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At least 19 records

A learned closure method applied to phase mixing in a turbulent gradient-driven gyrokinetic system in simple geometry

We present a new method for formulating closures that learn from kinetic simulation data. We apply this method to phase mixing in a simple gyrokinetic turbulent system – temperature-gradient-driven turbulence in an unsheared slab. The closure, called the learned multi-mode (LMM) closure, is constructed by, first, extracting an optimal basis from a nonlinear kinetic simulation using singular value decomposition. Subsequent nonlinear fluid simulations are projected onto this basis and the results are used to formulate the closure. We compare the closure with other closures schemes over a broad range of the relevant two-dimensional parameter space (collisionality and gradient drive). We find that the turbulent kinetic system produces phase-mixing rates much lower than the linear expectations, which the LMM closure is capable of capturing. We also compare radial heat fluxes. A Hammett–Perkins closure, generalized to include collisional effects, is quite successful throughout the parameter space, producing ${\sim }14\,\%$ root-mean-square (r.m.s.) error. The LMM closure is also very effective: when trained at three (two) points (in a 35 point parameter grid), the LMM closure produces $8\,\%$ ( $12\,\%$ ) r.m.s. errors. The LMM procedure can be readily generalized to other closure problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Revisiting leptonic nonunitarity

In the presence of extra neutrino states at high scales, the low-energy effective 3 × 3 leptonic mixing matrix (LMM) is in general nonunitary. We revisit the question of what is our current knowledge of individual LMM matrix elements without assuming unitarity. We first demonstrate that a minimal set of experimental constraints suffices in bounding LMM nonunitarity parameters to the level of O ( 10 − 3 ) , without the use of neutrino oscillation data. We then revisit oscillation results as a complementary cross-check, using different physics and different experimental techniques to probe a similar parameter space. We correct some common misconceptions in the neutrino nonunitarity literature resulting from an incautious treatment of input parameters. We find that neutrino oscillation experiments can constrain LMM nonclosure, but, contrary to claims in the literature, are completely insensitive to the overall normalization of the LMM. Thus, we conclude that oscillation experiments, including the future DUNE experiment, have no power in excluding nonunitarity altogether. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Development of a discontinuous approach for modeling fluid flow in heterogeneous media using the numerical manifold method

Summary In the numerical modeling of fluid flow in heterogeneous geological media, large material contrasts associated with complexly intersected material interfaces are challenging, not only related to mesh discretization but also for the accurate realization of the corresponding boundary constraints. To address these challenges, we developed a discontinuous approach for modeling fluid flow in heterogeneous media using the numerical manifold method (NMM) and the Lagrange multiplier method (LMM) for modeling boundary constraints. The advantages of NMM include meshing efficiency with fixed mathematical grids (covers), the convenience of increasing the approximation precision, and the high integration precision provided by simplex integration. In this discontinuous approach, the elements intersected by material interfaces are divided into different elements and linked together using the LMM. We derive and compare different forms of LMMs and arrive at a new LMM that is efficient in terms of not requiring additional Lagrange multiplier topology, yet stringently derived by physical principles, and accurate in numerical performance. To demonstrate the accuracy and efficiency of the NMM with the developed LMM for boundary constraints, we simulate a number of verification and demonstration examples, involving a Dirichlet boundary condition and dense and intersected material interfaces. Last, we applied the developed model for modeling fluid flow in heterogeneous media with several material zones containing a fault and an opening. We show that the developed discontinuous approach is very suitable for modeling fluid flow in strongly heterogeneous media with good accuracy for large material contrasts, complex Dirichlet boundary conditions, or complexly intersected material interfaces. Copyright © 2015 John Wiley & Sons, Ltd.

Hu, Mengsu↗

High Performance Flow Battery with Inexpensive Inorganic Reactants: DAYS Program (Final Technical Report)

