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At least 631 records · Page 35

Angular alignment and fidelity of neutron phase-gratings for improved interferometer fringe visibility

The recent development of phase-grating moiré neutron interferometry promises a wide range of impactful experiments from dark-field imaging of material microstructure to precise measurements of fundamental constants. However, the contrast of 3% obtained using this moiré interferometer was well below the theoretical prediction of 30% using ideal gratings. It is suspected that non-ideal aspects of the phase-gratings was a leading contributor to this deficiency and that phase-gratings needed to be quantitatively assessed and optimized. Here we characterize neutron diffraction from phase-gratings using Bragg diffraction crystals to determine the optimal phase-grating orientations. We show well-defined diffraction peaks and explore perturbations to the diffraction peaks and the effects on interferometer contrast as a function of grating alignment. This technique promises to improve the contrast of the grating interferometers by providing in-situ aides to grating alignment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

One-directional thermal transport in densely aligned single-wall carbon nanotube films

Individual carbon nanotubes (CNTs) possess extremely high thermal conductivities. However, the thermal conductivities and their anisotropy of macroscopic assemblies of CNTs have so far remained small. Here, we report the results of directional thermal transport measurements on a nearly perfectly aligned CNT film fabricated via controlled vacuum filtration. We found the thermal conductivity to be 43 ± 2.2 W m -1 K -1 with a record-high thermal anisotropy of 500. From the temperature dependence of the thermal conductivity and its agreement with the atomistic phonon transport calculation, we conclude that the effect of intertube thermal resistance on heat conduction in the alignment direction is negligible because of the large contact area between CNTs. These observations thus represent ideal unidirectional thermal transport, i.e., the thermal conductivity of the film is determined solely by that of individual CNTs.

42 ENGINEERING↗

Rotational self-alignment of graphene seeds for nanoribbon synthesis on Ge(001) via chemical vapor deposition

The chemical vapor deposition of CH 4 on Ge(001) results in the anisotropic synthesis of graphene nanoribbons that are aligned to Ge$\langle$110$\rangle$ and have faceted armchair edges, sub-10 nm widths, and lengths greater than 100 nm. The utilization of small graphene seeds to initiate nanoribbon synthesis provides control over the nanoribbon placement and orientation. However, in order to exclusively grow nanoribbons and suppress the concomitant growth of lower aspect ratio crystals, it is imperative to control the crystallographic orientation of the seeds with respect to the Ge lattice. Here, we demonstrate that when seeds are less than 18 nm in diameter, they are able to rotate upon annealing at 910 °C prior to nanoribbon synthesis. The effect of this rotation on the resulting nanoribbons’ orientation is characterized as a function of the diameter and initial crystallographic orientation of the seeds. The seeds preferentially rotate to an orientation in which an armchair direction of their lattice is parallel to Ge$\langle$110$\rangle$—subsequently maximizing the anisotropy in growth kinetics. By exploiting this seed rotation phenomenon, we demonstrate the fabrication of seamless nanoribbon meshes and gain understanding that will affect future efforts to create arrays of unidirectionally aligned nanoribbons.

36 MATERIALS SCIENCE↗

Roles of bandgrading, lifetime, band alignment, and carrier concentration in high-efficiency CdSeTe solar cells

CdSeTe alloying has significantly increased the efficiency of CdTe-based solar technology. Here, computational modeling compares how different CdSeTe bandgrading, carrier lifetimes, band alignment, and carrier concentrations contribute to transport, recombination, and performance. We find that the gain in photocurrent caused by bandgap narrowing alone is insufficient to describe experimental efficiency gains. Performance can be increased by adjusting CdSeTe compositions and bandgrading depths. However, these performance gains are small relative to the contributions of enhanced lifetime by Se alloying, which can explain record cell efficiency gains with minimal open-circuit voltage loss despite significant bandgap narrowing. Similarly, CdSeTe band alignment shifts can significantly increase performance if front interface recombination is prevalent. For a wide range of CdSeTe grading profiles, the hole density is a critical component to achieve efficiencies exceeding 25%.

