly refine grids, explore the use of advanced turbulence models, and generate databases when it takes weeks of dedicated computer time for a single solution. Chaderjian, Ahmad, Pandya, and Murman have focused on reducing the time-to-solution for this very difficult and complex problem through process automation and exploitation of parallel computing. They began with the Harrier geometry reported, and added a deflected wing flap and empennage for greater realism. To date more than 80 solutions have been carried out. This paper will describe this process and progress made in reducing the time required to generate a simple longitudinal force and moment database for a Harrier in ground effect. It shows a typical snap-shot from an unsteady streakline animation, where fluid particles are colored by temperature. The ground vortex and a jet-fountain vortex are highlighted. It also shows a similar streakline image, where HGI occurs due to the vehicle in close proximity to the ground. It is show the mean lift coefficient as a function of angle of attack and height. The angle of attack range was 4 deg less than or = alpha less than or = 10 deg with an increment of 1 degree, and the height range was 10 ft less than or = h less than or = 30ft with an increment of 5 feet. This 35 solution database was extended to over 2500 cases using a monotone cubic-spline interpolation procedure. The suck-down effect (reduction of lift near the ground) is highlighted in the figure. The "cushion effect," the conventional reduction of lift as the vehicle moves out of ground effect, is also indicated. All 35 RANS solutions were obtained using 952 Silicon Graphics Origin 2000 and 3000 processors in dedicated mode for one week. Typically, 112 processors were assigned to each case. Some other cases used fewer processors to utilize all available CPUS. The final paper will report on the automation of the solution process, including: grid generation, job monitoring, solution completion criteria, and post processing. Moreover, improvements in parallel efficiency for a dual time-step algorithm for the RANS equations will also be presented. Results will be discussed in detail using unsteady streakline flow visualization to correlate unsteady flow structures with dominant aerodynamic frequencies. The stability derivatives, CL, and CL, will also be presented.

Chaderjian, Neal M.↗

A case for radio galaxies as the sources of IceCube's astrophysical neutrino flux

We present an argument that radio galaxies (active galaxies with mis-aligned jets) are likely to be the primary sources of the high-energy astrophysical neutrinos observed by IceCube. In particular, if the gamma-ray emission observed from radio galaxies is generated through the interactions of cosmic-ray protons with gas, these interactions can also produce a population of neutrinos with a flux and spectral shape similar to that measured by IceCube. We present a simple physical model in which high-energy cosmic rays are confined within the volumes of radio galaxies, where they interact with gas to generate the observed diffuse fluxes of neutrinos and gamma rays. In addition to simultaneously accounting for the observations of Fermi and IceCube, radio galaxies in this model also represent an attractive class of sources for the highest energy cosmic rays.

79 ASTRONOMY AND ASTROPHYSICS↗

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Topological structure enhanced nanostructure of high temperature polymer exhibiting more than ten times enhancement of dipolar response

Nanofillers in polymer composites will induce interface regions in the polymer with non-uniform nanostructures which can be approximated as multilayer shells surrounding nanofillers. This paper studies topological nanostructures in polymers that interface with one-dimensional (1-D) and zero-dimensional (0-D) nanofillers. This new class of dielectric polymer nanocomposites involves nanofillers at ultra-low volume loading (< 1 vol percent) that generate large dielectric enhancement. The results show that the dipolar response of polyetherimide, a high temperature dielectric polymer, is increased by more than ten times with ultra-low (0.75 vol %) loading of 1-D nanofillers. The results reveal that 1-D nanofillers induce cylindrical shell-topology in the polymer matrix which is more effective in enhancing the high dielectric constant interfacial region than the spherical shell-topology generated by 0-D fillers. Furthermore, the cylindrical shells generated by 1-D fillers provide much higher dielectric enhancement over a broader interfacial region in the polymer matrix, as compared to the spherical shells induced by 0-D nanofillers.

