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At least 613 records · Page 34

Electron residual energy due to stochastic heating in field-ionized plasma

The electron residual energy originated from the stochastic heating in under-dense field-ionized plasma is investigated here. Initially, the optical response of plasma is modeled by using two counter-propagating electromagnetic waves. In this case, the solution of motion equation of a single electron indicates that by including the ionization, the electron with higher residual energy compared with that without ionization could be obtained. In agreement with chaotic nature of the motion, it is found that the electron residual energy will be significantly changed by applying a minor change in the initial conditions. Extensive kinetic 1D-3V particle-in-cell simulations have been performed in order to resolve full plasma reactions. In this way, two different regimes of plasma behavior are observed by varying the pulse length. The results indicate that the amplitude of scattered fields in a proper long pulse length is high enough to act as a second counter-propagating wave and trigger the stochastic electron motion. On the contrary, the analyses of intensity spectrum reveal the fact that the dominant scattering mechanism tends to Thomson rather than Raman scattering by increasing the pulse length. A covariant formalism is used to describe the plasma heating so that it enables us to measure electron temperature inside and outside of the pulse region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Effects of residual hydrogen in sputtering atmosphere on structures and properties of amorphous In-Ga-Zn-O thin films

We investigated the effects of residual hydrogen in sputtering atmosphere on subgap states and carrier transport in amorphous In-Ga-Zn-O (a-IGZO) using two sputtering systems with different base pressures of ∼10{sup −4} and 10{sup −7 }Pa (standard (STD) and ultrahigh vacuum (UHV) sputtering, respectively), which produce a-IGZO films with impurity hydrogen contents at the orders of 10{sup 20} and 10{sup 19 }cm{sup −3}, respectively. Several subgap states were observed by hard X-ray photoemission spectroscopy, i.e., peak-shape near-valence band maximum (near-VBM) states, shoulder-shape near-VBM states, peak-shape near-conduction band minimum (near-CBM) states, and step-wise near-CBM states. It was confirmed that the formation of these subgap states were affected strongly by the residual hydrogen (possibly H{sub 2}O). The step-wise near-CBM states were observed only in the STD films deposited without O{sub 2} gas flow and attributed to metallic In. Such step-wise near-CBM state was not detected in the other films including the UHV films even deposited without O{sub 2} flow, substantiating that the metallic In is segregated by the strong reduction effect of the hydrogen/H{sub 2}O. Similarly, the density of the near-VBM states was very high for the STD films deposited without O{sub 2}. These films had low film density and are consistent with a model that voids in the amorphous structure form a part of the near-VBM states. On the other hand, the UHV films had high film densities and much less near-VBM states, keeping the possibility that some of the near-VBM states, in particular, of the peak-shape ones, originate from –OH and weakly bonded oxygen. These results indicate that 2% of excess O{sub 2} flow is required for the STD sputtering to compensate the effects of the residual hydrogen/H{sub 2}O. The high-density near-VBM states and the metallic In segregation deteriorated the electron mobility to 0.4 cm{sup 2}/(V s)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The residual zonal flows in anisotropic tokamak plasmas

The gyro-kinetic equation is analytically solved based on the anisotropic two-temperature distribution, in which the ions' parallel temperature is a flux function while the perpendicular temperature depends on the poloidal angle. The residual level of collisionless zonal flows (ZFs) is derived and calculated in the large aspect circular limit. Our result shows that the anisotropy plays a remarkable role in determining the residual value of ZFs. Even weak anisotropy can significantly change the residual level.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Residual stress determination in oxide layers at different length scales combining Raman spectroscopy and X-ray diffraction: Application to chromia-forming metallic alloys

In oxidizing environments, the protection of metals and alloys against further oxidation at high temperature is provided by the oxide film itself. This protection is efficient only if the formed film adheres well to the metal (substrate), i.e., without microcracks and spalls induced by thermomechanical stresses. In this study, the residual stresses at both macroscopic and microscopic scales in the oxide film adhering to the substrate and over the damaged areas have been rigorously determined on the same samples for both techniques. Ni-30Cr and Fe-47Cr alloys have been oxidized together at 900 and 1000 °C, respectively, to create films with a thickness of a few microns. A multi-scale approach was adopted: macroscopic stress was determined by conventional X-ray diffraction and Raman spectroscopy, while microscopic residual stress mappings were performed over different types of bucklings using Raman micro-spectroscopy and synchrotron micro-diffraction. A very good agreement is found at macro- and microscales between the residual stress values obtained with both techniques, giving confidence on the reliability of the measurements. In addition, relevant structural information at the interface between the metallic substrate and the oxide layer was collected by micro-diffraction, a non-destructive technique that allows mapping through the oxide layer, and both the grain size and the crystallographic orientation of the supporting polycrystalline metal located either under a buckling or not were measured.