36 MATERIALS SCIENCE↗

Pressure–strain interaction. II. Decomposition in magnetic field-aligned coordinates

In weakly collisional and collisionless magnetized plasmas, the pressure–strain interaction describes the rate of conversion between bulk flow and thermal energy density. In this study, we derive an analytical expression for the pressure–strain interaction in a coordinate system with an axis aligned with the local magnetic field. The result is eight groups of terms corresponding to different physical mechanisms that can contribute to the pressure–strain interaction. We provide a physical description of each term. Here, the results are immediately of interest to weakly collisional and collisionless magnetized plasmas and the fundamental processes that happen therein, including magnetic reconnection, magnetized plasma turbulence, and collisionless shocks. The terms in the field-aligned coordinate decomposition are likely accessible to measurement with satellite observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dangling bonds, the charge neutrality level, and band alignment in semiconductors

We present a systematic study of the electronic properties of dangling bonds (DBs) in a variety of semiconductors and examine the relationship between DBs and the charge neutrality level (CNL) in the context of band alignments of semiconductors. We use first-principles calculations based on density functional theory to assess the energetics of DBs in a set of diamond-structure group-IV and III–V or II–VI zinc-blende-structure semiconductors, considering both cation and anion-derived states. We examine the charge-state transition levels of DBs to assess whether they can serve as a CNL to align band structures, by comparing with offsets calculated from interface calculations. Our results show that this approach for evaluating the CNL yields quantitative results for band offsets and provides useful insights. We discuss the relation with alternative approaches for determination of CNLs based on branch-point energies or transition levels of interstitial hydrogen.

36 MATERIALS SCIENCE↗

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES↗

MODELING THE JET KINEMATICS OF THE BLACK HOLE MICROQUASAR XTE J1550-564: A CONSTRAINT ON SPIN-ORBIT ALIGNMENT

Measurements of black hole spin made using the continuum-fitting method rely on the assumption that the inclination of the black hole's spin axis to our line of sight is the same as the orbital inclination angle i of the host binary system. The X-ray and radio jet data available for the microquasar XTE J1550-564 offer a rare opportunity to test this assumption. Following the work of others, we have modeled these data and thereby determined the inclination angle {theta} of the jet axis, which is presumed to be aligned with the black hole's spin axis. We find {theta} Almost-Equal-To 71 Degree-Sign and place an upper limit on the difference between the spin and orbital inclinations of |{theta} - i| < 12 Degree-Sign (90% confidence). Our measurement tests for misalignment along the line of sight while providing no constraint perpendicular to this plane. Our constraint on the misalignment angle supports the prediction that the spinning black hole in XTE J1550-564 has aligned itself with the orbital plane and provides support for the measurement of its spin via the continuum-fitting method. Our conclusions are based on a simple and reasonable model of a pair of symmetric jets propagating into a low-density cavity whose western wall is Almost-Equal-To 20% closer to XTE J1550-564 than its eastern wall.

79 ASTRONOMY AND ASTROPHYSICS↗

No evidence for Bardeen-Petterson alignment in GRMHD simulations and semi-analytic models of moderately thin, prograde, tilted accretion disks

In this paper, we introduce the first results that use data extracted directly from numerical simulations as inputs to the analytic twisted disk model of Zhuravlev and Ivanov. In both numerical and analytic approaches, fully relativistic models of tilted and twisted disks having a moderate effective viscosity around a slowly rotating Kerr black hole are considered. Qualitatively, the analytic model demonstrates the same dynamics as the simulations, although with some quantitative offset. Namely, the general relativistic magnetohydrodynamic simulations typically give smaller variations of tilt and twist across the disk. When the black hole and the disk rotate in the same direction, the simulated tilted disk and analytic model show no sign of Bardeen-Petterson alignment, even in the innermost parts of the disk where the characteristic time for relaxation to a quasi-stationary configuration is of the same order as the computation time. In the opposite case, when the direction of the disk's rotation is opposite to that of the black hole, a partial alignment is observed, in agreement with previous theoretical estimates. Thus, both fully numerical and analytic schemes demonstrate that the Bardeen-Petterson effect may not be possible for the case of prograde rotation provided that disk's effective viscosity is sufficiently small. This may have implications in modeling of different astrophysical phenomena such as disk spectra and jet orientation.

79 ASTRONOMY AND ASTROPHYSICS↗

FORMATION AND ALIGNMENT OF ELONGATED, FRACTAL-LIKE WATER-ICE GRAINS IN EXTREMELY COLD, WEAKLY IONIZED PLASMA

Elongated, fractal-like water-ice grains are observed to form spontaneously when water vapor is injected into a weakly ionized laboratory plasma formed in a background gas cooled to an astrophysically relevant temperature. The water-ice grains form in 1–2 minutes, levitate with regular spacing, and are aligned parallel to the sheath electric field. Water-ice grains formed in plasma where the neutrals and ions have low mass, such as hydrogen and helium, are larger, more elongated, and more fractal-like than water-ice grains formed in plasmas where the neutrals and ions have high mass such as argon and krypton. Typical aspect ratios (length to width ratio) are as great as 5 while typical fractal dimensions are ∼1.7. Water-ice grain lengths in plasmas with low neutral and ion masses can be several hundred microns long. Infrared absorption spectroscopy reveals that the water-ice grains are crystalline and so are similar in constitution to the water-ice grains in protoplanetary disks, Saturn’s rings, and mesospheric clouds. The properties and behavior of these laboratory water-ice grains may provide insights into morphology and alignment behavior of water-ice grains in astrophysical dusty plasmas.

