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At least 1,135 records · Page 63

Structural and mechanistic basis of mammalian Nudt12 RNA deNADding

We recently demonstrated that mammalian cells harbor nicotinamide adenine dinucleotide (NAD)-capped messenger RNAs that are hydrolyzed by the DXO deNADding enzyme. Here, we report that the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targeting different RNAs. Here, the crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg 2+ ions at 1.6 Å resolution provides insights into the molecular basis of the deNADding activity in the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells, and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to nutrient or environmental stress manifests changes in NAD-capped RNA levels that are selectively responsive to Nudt12 or DXO, respectively, indicating an association of deNADding to cellular metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Non-invasive ventral cervical magnetoneurography as a proxy of in vivo lipopolysaccharide-induced inflammation

Maintenance of autonomic homeostasis is continuously calibrated by sensory fibers of the vagus nerve and sympathetic chain that convey compound action potentials (CAPs) to the central nervous system. Lipopolysaccharide (LPS) intravenous challenge reliably elicits a robust inflammatory response that can resemble systemic inflammation and acute endotoxemia. Here, we administered LPS intravenously in nine healthy subjects while recording ventral cervical magnetoneurography (vcMNG)-derived CAPs at the rostral Right Nodose Ganglion (RNG) and the caudal Right Carotid Artery (RCA) with optically pumped magnetometers (OPM). We observed vcMNG RNG and RCA neural firing rates that tracked changes in TNF-α levels in the systemic circulation. Further, endotype subgroups based on high and low IL-6 responders segregate RNG CAP frequency (at 30-120 min) and based on high and low IL-10 response discriminate RCA CAP frequency (at 0-30 min). These vcMNG tools may enhance understanding and management of the neuroimmune axis that can guide personalized treatment based on an individual’s distinct endophenotype.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of the oxide layer on current-induced spin-orbit torques in Hf|CoFeB|MgO and Hf|CoFeB|TaO{sub x} structures

We study the effect of the oxide layer on the current-induced spin-orbit torques (SOTs) in perpendicularly magnetized Hf|CoFeB|MgO (MgO-capped) or Hf|CoFeB|TaO{sub x} (TaO{sub x}-capped) structures. The effective fields corresponding to both the field-like and damping-like current-induced SOTs are characterized using electric transport measurements. Both torques are found to be significantly stronger in MgO-capped structures than those in TaO{sub x}-capped structures. The difference in field-like and damping-like SOTs in the different structures may be attributed to the different Rashba-like Hamiltonian, arising from the difference in the electric potential profiles across the oxide|ferromagnet interfaces in the two cases, as well as possible structural and oxidation differences in the underlying CoFeB and Hf layers. Our results show that the oxide layer in heavy-metal|ferromagnet|oxide trilayer structures has a very significant effect on the generated SOTs for manipulation of ferromagnetic layers. These findings could potentially be used to engineer SOT devices with enhanced current-induced switching efficiency.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Generalized gradient approximation exchange energy functional with correct asymptotic behavior of the corresponding potential

A new non-empirical exchange energy functional of the generalized gradient approximation (GGA) type, which gives an exchange potential with the correct asymptotic behavior, is developed and explored. In combination with the Perdew-Burke-Ernzerhof (PBE) correlation energy functional, the new CAP-PBE (CAP stands for correct asymptotic potential) exchange-correlation functional gives heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies on standard test sets that are fully competitive with those obtained from other GGA-type functionals that do not have the correct asymptotic exchange potential behavior. Distinct from them, the new functional provides important improvements in quantities dependent upon response functions, e.g., static and dynamic polarizabilities and hyperpolarizabilities. CAP combined with the Lee-Yang-Parr correlation functional gives roughly equivalent results. Consideration of the computed dynamical polarizabilities in the context of the broad spectrum of other properties considered tips the balance to the non-empirical CAP-PBE combination. Intriguingly, these improvements arise primarily from improvements in the highest occupied and lowest unoccupied molecular orbitals, and not from shifts in the associated eigenvalues. Those eigenvalues do not change dramatically with respect to eigenvalues from other GGA-type functionals that do not provide the correct asymptotic behavior of the potential. Unexpected behavior of the potential at intermediate distances from the nucleus explains this unexpected result and indicates a clear route for improvement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Strain engineering of quantum dots for long wavelength emission: Photoluminescence from self-assembled InAs quantum dots grown on GaAs(001) at wavelengths over 1.55 μm