36 MATERIALS SCIENCE↗

Current capabilities of the residual stress diffractometer at the high flux isotope reactor

The engineering diffractometer 2nd Generation Neutron Residual Stress Facility (NRSF2) at the Oak Ridge National Laboratory’s High Flux Isotope Reactor was built specifically for the mapping of residual strains. NRSF2 is optimized to investigate a wide range of engineering materials by providing the user a selection of monochromatic neutron wavelengths to maintain the selected Bragg reflection near 2θ = 90°, which is the optimal scattering geometry for strain mapping. Here in this work, details of the instrument configuration and operation are presented, and considerations for experimental planning are also discussed. Selected examples of recent residual stress work completed with NRSF2 are presented to highlight capabilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Excitation of low-frequency residual currents at combination frequencies of an ionising two-colour laser pulse

We have studied the processes of excitation of low-frequency residual currents in a plasma produced through ionisation of gases by two-colour laser pulses in laser-plasma schemes for THz generation. We have developed an analytical approach that allows one to find residual currents in the case when one of the components of a two-colour pulse is weak enough. The derived analytical expressions show that the effective generation of the residual current (and hence the effective THz generation) is possible if the ratio of the frequencies in the two-colour laser pulse is close to a rational fraction with a not very big odd sum of the numerator and denominator. The results of numerical calculations (including those based on the solution of the three-dimensional time-dependent Schrödinger equation) agree well with the analytical results. (extreme laser radiation: physics and fundamental applications)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition

Methylation of the small ribosome subunit rRNA in the ribosomal decoding center results in exceptionally high-level aminoglycoside resistance in bacteria. Enzymes that methylate 16S rRNA on N7 of nucleotide G1405 (m 7 G1405) have been identified in both aminoglycoside-producing and clinically drug-resistant pathogenic bacteria. Using a fluorescence polarization 30S-binding assay and a new crystal structure of the methyltransferase RmtC at 3.14 Å resolution, here we report a structure-guided functional study of 30S substrate recognition by the aminoglycoside resistance-associated 16S rRNA (m 7 G1405) methyltransferases. We found that the binding site for these enzymes in the 30S subunit directly overlaps with that of a second family of aminoglycoside resistance-associated 16S rRNA (m 1 A1408) methyltransferases, suggesting that both groups of enzymes may exploit the same conserved rRNA tertiary surface for docking to the 30S. Within RmtC, we defined an N-terminal domain surface, comprising basic residues from both the N1 and N2 subdomains, that directly contributes to 30S-binding affinity. In contrast, additional residues lining a contiguous adjacent surface on the C-terminal domain were critical for 16S rRNA modification but did not directly contribute to the binding affinity. The results from our experiments define the critical features of m 7 G1405 methyltransferase–substrate recognition and distinguish at least two distinct, functionally critical contributions of the tested enzyme residues: 30S-binding affinity and stabilizing a binding-induced 16S rRNA conformation necessary for G1405 modification. Our study sets the scene for future high-resolution structural studies of the 30S-methyltransferase complex and for potential exploitation of unique aspects of substrate recognition in future therapeutic strategies.

(ribosomal RNA) ribosome RNA methylation↗

FOCAL PLANE WAVEFRONT SENSING USING RESIDUAL ADAPTIVE OPTICS SPECKLES

Optical imperfections, misalignments, aberrations, and even dust can significantly limit sensitivity in high-contrast imaging systems such as coronagraphs. An upstream deformable mirror (DM) in the pupil can be used to correct or compensate for these flaws, either to enhance the Strehl ratio or suppress the residual coronagraphic halo. Measurement of the phase and amplitude of the starlight halo at the science camera is essential for determining the DM shape that compensates for any non-common-path (NCP) wavefront errors. Using DM displacement ripples to create a series of probe and anti-halo speckles in the focal plane has been proposed for space-based coronagraphs and successfully demonstrated in the lab. We present the theory and first on-sky demonstration of a technique to measure the complex halo using the rapidly changing residual atmospheric speckles at the 6.5 m MMT telescope using the Clio mid-IR camera. The AO system's wavefront sensor measurements are used to estimate the residual wavefront, allowing us to approximately compute the rapidly evolving phase and amplitude of speckle halo. When combined with relatively short, synchronized science camera images, the complex speckle estimates can be used to interferometrically analyze the images, leading to an estimate of the static diffraction halo with NCP effects included. In an operational system, this information could be collected continuously and used to iteratively correct quasi-static NCP errors or suppress imperfect coronagraphic halos.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effect of polymer residues on the electrical properties of large-area graphene–hexagonal boron nitride planar heterostructures