79 ASTRONOMY AND ASTROPHYSICS↗

Intermittency and alignment in strong RMHD turbulence

We develop an analytic model of intermittent, three-dimensional, strong, reduced magnetohydrodynamic (RMHD) turbulence with zero cross helicity. We take the fluctuation amplitudes to have a log-Poisson distribution and incorporate into the model a new phenomenology of scale-dependent dynamic alignment between the Elsässer variables z{sup ±}. We find that the structure function 〈|Δz{sub λ}{sup ±}|{sup n}〉 scales as λ{sup 1−β{sup n}}, where Δz{sub λ}{sup ±} is the variation in z{sup ±} across a distance λ perpendicular to the magnetic field. We calculate the value of β to be ≃ 0.69 based on our assumption that the most intense coherent structures are two-dimensional with a volume filling factor ∝ λ. Two consequences of this structure-function scaling are that the total-energy power spectrum is ∝ k{sub ⊥}{sup −1.52} and the kurtosis of the fluctuations is ∝ λ{sup −0.27}. Our model resolves the problem that alignment angles defined in different ways exhibit different scalings. Specifically, we find that the energy-weighted average angle between the velocity and magnetic-field fluctuations is ∝ λ{sup 0.21}, the energy-weighted average angle between Δz{sup +} and Δz{sup −} is ∝ λ{sup 0.10}, and the average angle between Δz{sup +} and Δz{sup −} without energy weighting is ∝ [ln(L/λ)]{sup −1/2} when L/λ≫1, where L is the outer scale. We also carry out a direct numerical simulation of RMHD turbulence. The scalings in our model are similar to the scalings in this simulation as well as the structure-function scalings observed in the slow solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗

Chemical Solution Derived Planarization Layers for Highly Aligned IBAD MgO Templates

The main goal of this research is to develop a chemical solution derived planarization layer to fabricate highly aligned IBAD-MgO templates for the development of high temperature superconductor (HTS) based coated conductors. The standard IBAD-MgO template needs an additional electrochemical polishing step of the mechanically polished 50- m-thick Hastelloy C-276 substrates to ensure a flat and smooth surface for subsequent growth of multi-layer buffer architectures, which include: sputtered 80-nm Al2O3; sputtered 7-nm Y2O3; IBAD 10-nm MgO; sputtered 30-nm homo-epi MgO; and sputtered 30-nm LaMnO3 (LMO) layers. We have successfully developed a solution planarization layer that removes the electrochemical polishing step and also acts as a barrier layer. Crack-free, smooth Al2O3 layers were prepared on mechanically polished Hastelloy substrates using a chemical solution process. A nearly 10-15-nm thick Al2O3 layer was formed with each coating and the coating was repeated several times to achieve the desired film thickness with intermediate heat-treatments after each coating. The Al2O3 planarization layer significantly reduced the surface roughness of the substrate. The average surface roughness value, Ra for a starting substrate was 9-10 nm. After 8 coatings of Al2O3 layer, the Ra was reduced to 2 nm. Highly aligned IBAD-MgO layers with out-of-plane and in-plane textures comparable to the standard IBAD-MgO layers were successfully deposited on top of the solution planarization Al2O3 layers with an Y2O3 nucleation layer using a reel-to-reel ion-beam sputtering system. Both homo-epi MgO and LMO layers were subsequently deposited on the IBAD-MgO layers using rf sputtering to complete the buffer stack required for the growth of HTS films. YBa2Cu3O7- (YBCO) films with a thickness of 0.8 m deposited on these IBAD-MgO templates by pulsed laser deposition showed a high self-field critical current density, Jc of 3.04 MA/cm2 at 77 K and 6.05 MA/cm2 at 65 K. These results demonstrate that a low-cost chemical-solution-based, high-throughput Al2O3 planarization layer can remove the electro-polishing step and replace sputtered Al2O3 layers for the production of high Jc YBCO-coated conductors.