Photoluminescence (PL) at wavelengths over 1.55 μm from self-assembled InAs quantum dots (QDs) grown on GaAs(001) is observed at room temperature (RT) and 4 K using a bilayer structure with thin cap. The PL peak has been known to redshift with decreasing cap layer thickness, although accompanying intensity decrease and peak broadening. With our strain-controlled bilayer structure, the PL intensity can be comparable to the ordinary QDs while realizing peak emission wavelength of 1.61 μm at 4 K and 1.73 μm at RT. The key issue lies in the control of strain not only in the QDs but also in the cap layer. By combining with underlying seed QD layer, we realize strain-driven bandgap engineering through control of strain in the QD and cap layers.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Silver nanoparticles with tunable work functions

To improve the efficiencies of electronic devices, materials with variable work functions are required to decrease the energy level differences at the interfaces between working layers. Here, we report a method to obtain silver nanoparticles with tunable work functions, which have the same silver core of 5 nm in diameter and are capped by myristates and 1-octanethoilates self-assembled monolayers, respectively. The silver nanoparticles capped by organic molecules can form a uniform two-dimensional sheet at air-water interface, and the sheet can be transferred on various hydrophobic substrates. The surface potential of the two-dimensional nanoparticle sheet was measured in terms of Kelvin probe force microscopy, and the work function of the sheet was then calculated from the surface potential value by comparing with a reference material. The exchange of the capping molecules results in a work function change of approximately 150–250 meV without affecting their hydrophobicity. We systematically discussed the origin of the work function difference and found it should come mainly from the anchor groups of the ligand molecules. The organic molecule capped nanoparticles with tunable work functions have a potential for the applications in organic electronic devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Hybrid grating reflectors: Origin of ultrabroad stopband

Hybrid grating (HG) reflectors with a high-refractive-index cap layer added onto a high contrast grating (HCG) provide a high reflectance close to 100% over a broader wavelength range than HCGs. The combination of a cap layer and a grating layer brings a strong Fabry-Perot (FP) resonance as well as a weak guided mode (GM) resonance. Most of the reflected power results from the FP resonance, while the GM resonance plays a key role in achieving a reflectance close to 100% as well as broadening the stopband. An HG sample with 7 InGaAlAs quantum wells included in the cap layer has been fabricated by directly wafer-bonding a III-V cap layer onto a Si grating layer. Its reflection property has been characterized. This heterogeneously integrated HG reflector may allow for a hybrid III-V on Si laser to be thermally efficient, which has promising prospects for silicon photonics light sources and high-speed operation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Crystallization growth rates and front propagation in amorphous solid water films

The growth rate of crystalline ice (CI) in amorphous solid water (ASW) films was investigated using reflection absorption infrared spectroscopy. Two different experiments were set up to measure rates of the crystallization front propagation from the underlying crystalline template upward and from the vacuum interface downward. In one set of experiments, layers of ASW (5% D 2 O in H 2 O) were grown on a CI template and capped with a decane layer. In isothermal experiments from 140 to 150 K, crystallization was observed from the onset (no induction time) and the extent of crystallization increased linearly with time. In a second set of experiments, uncapped ASW films without a CI template were studied. The films were created by placing a 100 ML isotopic layer (5% D 2 O in H 2 O) at various positions in a 1000 ML ASW (H 2 O) film. The CI growth rates obtained from the two configurations (capped films with a CI template and uncapped films without a CI template) are in quantitative agreement. The results support the idea that for ASW films in a vacuum, a crystalline layer forms at the surface that then acts as a CI template for a growth front that moves downward into the film.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental setup combining in situ hard X-ray photoelectron spectroscopy and real-time surface X-ray diffraction for characterizing atomic and electronic structure evolution during complex oxide heterostructure growth