Polymer residue plays an important role in the performance of 2D heterostructured materials. Herein, we study the effect of polymer residual impurities on the electrical properties of graphene–boron nitride planar heterostructures. Large-area graphene (Gr) and hexagonal boron nitride (h-BN) monolayers were synthesized using chemical vapor deposition techniques. Atomic van-der-Waals heterostructure layers based on varied configurations of Gr and h-BN layers were assembled. The average interlayer resistance of the heterojunctions over a 1 cm 2 area for several planar heterostructure configurations was assessed by impedance spectroscopy and modeled by equivalent electrical circuits. As a result, conductive AFM measurements showed that the presence of polymer residues on the surface of the Gr and h-BN monolayers resulted in significant resistance deviations over nanoscale regions.

36 MATERIALS SCIENCE↗

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA) published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus

Abstract Cellulases are largely afflicted by inhibition from their reaction products, especially at high-substrate loading, which represents a major challenge for biomass processing. This challenge was overcome for endoglucanase 1 (E1) from Acidothermus cellulolyticus by identifying a large conformational change involving distal residues upon binding cellobiose. Having introduced alanine substitutions at each of these residues, we identified several mutations that reduced cellobiose inhibition of E1, including W212A, W213A, Q247A, W249A and F250A. One of the mutations (W212A) resulted in a 47-fold decrease in binding affinity of cellobiose as well as a 5-fold increase in the kcat. The mutation further increased E1 activity on Avicel and dilute-acid treated corn stover and enhanced its productivity at high-substrate loadings. These findings were corroborated by funnel metadynamics, which showed that the W212A substitution led to reduced affinity for cellobiose in the +1 and +2 binding sites due to rearrangement of key cellobiose-binding residues.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamical ejecta from binary neutron star mergers: Impact of a small residual eccentricity and of the equation of state implementation

Predicting the properties of the matter ejected during and after a neutron star merger is crucial to our ability to use electromagnetic observations of these mergers to constrain the masses of the neutron stars, the equation of state of dense matter, and the role of neutron star mergers in the enrichment of the Universe in heavy elements. Furthermore, our ability to reliably provide such predictions is however limited by a broad range of factors, including the finite resolution of numerical simulations, their treatment of magnetic fields, neutrinos, and neutrino-matter interactions, and the approximate modeling of the equation of state of dense matter. In this manuscript, we study specifically the role that a small residual eccentricity and different implementations of the same equation of state have on the matter ejected during the merger of a 1.3M ⊙ –1.4M ⊙ binary neutron star system. We find that a residual eccentricity e ~ 0.01, as measured ~ 4–6 orbits before merger, causes O(25%–30%) changes in the amount of ejected mass, mainly due to changes in the amount of matter ejected as a result of core bounces during merger. We note that O(1%) residual eccentricities have regularly been used in binary neutron star merger simulations as proxy for circular binaries, potentially creating an additional source of error in predictions for the mass of the dynamical ejecta.

79 ASTRONOMY AND ASTROPHYSICS↗

Main-ion intrinsic toroidal rotation profile driven by residual stress torque from ion temperature gradient turbulence in the DIII-D tokamak

Intrinsic toroidal rotation of the deuterium main ions in the core of the DIII-D tokamak is observed to transition from flat to hollow, forming an off-axis peak, above a threshold level of direct electron heating. Nonlinear gyrokinetic simulations show that the residual stress associated with electrostatic ion temperature gradient turbulence possesses the correct radial location and stress structure to cause the observed hollow rotation profile. Residual stress momentum flux in the gyrokinetic simulations is balanced by turbulent momentum diffusion, with negligible contributions from turbulent pinch. Finally, the prediction of the velocity profile by integrating the momentum balance equation produces a rotation profile that qualitatively and quantitatively agrees with the measured main-ion profile, demonstrating that fluctuation-induced residual stress can drive the observed intrinsic velocity profile.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the nonlinear temperature dependence of residual stresses in solid oxide fuel cells

The residual stresses in a dense yttria-stabilized zirconia (YSZ) layer bonded to a porous NiO-YSZ substrate were measured by X-ray diffraction in air between 25°C and 900°C. In this work, it was found that the residual stresses on the outer surface of the YSZ layer were compressive, that their magnitude increased with decreasing temperature, and that the temperature dependence was nonlinear particularly at temperatures below 600°C. An elastic model that incorporates micromechanics and laminate theory was formulated to successfully predicts the nonlinearity of the temperature dependence of the residual stresses by accounting for the effect of the order-disorder transition experienced by YSZ around 600°C and the magnetic transition of NiO at the Néel temperature around 265°C, on the properties of these materials. The implications of the results for the reliability of solid oxide fuel cells are discussed.