Paranthaman, Mariappan Parans↗

Aligning thermal and current quenches with a high density low-Z injection

The conventional approach for thermal quench (TQ) mitigation in a tokamak disruption is through a high- Z impurity injection that radiates away the plasma’s thermal energy before it reaches the wall. The downside is a robust Ohmic-to-runaway current conversion due to the radiatively clamped low post-thermal-quench electron temperature. An alternative approach is to deploy a low- Z (either deuterium or hydrogen) injection that aims to slow down the TQ, and ideally aligns it with the current quench (CQ). This approach has been investigated here via 3D MHD simulations using the PIXIE3D code. By boosting the hydrogen density, a fusion-grade plasma is dilutionally cooled at approximately the original pressure. Energy loss to the wall is controlled by a Bohm outflow condition at the boundary where the magnetic field intercepts a thin plasma sheath at the wall, in addition to Bremsstrahlung bulk losses. Robust MHD instabilities proceed as usual, while the collisionality of the plasma has been greatly increased and parallel transport is now in the Braginskii regime. The main conclusion of this study is that the decreased transport loss along open field lines due to a sufficient low- Z injection slows down the TQ rate to the order of 20 ms, aligned with the CQ timescale for a 15 MA ITER plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Web-based application for the collection, management and release of Alignment and Calibration configurations used in data processing at the Compact Muon Solenoid experiment

The Compact Muon Solenoid (CMS) experiment makes a vast use of alignment and calibration measurements in several data processing workflows: in the High Level Trigger, in the processing of the recorded collisions and in the production of simulated events for data analysis and studies of detector upgrades. A complete alignment and calibration scenario is factored in approximately three-hundred records, which are updated independently and can have a time-dependent content, to reflect the evolution of the detector and data taking conditions. Given the complexity of the CMS condition scenarios and the large number (50) of experts who actively measure and release calibration data, in 2015 a novel web-based service has been developed to structure and streamline their management. The cmsDbBrowser provides an intuitive and easily accessible entry point for the navigation of existing conditions by any CMS member, for the bookkeeping of record updates and for the actual composition of complete calibration scenarios. This paper describes the design, choice of technologies and the first year of usage in production of the cmsDbBrowser.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ultrafast infrared plasmon switching in aligned carbon-nanotube optical resonators

Reconfigurable plasmonic materials are crucial components in active photonic devices for optical communication, signal processing, and sensing applications. Certain candidates including transparent conducting oxides, small-bandgap semiconductors (i.e. Ge, InSb), and conducting polymers can exhibit switchable free carrier concentrations triggered by optical, electrical or thermal excitations. Here, we show that aligned films of single-walled carbon nanotubes (SWCNTs) can serve as all-optically tunable plasmonic material in the mid-infrared range, thereby adding them to the library of switchable plasmonic materials. Interband optical pumping with femtosecond laser pulses results in the photoexcitation of free charge carriers, which transiently blueshifts the plasmon resonances of patterned, periodic SWCNT nano-resonators spanning the mid-infrared spectral range from 1700 to 2700 cm -1 . Furthermore. the ultrafast plasmon modulation exhibits a nearly single-picosecond decay time, attributed to interband carrier relaxation and inter-tube charge transfer. Given that aligned films of SWCNTs have high thermal stability, excellent photostability, epsilon-near-zero property, and extremely large optical anisotropy, their dynamic tunability represents a promising pathway towards active optical devices in the technologically important mid-infrared range.

single-walled carbon nanotubes↗

CoverM: read alignment statistics for metagenomics

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.

Aroney, Samuel T N↗

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.

59 BASIC BIOLOGICAL SCIENCES↗

Alignment of the magnetic field in star-forming regions and why it might be difficult to observe

ABSTRACT Magnetic fields are an important component of the interstellar medium (ISM) and exhibit strongly varying field strengths and a non-trivial correlation with the gas density. Its dynamical impact varies between individual regions of the ISM and correlates with the orientation of the field with respect to the gas structures. Using high-resolution magneto-hydrodynamical simulations of the ISM, we explore the connection between the orientation of the field and the dynamical state of the gas. We find that the onset of gravitational instability in molecular gas above a density of $\rho \sim 10^{-21}\, \mathrm{g\, cm}^{-3}$$(n\sim 400\, \mathrm{cm}^{-3})$ coincides with an alignment of the magnetic field lines and the gas flow. At this transition, the gradient of the density changes from mainly perpendicular to preferentially parallel to the field lines. A connection between the three-dimensional alignment and projected two-dimensional observables is non-trivial, because of a large dispersion of the magnetic field orientation along the line of sight. The turbulent correlation lengths can be small compared to the typical integration lengths. As a consequence, the small-scale signal of the orientation can sensitively depend on the line of sight or the dynamical state of the cloud can fluctuate stochastically or be completely averaged out. With higher spatial resolution more small-scale structures are resolved, which aggravates the link between magneto-hydrodynamical quantities and projected observables.

Girichidis, Philipp (ORCID:0000000293009914)↗