We describe the next-generation system for in situ characterization of a complex oxide thin film and heterostructure growth by pulsed laser deposition (PLD) using synchrotron hard X-rays. The system consists of a PLD chamber mounted on a diffractometer allowing both real-time surface X-ray diffraction (SXRD) and in situ hard X-ray photoelectron spectroscopy (HAXPES). HAXPES is performed in the incident X-ray energy range from 4 to 12 keV using a Scienta EW4000 electron energy analyzer mounted on the PLD chamber fixed parallel with the surface normal. In addition to the standard application mode of HAXPES for disentangling surface from bulk properties, the increased penetration depth of high energy photoelectrons is used for investigation of the electronic structure changes through thin films grown deliberately as variable thickness capping layers. Such heterostructures represent model systems for investigating a variety of critical thickness and dead layer phenomena observed at complex oxide interfaces. In this new mode of operation, in situ HAXPES is used to determine the electronic structure associated with unique structural features identified by real-time SXRD during thin film growth. The system is configured for using both laboratory excitation sources off-line and on-line operation at beamline 33-ID-D at the Advanced Photon Source. We illustrate the performance of the system by preliminary scattering and spectroscopic data on oxygen vacancy ordering induced perovskite-to-brownmillerite reversible phase transformation in La 2/3 Sr 1/3 MnO 3 films capped with oxygen deficient SrTiO 3–δ (100) layers of varying thickness.

47 OTHER INSTRUMENTATION↗

Managing photoinduced electron transfer in AgInS2–CdS heterostructures

Ternary semiconductors such as AgInS2, with their interesting photocatalytic properties, can serve as building blocks to design light harvesting assemblies. The intraband transitions created by the metal ions extend the absorption well beyond the bandgap transition. The interfacial electron transfer of AgInS2 with surface bound ethyl viologen under bandgap and sub-bandgap irradiation as probed by steady state photolysis and transient absorption spectroscopy offers new insights into the participation of conduction band and trapped electrons. Capping AgInS2 with CdS shifts emission maximum to the blue and increases the emission yield as the surface defects are remediated. CdS capping also promotes charge separation as evident from the efficiency of electron transfer to ethyl viologen, which increased from 14% to 29%. The transient absorption measurements that elucidate the kinetic aspects of electron transfer processes in AgInS2 and CdS capped AgInS2 are presented. The improved performance of CdS capped AgInS2 offers new opportunities to employ them as photocatalysts.

Kipkorir, Anthony↗

Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

We report crystal structures of the antibacterial lasso peptides microcin J25 (MccJ25) and capistruin (Cap) bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). Both peptides bind within the RNAP secondary channel, through which NTP substrates enter the RNAP active site, and sterically block trigger-loop folding, which is essential for efficient catalysis by the RNAP. MccJ25 binds deep within the secondary channel in a manner expected to interfere with NTP substrate binding, explaining the partial competitive mechanism of inhibition with respect to NTPs found previously [Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH (2004) Mol Cell 14:739–751]. The Cap binding determinant on RNAP overlaps, but is not identical to, that of MccJ25. Cap binds further from the RNAP active site and does not sterically interfere with NTP binding, and we show that Cap inhibition is partially noncompetitive with respect to NTPs. This work lays the groundwork for structure determination of other lasso peptides that target the bacterial RNAP and provides a structural foundation to guide lasso peptide antimicrobial engineering approaches.

