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At least 217 records · Page 12

MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Motivation: Alignment of protein–protein interaction networks can be used for the unsupervised prediction of functional modules, such as protein complexes and signaling pathways, that are conserved across different species. To date, various algorithms have been proposed for biological network alignment, many of which attempt to incorporate topological similarity between the networks into the alignment process with the goal of constructing accurate and biologically meaningful alignments. Especially, random walk models have been shown to be effective for quantifying the global topological relatedness between nodes that belong to different networks by diffusing node-level similarity along the interaction edges. However, these schemes are not ideal for capturing the local topological similarity between nodes. Results: Here, we propose MONACO, a novel and versatile network alignment algorithm that finds highly accurate pairwise and multiple network alignments through the iterative optimal matching of ‘local’ neighborhoods around focal nodes. Extensive performance assessment based on real networks as well as synthetic networks, for which the ground truth is known, demonstrates that MONACO clearly and consistently outperforms all other state-of-the-art network alignment algorithms that we have tested, in terms of accuracy, coherence and topological quality of the aligned network regions. Furthermore, despite the sharply enhanced alignment accuracy, MONACO remains computationally efficient and it scales well with increasing size and number of networks.

97 MATHEMATICS AND COMPUTING↗

Dynamic Aperture of the PIP-II Accumulator Ring (PAR)

The Proton Improvement Plan-II (PIP-II) will include a superconducting linear accelerator which will accelerate H- ions to 800MeV, at an intensity never seen before. A proposed PIP-II Accumulator Ring (PAR) can reduce the injection losses to the booster, enhance the ramp up of the Long Baseline Neutrino Facility (LBNF) and support experiments in Dark Sector Physics. When the beam is circulating in PAR at its full intensity, it will then be transferred to the Booster via single turn injection. Strong PAR focusing results in larger phase advances, shorter focal lengths and higher machine tunes, which creates robust beam envelope control. Particles will be able to survive modest excursions from the elliptical phase-space trajectories of linear optics, and any loss of particles would be due to reduced dynamic aperture. The values for tunes and chromaticities are flexible and will continue to evolve as the lattice matures. Since there will be non-linear terms impacting the particles’ trajectories, tracking will include realistic magnetic field errors and installation alignment errors to determine the dynamic aperture as a function of the machine tunes. This will allow us to determine the optimum operating point in phase-space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulation of Plasma Emission in Magnetized Plasmas

The recent Parker Solar Probe observations of type III radio bursts show that the effects of the finite background magnetic field can be an important factor in the interpretation of data. In the present paper, the effects of the background magnetic field on the plasma-emission process, which is believed to be the main emission mechanism for solar coronal and interplanetary type III radio bursts, are investigated by means of the particle-in-cell simulation method. The effects of the ambient magnetic field are systematically surveyed by varying the ratio of plasma frequency to electron gyrofrequency. The present study shows that for a sufficiently strong ambient magnetic field, the wave–particle interaction processes lead to a highly field-aligned longitudinal mode excitation and anisotropic electron velocity distribution function, accompanied by a significantly enhanced plasma emission at the second-harmonic plasma frequency. For such a case, the polarization of the harmonic emission is almost entirely in the sense of extraordinary mode. On the other hand, for moderate strengths of the ambient magnetic field, the interpretation of the simulation result is less clear. The underlying nonlinear-mode coupling processes indicate that to properly understand and interpret the simulation results requires sophisticated analyses involving interactions among magnetized plasma normal modes, including the two transverse modes of the magneto-active plasma, namely, the extraordinary and ordinary modes, as well as electron-cyclotron-whistler, plasma oscillation, and upper-hybrid modes. At present, a nonlinear theory suitable for quantitatively analyzing such complex-mode coupling processes in magnetized plasmas is incomplete, which calls for further theoretical research, but the present simulation results could provide a guide for future theoretical efforts.

79 ASTRONOMY AND ASTROPHYSICS↗

An automated system for the alignment of large area modular solar simulators

A real-time optical alignment and diagnostic system is being assembled for installation at the Space Environment Simulation Laboratory. This system will be used to measure and analyze the performance of optical components, assemblies, and full modules. This information, in turn, is used to align assemblies and modules. The system capability includes such functions as the generation and updating of a catalog, which serves as permanent record, in addition to providing the capability to predict in-chamber performance of optics combinations before they are mounted in the chamber.