RTRC’s DAYS projects focused on new flow battery (FB) chemistries for long duration energy storage: one that pairs aqueous polysulfide and manganese active materials in strongly alkaline electrolytes (S/Mn); another explores ligand-modified metal (LMM) chemistries in moderate pH electrolyte conditions. The S/Mn chemistry met durability targets by running for over 500 cycles and 1000 hours. Combined with this durability, power densities of up to 60 mW/cm2 at 80% round-trip efficiency, and exceptionally low-cost S and Mn active materials, the S/Mn FB offers a pathway to meeting the <5¢/kW-hr levelized cost of storage (LCOS) target first proposed by the DAYS Program and accepted by the DOE Energy Storage Grand Challenge. The LMM chemistry made impressive progress as well, including durability tests that retained performance over 600 hours of cycling. Cell optimization allowed this chemistry to operate as high as 500 mW/cm2 at 80% round-trip efficiency, nearly 10x the power density of S/Mn and comparable to the power density achieved in RTRC’s flow battery stacks using acidic vanadium battery solutions. This enabled the LMM chemistry to also offer a pathway to the <5¢/kW-hr LCOS DAYS and DOE targets. The promising results from the LMM chemistry have led to a recent DOE AMO award to advance the technology to a 5 kW, 20 kW-hr prototype.

25 ENERGY STORAGE↗

X-ray photoelectron spectroscopic study on interface bonding between Pt and Zn- and O-terminated ZnO

Interface bonding between Pt and Zn- and O-terminated ZnO surfaces was investigated by precise analysis of x-ray photoelectron spectra. The interfaces were formed by vapor depositing Pt onto the ZnO surfaces in ultrahigh vacuum. The changes in the Zn 2p{sub 3/2}, O 1s, Zn LMM Auger, and Pt 4f{sub 7/2} spectra upon Pt deposition were observed. The changes in the shape of the Zn LMM spectra and the shifts in the binding energy of Zn 2p{sub 3/2} and O 1s revealed that there was a metallic Zn component in the Zn LMM and Zn 2p{sub 3/2} spectra for Zn-terminated ZnO and a Pt-O component in the O 1s spectra for both Zn- and O-terminated ZnO. Peaks were fitted with multiple components accordingly. The binding energy shifts of Zn 2p{sub 3/2} and O 1s for the ZnO component were almost the same, which confirmed that the fitting was reasonable. From the fitting results, the interface bonding was concluded to be O-terminated, i.e., Zn-O-Pt bond formation occurred at the interface for both Zn- and O-terminated ZnO. This clearly demonstrated that the stable interface bonding occurring between Pt and ZnO is Zn-O-Pt bonding whether the ZnO substrate is initially Zn-terminated or O-terminated.

36 MATERIALS SCIENCE↗

Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum

Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.

genomics↗

A composite approach towards a complete model of the myosin rod

Sarcomeric myosins have the remarkable ability to form regular bipolar thick filaments that, together with actin thin filaments, constitute the fundamental contractile unit of skeletal and cardiac muscle. This has been established for over 50 years and yet a molecular model for the thick filament has not been attained. In part this is due to the lack of a detailed molecular model for the coiled–coil that constitutes the myosin rod. The ability to self–assemble resides in the C–terminal section of myosin known as light meromyosin (LMM) which exhibits strong salt–dependent aggregation that has inhibited structural studies. Here we evaluate the feasibility of generating a complete model for the myosin rod by combining overlapping structures of five sections of coiled–coil covering 164 amino acid residues which constitute 20% of LMM. Each section contains ~7–9 heptads of myosin. The problem of aggregation was overcome by incorporating the globular folding domains, Gp7 and Xrcc4 which enhance crystallization. The effect of these domains on the stability and conformation of the myosin rod was examined through biophysical studies and overlapping structures. In addition, a computational approach was developed to combine the sections into a contiguous model. The structures were aligned, trimmed to form a contiguous model, and simulated for >700 ns to remove the discontinuities and achieve an equilibrated conformation that represents the native state. As a result, this experimental and computational strategy lays the foundation for building a model for the entire myosin rod.

59 BASIC BIOLOGICAL SCIENCES↗

Real-world outcomes in patients with unresected stage III non-small cell lung cancer

This study examined real-world clinical outcomes such as progression-free survival (PFS), time to metastasis (TTM), overall survival (OS), and health-related quality of life (HRQOL) in patients with unresected stage III non-small cell lung cancer (NSCLC) treated in the community setting. A retrospective review of medical records extracted from 10 US community oncology practices was conducted. Eligible patients were adults diagnosed with stage III NSCLC from 1/1/2011 to 3/1/2016 without evidence of surgical resection within 6 months after stage III NSCLC diagnosis (index date). PFS, OS, and TTM were assessed from the index date, and were analyzed using Kaplan–Meier and Cox regression analyses. HRQOL was assessed for a subset of patients using a patient-reported measure, the 86-item Patient Care Monitor (PCM). Linear mixed models (LMM) were used to assess the impact of patient characteristics and change in PCM scores associated with progression. Among the sample of 478 patients, median PFS (95% confidence interval) was 10 months (9–11), median OS was 20 months (17–22), and median TTM was 30 months (23–45). Most patients (58.2%) experienced disease progression, which the LMM showed to be associated with significant worsening of physical symptoms and psychological states (p < 0.001). This study documented PFS and OS consistent with published literature. The majority of patients experienced disease progression, which was associated with worsening of HRQOL. These findings highlighted the need for better therapeutic options in patients with unresected stage III NSCLC with potential to improve patient outcomes and HRQOL.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Structure and Mechanism of LcpA, a Phosphotransferase That Mediates Glycosylation of a Gram-Positive Bacterial Cell Wall-Anchored Protein