59 BASIC BIOLOGICAL SCIENCES↗

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library. Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s{sup −1}) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Highly Reliable Multi-Port Smart Inverter Modules for PV-Based Energy Systems

Generally, large electrolytic capacitors (E-caps) are required to decouple the double-line frequency power fluctuation inherent in all single-phase dc-ac or ac-dc converters. These E-caps pose the weak link in the photovoltaic (PV) inverter because they have poor reliability as a result of short life expectancy and higher equivalent series resistance (ESR) which leads to lower system efficiency. In this paper, multiport smart dual-inverter modules are proposed for residential PV inverter systems with balanced outputs to eliminate the requirement of large decoupling capacitors, thus leading to more reliable and highly efficient inverter modules. The balanced dual outputs are controlled in phase quadrature such that the double frequency current is completely eliminated. One phase supports the standalone residential loads, and the other phase interfaces with the grid, which is synchronized to the utility grid. Also, the proposed modular configuration is scalable to accommodate higher power rating by stacking and paralleling multiple modules. Simulation results for the dual-inverter modules rated for 1 kW each are presented to validate the proposed concept. Experimental results from a controller hardware-in-the-loop (CHIL) platform also verify its feasibility.

14 SOLAR ENERGY↗

Glass production rate in electric furnaces for radioactive waste vitrification

Correlating the melting rates of feeds in electric melters with results of simple laboratory experiments can help evaluate melter feed additives and their effects on melting rate, and support the feed scheduling and plant operation. A recently proposed melting rate correlation (MRC) equation, relating the melting rate to melt viscosity, feed-to-glass conversion heat, and cold-cap bottom temperature, was tested using data from experiments covering various feed compositions and melter operating parameters. The MRC equation is shown to reasonably represent the measured data and thus can be used to quantify how individual variables (melt viscosity, cold-cap bottom temperature, conversion heat, melter operating temperature, and bubbling rate) affect the glass production rate.

Lee, Seung Min↗

Experimental quantification of vent mechanism flow parameters in 18650 format lithium ion batteries

Lithium ion batteries have a well documented tendency to fail energetically under various abuse conditions. These conditions frequently result in decomposition of the electrochemical components within the battery resulting in gas generation and increased internal pressure which can lead to an explosive case rupture. The 18650 format cell incorporates a vent mechanism located within a crimped cap to relieve pressure and mitigate the risk of case rupture. Cell venting, however, introduces additional safety concerns associated with the flow of flammable gases and liquid electrolyte into the environment. Experiments to quantify key parameters are performed to elucidate the external dynamics of battery venting. A first experiment measures the vent burst pressure. Burst vent caps are then tested with a second experimental fixture to measure vent opening area and discharge coefficient during choked-flow venting, which occurs during battery failure. Vent opening area and discharge coefficient are calculated from stagnation temperature, stagnation pressure, and static pressure measurements along with compressible-isentropic flow equations and conservation of mass. Commercially-sourced vent caps are used with repeated tests run to quantify repeatability and variability. Validation experiments confirmed accuracy of opening area and discharge coefficient measurement. Moreover, trials conducted on vent caps from two sources demonstrate the potential for variation between manufacturers.

25 ENERGY STORAGE↗

Comparison of B{sub 2}O{sub 3} and BN deposited by atomic layer deposition for forming ultrashallow dopant regions by solid state diffusion