25 ENERGY STORAGE↗

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process

Anaerobic digestion of organic residues offers economic benefits via biogas production, still methane (CH 4 ) yield relies on the development of a robust microbial consortia for adequate substrate degradation, among other factors. In this study, we monitor biogas production and changes in the microbial community composition in two semi-continuous stirred tank reactors during the setting process under mesophilic conditions (35°C) using a 16S rDNA high-throughput sequencing method. Reactors were initially inoculated with anaerobic granular sludge from a brewery wastewater treatment plant, and gradually fed organic urban residues (4·0 kg VS m -3 day -1 ) . The inocula and biomass samples showed changes related to adaptations of the community to urban organic wastes including a higher relative proportion of Clostridiales, with Ruminococcus spp. and Syntrophomonas spp. as recurrent species. Candidatus Cloacamonas spp. (Spirochaetes) also increased from ~2·2% in the inoculum to >10% in the reactor biomass. The new community consolidated the cellulose degradation and the propionate and amino acids fermentation processes. Acetoclastic methanogens were more abundant in the reactor, where Methanosaeta spp. was found as a key player. This study demonstrates a successful use of brewery treatment plant granular sludge to obtain a robust consortium for methane production from urban organic solid waste in Mexico.This study describes the selection of relevant bacteria and archaea in anaerobic digesters inoculated with anaerobic granular sludge from a brewery wastewater treatment plant. Generally, these sludge granules are used to inoculate reactors digesting organic urban wastes. Though, it is still not clearly understood how micro-organisms respond to substrate variations during the reactor start-up process. After feeding two reactors with organic urban residues, it was found that a broader potential for cellulose degradation was developed including Bacteroidetes, Firmicutes and Spirochaetes. These results clarify the bacterial processes behind new reactors establishment for treating organic wastes in urban areas.

59 BASIC BIOLOGICAL SCIENCES↗

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

SU-D-16A-06: Modeling Biological Effects of Residual Uncertainties For Stereotactic Radiosurgery

Purpose: Residual uncertainties on the order of 1-2 mm are frequently observed when delivering stereotactic radiosurgery via on-line imaging guidance with a relocatable frame. In this study, a predictive model was developed to evalute potentiral late radiation effects associated with such uncertainties. Methods: A mathematical model was first developed to correlate the peripherial isodose volume with the internal and/or setup margins for a radiosurgical target. Such a model was then integrated with a previoulsy published logistic regression normal tissue complication model for determining the symptomatic radiation necrosis rate at various target sizes and prescription dose levels. The model was tested on a cohort of 15 brain tumor and tumor resection cavity patient cases and model predicted results were compared with the clinical results reported in the literature. Results: A normalized target diameter (D{sub 0}) in term of D{sub 0} = 6V/S, where V is the volume of a radiosurgical target and S is the surface of the target, was found to correlate excellently with the peripheral isodose volume for a radiosurgical delivery (logarithmic regression R{sup 2} > 0.99). The peripheral isodose volumes were found increase rapidly with increasing uncertainties levels. In general, a 1-mm residual uncertainties as calculated to result in approximately 0.5%, 1%, and 3% increases in the symptomatic radiation necrosis rate for D{sub 0} = 1 cm, 2 cm, and 3 cm based on the prescription guideline of RTOG 9005, i.e., 21 Gy to a lesion of 1 cm in diameter, 18 Gy to a lesion 2 cm in diameter, and 15 Gy to a lesion 3 cm in diameter respectively. Conclusion: The results of study suggest more stringent criteria on residual uncertainties are needed when treating a large target such as D{sub 0}≤ 3 cm with stereotactic radiosurgery. Dr. Ma and Dr. Sahgal are currently serving on the board of international society of stereotactic radiosurgery (ISRS)

60 APPLIED LIFE SCIENCES↗

Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation

Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative “cap helix” region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. Ultimately, this study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