ABSTRACT The widely conserved LytR-CpsA-Psr (LCP) family of enzymes in Gram-positive bacteria is known to attach glycopolymers, including wall teichoic acid, to the cell envelope. However, it is undetermined if these enzymes are capable of catalyzing glycan attachment to surface proteins. In the actinobacterium Actinomyces oris , an LCP homolog here named LcpA is genetically linked to GspA, a glycoprotein that is covalently attached to the bacterial peptidoglycan by the housekeeping sortase SrtA. Here we show by X-ray crystallography that LcpA adopts an α-β-α structural fold, akin to the conserved LCP domain, which harbors characteristic catalytic arginine residues. Consistently, alanine substitution for these residues, R149 and R266, abrogates GspA glycosylation, leading to accumulation of an intermediate form termed GspA LMM , which is also observed in the lcpA mutant. Unlike other LCP proteins characterized to date, LcpA contains a stabilizing disulfide bond, mutations of which severely affect LcpA stability. In line with the established role of disulfide bond formation in oxidative protein folding in A. oris , deletion of vkor , coding for the thiol-disulfide oxidoreductase VKOR, also significantly reduces LcpA stability. Biochemical studies demonstrated that the recombinant LcpA enzyme possesses pyrophosphatase activity, enabling hydrolysis of diphosphate bonds. Furthermore, this recombinant enzyme, which weakly interacts with GspA in solution, catalyzes phosphotransfer to GspA LMM . Altogether, the findings support that A. oris LcpA is an archetypal LCP enzyme that glycosylates a cell wall-anchored protein, a process that may be conserved in Actinobacteria , given the conservation of LcpA and GspA in these high-GC-content organisms. IMPORTANCE In Gram-positive bacteria, the conserved LCP family enzymes studied to date are known to attach glycopolymers, including wall teichoic acid, to the cell envelope. It is unknown if these enzymes catalyze glycosylation of surface proteins. We show here in the actinobacterium Actinomyces oris by X-ray crystallography and biochemical analyses that A. oris LcpA is an LCP homolog, possessing pyrophosphatase and phosphotransferase activities known to belong to LCP enzymes that require conserved catalytic Arg residues, while harboring a unique disulfide bond critical for protein stability. Importantly, LcpA mediates glycosylation of the surface protein GspA via phosphotransferase activity. Our studies provide the first experimental evidence of an archetypal LCP enzyme that promotes glycosylation of a cell wall-anchored protein in Gram-positive bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Low-bandgap, monolithic, multi-bandgap, optoelectronic devices

Low bandgap, monolithic, multi-bandgap, optoelectronic devices (10), including PV converters, photodetectors, and LED's, have lattice-matched (LM), double-heterostructure (DH), low-bandgap GaInAs(P) subcells (22, 24) including those that are lattice-mismatched (LMM) to InP, grown on an InP substrate (26) by use of at least one graded lattice constant transition layer (20) of InAsP positioned somewhere between the InP substrate (26) and the LMM subcell(s) (22, 24). These devices are monofacial (10) or bifacial (80) and include monolithic, integrated, modules (MIMs) (190) with a plurality of voltage-matched subcell circuits (262, 264, 266, 270, 272) as well as other variations and embodiments.

42 ENGINEERING↗

Low-bandgap, monolithic, multi-bandgap, optoelectronic devices

Low bandgap, monolithic, multi-bandgap, optoelectronic devices (10), including PV converters, photodetectors, and LED's, have lattice-matched (LM), double-heterostructure (DH), low-bandgap GaInAs(P) subcells (22, 24) including those that are lattice-mismatched (LMM) to InP, grown on an InP substrate (26) by use of at least one graded lattice constant transition layer (20) of InAsP positioned somewhere between the InP substrate (26) and the LMM subcell(s) (22, 24). These devices are monofacial (10) or bifacial (80) and include monolithic, integrated, modules (MIMs) (190) with a plurality of voltage-matched subcell circuits (262, 264, 266, 270, 272) as well as other variations and embodiments.