42 ENGINEERING↗

Toughening by Nanodroplets: Polymer–Droplet Biocomposite with Anomalous Toughness

The development of new polymer composites is highly dependent on the design of novel fillers that can bring more benefits in the design and control of structure–property–function than conventional solid particles. Here, inspired by the unique coupling structures of tough mussel byssus, we employ nanodroplets of high-boiling-point oligomers as the liquid filler to fabricate a new class of polymer–droplet composites (PDCs). The combination of nanodroplets and chain end/tail modifier in PDCs finally generates soft-coupling structures with chain ends coupled by the nanodroplets. With this strategy, brittle poly(lactic acid) is successfully transformed into a tough bioplastic with toughness improved by over 2000% via a minimal amount of the modifiers (1.5 wt %). Moreover, the composites show unexpected speed-enhanced energy absorption capability. A soft-coupling toughening mechanism is further proposed for the first time to understand the PDCs’ mechanical properties. This work also indicates the potential of nanodroplets as a new tool for tuning the mechanical properties and even functions of polymer composites.

36 MATERIALS SCIENCE↗

Growth of concomitant laser-driven collisionless and resistive electron filamentation instabilities over large spatiotemporal scales

Collective processes in plasmas often induce microinstabilities that play an important role in many space or laboratory plasma environments. Particularly of note is the Weibel-type current filamentation instability, which is believed to drive the creation of collisionless shocks in weakly magnetized astrophysical plasmas. In this paper, this instability class is studied through interactions of ultraintense and short laser pulses with solid foils, leading to localized generation of megaelectronvolt electrons. Proton radiographic measurements of both low- and high-resistivity targets show two distinct, superimposed electromagnetic field patterns arising from the interpenetration of the megaelectronvolt electrons and the background plasma. Particle-in-cell simulations and theoretical estimates suggest that the collisionless Weibel instability building up in the dilute expanding plasmas formed at the target surfaces causes the observed azimuthally symmetric electromagnetic filaments. For a sufficiently high resistivity of the target foil, an additional resistive instability is triggered in the bulk target, giving rise to radially elongated filaments. The data reveal the growth of both filamentation instabilities over large temporal (tens of picoseconds) and spatial (hundreds of micrometres) scales.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood–Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community’s capacity, with up to 9.9% of fermentation, 6.4% of the Wood–Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

Candidatus↗

Strong-field physics in three-dimensional topological insulators

We investigate theoretically the strong-field regime of light-matter interactions in the topological-insulator class of quantum materials. In particular, we focus on the process of nonperturbative high-order harmonic generation from the paradigmatic three-dimensional topological insulator bismuth selenide (Bi 2 Se 3 ) subjected to intense midinfrared laser fields. We analyze the contributions from the spin-orbit-coupled bulk states and the topological surface bands separately and reveal a major difference in how their harmonic yields depend on the ellipticity of the laser field. Furthermore, bulk harmonics show a monotonic decrease in their yield as the ellipticity increases, in a manner reminiscent of high harmonic generation in gaseous media. However, the surface contribution exhibits a highly nontrivial dependence, culminating with a maximum for circularly polarized fields. We attribute the observed anomalous behavior to (i) the enhanced amplitude and the circular pattern of the interband dipole and the Berry connections in the vicinity of the Dirac point and (ii) the influence of the higher-order, hexagonal warping terms in the Hamiltonian, which are responsible for the hexagonal deformation of the energy surface at higher momenta. The latter are associated directly with spin-orbit-coupling parameters. Our results thus establish the sensitivity of strong-field-driven high harmonic emission to the topology of the band structure as well as to the manifestations of spin-orbit interaction.

74 ATOMIC AND MOLECULAR PHYSICS↗

Walking the ‘design–build–test–learn’ cycle: flux analysis and genetic engineering reveal the pliability of plant central metabolism