In this study, the authors investigated atomic layer deposition (ALD) of B{sub 2}O{sub 3} and BN for conformal, ultrashallow B doping applications and compared the effect of dopant-containing overlayers on sheet resistance (R{sub s}) and B profiles for both types of films subjected to a drive-in thermal anneal. For the deposition of B{sub 2}O{sub 3}, tris(dimethylamido)borane and O{sub 3} were used as coreactants and for the deposition of BN, BCl{sub 3} and NH{sub 3} were used as coreactants. Due to the extreme air instability of B{sub 2}O{sub 3} films, physical analysis was performed on B{sub 2}O{sub 3} films, which were capped in-situ with ∼30 Å ALD grown Al{sub 2}O{sub 3} layers. For the BN films, in-situ ALD grown Si{sub 3}N{sub 4} capping layers (∼30 Å) were used for comparison. From spectroscopic ellipsometry, a thickness decrease was observed after 1000 °C, 30 s anneal for the B{sub 2}O{sub 3} containing stack with 60 ALD cycles of B{sub 2}O{sub 3}, whereas the BN containing stacks showed negligible thickness decrease after the annealing step, regardless of the number of BN cycles tested. The postanneal reduction in film thickness as well as decrease in R{sub s} for the B{sub 2}O{sub 3} containing stack suggests that the solid state diffusion dopant mechanism is effective, whereas for the BN containing stacks this phenomenon seems to be suppressed. Further clarification of the effectiveness of the B{sub 2}O{sub 3} containing layer compared to the film stacks with BN was evidenced in backside secondary ion mass spectrometry profiling of B atoms. Thus, B{sub 2}O{sub 3} formed by an ALD process and subsequently capped in-situ followed by a drive-in anneal offers promise as a dopant source for ultrashallow doping, whereas the same method using BN seems ineffective. An integrated approach for B{sub 2}O{sub 3} deposition and annealing on a clustered tool also demonstrated controllable R{sub s} reduction without the use of a capping layer.

36 MATERIALS SCIENCE↗

Characterizing the Impact of GPU Power Management on an Exascale System

As GPU-accelerated high-performance computing (HPC) systems approach exascale performance, controlling energy consumption without compromising throughput is essential. Architectures such as the AMD MI250X-based Frontier supercomputer provide runtime mechanisms like frequency and power capping, enabling energy tuning without modifying application code. Although both target energy reduction, they operate via distinct hardware control paths and influence workloads differently. We present a comprehensive evaluation of these strategies on a leadership-class system using diverse HPC proxy applications representative of production workloads. Our study analyzes performance–energy trade-offs across multiple capping levels, node counts (1 and 32), and application profiles. Results show that frequency capping generally achieves higher energy efficiency and scalability, with gains of up to 13.2% without performance loss, while power capping is more effective for single-node runs or bursty GPU utilization. We also provide practical guidelines to help system administrators and users balance energy efficiency and performance in large-scale scientific workloads.

Costa, Mariana [Universidade Federal do Rio Grande↗

Analysis of Factors that Influence Infiltration Rates using the HELP Model

The Hydrologic Evaluation of Landfill Performance (HELP) model is used by Savannah River National Laboratory (SRNL) in conjunction with PORFLOW groundwater flow simulation software to make longterm predictions of the fate and transport of radionuclides in the environment at radiological waste sites. The work summarized in this report supports preparation of the planned 2018 Performance Assessment for the E-Area Low-Level Waste Facility (LLWF) at the Savannah River Site (SRS). More specifically, this project focused on conducting a sensitivity analysis of infiltration (i.e., the rate at which water travels vertically in soil) through the proposed E-Area LLWF closure cap. A sensitivity analysis was completed using HELP v3.95D to identify the cap design and material property parameters that most impact infiltration rates through the proposed closure cap for a 10,000-year simulation period. The results of the sensitivity analysis indicate that saturated hydraulic conductivity (Ksat) for select cap layers, precipitation rate, surface vegetation type, and geomembrane layer defect density are dominant factors limiting infiltration rate. Interestingly, calculated infiltration rates were substantially influenced by changes in the saturated hydraulic conductivity of the Upper Foundation and Lateral Drainage layers. For example, an order-of-magnitude decrease in Ksat for the Upper Foundation layer lowered the maximum infiltration rate from a base-case 11 inches per year to only two inches per year. Conversely, an order-of-magnitude increase in Ksat led to an increase in infiltration rate from 11 to 15 inches per year. This work and its results provide a framework for quantifying uncertainty in the radionuclide transport and dose models for the planned 2018 E-Area Performance Assessment. Future work will focus on the development of a nonlinear regression model for infiltration rate using Minitab 17® to facilitate execution of probabilistic simulations in the GoldSim® overall system model for the E-Area LLWF.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