14 SOLAR ENERGY↗

Low-bandgap, monolithic, multi-bandgap, optoelectronic devices

Low bandgap, monolithic, multi-bandgap, optoelectronic devices (10), including PV converters, photodetectors, and LED's, have lattice-matched (LM), double-heterostructure (DH), low-bandgap GaInAs(P) subcells (22, 24) including those that are lattice-mismatched (LMM) to InP, grown on an InP substrate (26) by use of at least one graded lattice constant transition layer (20) of InAsP positioned somewhere between the InP substrate (26) and the LMM subcell(s) (22, 24). These devices are monofacial (10) or bifacial (80) and include monolithic, integrated, modules (MIMs) (190) with a plurality of voltage-matched subcell circuits (262, 264, 266, 270, 272) as well as other variations and embodiments.

30 DIRECT ENERGY CONVERSION↗

In Situ Monitoring of H 2 -Induced Nonstoichiometry in Cu 2 O

Nonstoichiometry plays a pivotal role in the functioning of oxide materials, but it is challenging to measure the non-stoichiometric formation and the resulting charge redistribution around the point defects. Using ambient-pressure X-ray photoelectron spectroscopy and Auger electron spectroscopy to monitor the reduction of Cu 2 O in H 2 , we identify the formation of an intermediate, oxygen-deficient Cu 2 O phase and its progressive inward growth into the deeper region of the oxide. Complemented by DFT modeling, we show that the oxygen-deficient Cu 2 O formation occurs via molecular H 2 adsorption at the Cu 2 O surface, which results in the loss of lattice O from the formation of H 2 O molecules that desorb spontaneously from the oxide surface. The resulting oxy-gen-deficient Cu 2 O is a stable intermediate that persists before the Cu 2 O is fully reduced to metallic Cu. The O vacancy induced charge redistribution of the coordinating Cu atoms results in a satellite feature in Cu LMM, which can be used a fingerprint to identify the nonstoichiometry and local charge transfer in non-stoichiometric oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characteristics of high-purity Cu thin films deposited on polyimide by radio-frequency Ar/H{sub 2} atmospheric-pressure plasma jet

With a view to fabricating future flexible electronic devices, an atmospheric-pressure plasma jet driven by 13.56 MHz radio-frequency power is developed for depositing Cu thin films on polyimide, where a Cu wire inserted inside the quartz tube was used as the evaporation source. A polyimide substrate is placed on a water-cooled copper heat sink to prevent it from being thermally damaged. With the aim of preventing oxidation of the deposited Cu film, we investigated the effect of adding H{sub 2} to Ar plasma on film characteristics. Theoretical fitting of the OH emission line in OES spectrum revealed that adding H{sub 2} gas significantly increased the rotational temperature roughly from 800 to 1500 K. The LMM Auger spectroscopy analysis revealed that higher-purity Cu films were synthesized on polyimide by adding hydrogen gas. A possible explanation for the enhancement in the Cu film deposition rate and improvement of purity of Cu films by H{sub 2} gas addition is that atomic hydrogen produced by the plasma plays important roles in heating the gas to promote the evaporation of Cu atoms from the Cu wire and removing oxygen from copper oxide components via reduction reaction.

36 MATERIALS SCIENCE↗

Tuning the band structure, magnetic and transport properties of the zigzag graphene nanoribbons/hexagonal boron nitride heterostructures by transverse electric field