Oilseeds are of great economic importance for food and animal feed and their contribution to renewable energy production. Soybean seeds (Glycine max (L.) Merr.) contain c. 40% protein, 20% oil, and 30% carbohydrate (Song et al., 2023). Due to the massive scale of soybean production worldwide, even small improvements in seed protein and oil content make economic sense (Song et al., 2023). Successful manipulation of seed composition largely depends on a thorough understanding of the processes and pathways involved in the biosynthesis of fatty acids and amino acids, which are the building blocks of lipids and proteins. Rational engineering of the synthesis of storage reserves, that is, the rerouting of metabolic flux in central metabolism, is difficult to accomplish due to the complexity of the central metabolic network, the intricate regulation of its enzymes at multiple levels, and the often-unpredictable effects of genetic manipulation (Sweetlove et al., 2017). Therefore, the advancement of our understanding of central metabolism and its control of carbon partitioning requires following an iterative ‘design–build–test–learn’ (DBTL) cycle (Lin & Eudes, 2020) where metabolic flux analysis and hypothesis testing by transgenic approaches are important components. Previous metabolic studies on soybeans using isotopic tracers and metabolic flux analysis have provided insight into how lipid and protein biosynthesis occurs simultaneously during seed development (Allen et al., 2009; Allen & Young, 2013; Kambhampati et al., 2021). In an article published in this issue of New Phytologist, Morley et al. (2023; 1834–1851) put the insights they have gained into the delivery of metabolic precursors and energy cofactors to oil synthesis to the test and arrive at a successful metabolic engineering design. They show that an increase in seed oil content in soybeans can be achieved by overexpression of malic enzyme (ME) during seed development. Malic enzyme refers to a class of decarboxylating malate dehydrogenase enzymes that oxidize malate with NAD + or NADP + as redox cofactor while generating pyruvate and CO 2 . Like higher plants in general, soybean has distinct NADH- or NADPH-producing ME isoforms localized to the cytosol, plastid, or mitochondria (Gerrard Wheeler et al., 2016). As Morley et al. show, an increase in seed oil can be achieved in particular when a NADP+-dependent enzyme isoform (EC 1.1.1.40) is overexpressed in the plastid. Given the complex compartmentalization of pyruvate, malate, and redox metabolism (Fig. 1), increased oil production appears to depend on additional pyruvate and reducing equivalents being produced in the same compartment where de novo fatty acid biosynthesis occurs: the plastid.

59 BASIC BIOLOGICAL SCIENCES↗

Creation of skyrmions in van der Waals ferromagnet Fe 3 GeTe 2 on (Co/Pd) n superlattice

Magnetic skyrmions are topological spin textures, which usually exist in noncentrosymmetric materials where the crystal inversion symmetry breaking generates the so-called Dzyaloshinskii-Moriya interaction. This requirement unfortunately excludes many important magnetic material classes, including the recently found two-dimensional van der Waals (vdW) magnetic materials, which offer unprecedented opportunities for spintronic technology. Using photoemission electron microscopy and Lorentz transmission electron microscopy, we investigated and stabilized Néel-type magnetic skyrmion in vdW ferromagnetic Fe 3 GeTe 2 on top of (Co/Pd) n in which the Fe 3 GeTe 2 has a centrosymmetric crystal structure. We demonstrate that the magnetic coupling between the Fe 3 GeTe 2 and the (Co/Pd) n could create skyrmions in Fe 3 GeTe 2 without the need of an external magnetic field. Our results open exciting opportunities in spintronic research and the engineering of topologically protected nanoscale features by expanding the group of skyrmion host materials to include these previously unknown vdW magnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Experiences Detecting Defective Hardware in Exascale Supercomputers

In May 2022, the newest supercomputer to top the TOP 500 list was Frontier at Oak Ridge National Laboratory, demonstrating the capability of computing more than 1.1 quintillion (1018) floating-point calculations every second. Driving this ground-breaking rate of computing is Frontier’s more than 37,000 graphics processing units (GPUs) and 9,408 central processing units (CPUs). In total, Frontier contains more than 60 million parts. At this scale, the smallest margin of error may generate hundreds of hardware errors across the system. These errors are capable of directly hindering world-class science performed on Frontier if not found. In this work, we describe and evaluate two strategies for finding hardware-level faults in Frontier’s 9,408 compute nodes. There are two strategies developed: the first uses the Slurm scheduler to scavenge available compute time to run the node screen, the second builds upon the lessons learned in the first strategy and enforces a weekly screen of each node. Using June 2023 as a case study, we find that the first scheduling strategy consumed more than ten times the resources as the second scheduling strategy, but successfully detected five hardware defects in Frontier. We summarize the lessons learned while developing and running a node screen on the world’s first exascale supercomputer.

Hagerty, Nick↗