The paper presents the results of ab initio study of the opportunities for tuning the band structure, magnetic and transport properties of zigzag graphene nanoribbon (8-ZGNR) on hexagonal boron nitride (h-BN(0001)) semiconductor heterostructure by transverse electric field (E{sub ext}). This study was performed within the framework of the density functional theory (DFT) using Grimme's (DFT-D2) scheme. We established the critical values of E{sub ext} for the 8-ZGNR/h-BN(0001) heterostructure, thereby providing for semiconductor-halfmetal transition in one of electron spin configurations. This study also showed that the degeneration in energy of the localized edge states is removed when E{sub ext} is applied. In ZGNR/h-BN (0001) heterostructure, value of the splitting energy was higher than one in ZGNRs without substrate. We determined the effect of low E{sub ext} applied to the 8-ZGNR/h-BN (0001) semiconductor heterostructure on the preserved local magnetic moment (LMM) (0.3μ{sub B}) of edge carbon atoms. The transport properties of the 8-ZGNR/h-BN(0001) semiconductor heterostructure can be controlled using E{sub ext}. In particular, at a critical value of the positive potential, the electron mobility can increase to 7× 10{sup 5} cm{sup 2}/V s or remain at zero in the spin-up and spin-down electron subsystems, respectively. We established that magnetic moments (MMs), band gaps, and carrier mobility can be altered using E{sub ext}. These abilities enable the use of 8-ZGNR/h-BN(0001) semiconductor heterostructure in spintronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal Control of the Energy-Saving Hybrid Hydraulic-Electric Architecture (HHEA) for Off-Highway Mobile Machines

Most off-highway constructions and agriculture equipment use hydraulics, which has unmatched power density, for power transmission and throttling as a means for control. A novel hybrid hydraulic-electric architecture (HHEA) has recently been proposed to improve efficiency for high-power machines that would have been cost-prohibitive to electrify directly. HHEA uses a set of common pressure rails (CPRs) to transmit the majority of power hydraulically and small electric motor drives to modulate that power and to achieve precise control. This article proposes a computationally efficient Lagrange multiplier method (LMM) for computing the optimal sequence of pressure rail selections to minimize energy use. This is needed to evaluate HHEA's energy-saving potential and for iterative architecture design and sizing. An interesting complication is that the cost function is not fully defined until the candidate control sequence is fully specified. This issue is dealt with by decomposing the original problem into a set of sub-problems with additional constraints that can be solved efficiently. Computational effort can be further reduced if actuators are optimized individually instead of together. However, additional steps are required to prevent the constraint functions from becoming discontinuous with respect to the Lagrange multipliers, which is necessary for meeting the constraints. Lastly, a case study of a construction machine demonstrates the efficacy of the method and shows that the HHEA reduces energy consumption by 68%-73% compared to the baseline load-sensing architecture.

Lagrange multiplier↗

Lithium-based transition-metal oxides for battery electrodes analyzed by x-ray photoelectron spectroscopy. I. LiNi 0.8 Co 0.15 0.05 O 2

X-ray photoelectron spectroscopy (XPS) was used to analyze fresh LiNi 0.8 Co 0.1 5Al 0.05 O 2 powder obtained from TODA America. XP spectra were obtained using incident monochromatic Al Kα radiation at 0.834 01 nm. A survey spectrum together with Ni 2p, Co 2p, Ni LMM, O 1s, C 1s, Al 2s, Ni 3s, Co 3s, Al 2p, Ni 3p, Co 3p, and Li 1s are presented. The spectra indicate the principal core level photoelectron and Auger electron signals and show carbon with only minor sulfur contamination. Making use of the O 1s, Al 2s, Ni 3p, Co 3p, Li 1s lines and neglecting the components related to surface contaminants, XPS quantitative analysis reveals an altered stoichiometry of the air-exposed powder surface of LiNi 0.2 Co 0.03 Al 0.1 O 0.7 .

25 ENERGY STORAGE↗

Lithium-based transition-metal oxides for battery electrodes analyzed by x-ray photoelectron spectroscopy. II. LiNi 0.8 Co 0.1 Mn 0.1 O 2

X-ray photoelectron spectroscopy (XPS) was used to analyze fresh LiNi 0.8 Co 0.1 Mn 0.1 O 2 powder obtained from Targray Technology International, Inc.. XP spectra were obtained using incident monochromatic Al Kα radiation at 0.834 01 nm. A survey spectrum together with Ni 2p, Co 2p, Mn 2p, Ni LMM, O 1s, C 1s, Al 2s, Ni 3s, Co 3s, Mn 3s, Ni 3p, Co 3p, Li 1s, and Mn 3p are presented. The spectra indicate the principal core level photoelectron and Auger electron signals and show only minor sulfur contamination. Making use of the O 1s, Ni 3p, Co 3p, Mn 3p, Li 1s lines and neglecting the components related to surface contaminants, XPS quantitative analysis reveals an altered stoichiometry of the air-exposed powder surface of LiNi 0.4 Co 0.02 Mn 0.1 O 0.8 .

25 ENERGY STORAGE↗