Vincent, J. P.↗

Precision navigation for approach and landing operations.

This paper summarizes some of the practical considerations and implementation techniques used in the development of the onboard software for an experimental navigation system. This software includes (1) a Kalman filter implementation in square-root form with gyro and accelerometer noises modeled as random forcing functions in the filter; (2) operational modes for inflight alignment, ground alignment, normal aided inertial navigation operation, and postflight analysis; (3) a sophisticated time-sharing system for obtaining a very flexible input-output capability during real-time operations; and (4) a problem formulation and scaling for complete operation in single-precision arithmetic using a 24-bit word. The paper emphasizes the procedures used in formulation, scaling, and time-sharing for the real-time Kalman filter application. Some flight results are presented to illustrate the performance of the filter during real-time operation.

Schmidt, S. F.↗

One-dimensional models of quasi-neutral parallel electric fields

Parallel electric fields can exist in the magnetic mirror geometry of auroral field lines if they conform to the quasineutral equilibrium solutions. Results on quasi-neutral equilibria and on double layer discontinuities were reviewed and the effects on such equilibria due to non-unique solutions, potential barriers and field aligned current flows using as inputs monoenergetic isotropic distribution functions were examined.

Stern, D. P.↗

Core plasma in the magnetosphere

The paper presents a review of new findings related to core plasma (which includes ions and electrons with energies less than 50 eV) identified in studies of magnetosphere during 1983-1986. These findings include the cleft ion fountain; the plasmaspheric heavy ion torus; core molecular ions; high core-plasma densities in the plasma-sheet boundary layer; intense transverse heating of core plasmas in the equatorial regions; the supersonic polar wind (H/+/ and He/+/); toroidal or ring heavy-ion distribution functions in the auroral region; conic-to-field-aligned ion signatures of inverted-V auroral events; and the large-scale electron density structure of the magnetosphere. The progress made on modeling core plasma includes simulation of thermal helium heating at the equator; kinetic models of the plasma transport from localized ionospheric regions; time-dependent hydrodynamic models of the polar wind and plasmasphere-ionosphere coupling; and kinetic models of plasmasphere refilling.

Horwitz, J. L.↗

Toward an IMU-based Space Suit Motion Capture System

Spacesuits are complex engineering systems that sustain human health and enable performance outside of Earth-like environments. These systems must support human mobility and physical workload demands while minimizing injury risk during extravehicular activity (EVA). Future EVA on the lunar surface during the Artemis program is expected to be more frequent and require higher physical workloads than previous EVAs during the ISS, Shuttle, or Apollo programs. Hence it is important to optimize future as well as current spacesuits to be efficient and comfortable for the success of space and planetary missions. To enable this, an efficient method is needed to test these spacesuits on the ground.When testing spacesuits in ground environments, it is often necessary to understand the kinematics of the suit to validate the design against relevant requirements or characterize the physical workload necessary to operate the suit. This is a challenging task for traditional optical motion capture (OMC) approaches: suit-mounted OMC markers are easily occluded by the subject or environment and may become detached during testing. Controlling lighting and reflectivity of objects in the motion capture volume is also difficult. Fixed-position OMC cameras also constrain testing to a small and contrived laboratory environment, disallowing kinematics capture in field environments.One promising alternative is the use of suit-mounted inertial measurement units (IMUs). These sensors are small, unobtrusive, and portable, but come at the cost of increased sensor noise and complexity of the software and mathematics to analyze the collected data. To this end, engineers at NASA are developing the Augmented Suit Inverse Kinematics (ASIK) system, a complete motion capture methodand inverse kinematics solver which relies solely on a network of wireless IMUs attached to the major kinematic segments of the spacesuit. The ASIK modeling language allows for the simple inclusion of probabilistic priors such as suit size and shape or IMU positions and rotations. Furthermore, to increase accuracy and reduce operational overhead to use this motion capture approach, the developed inverse kinematics solver exploits so-called self-calibratingalgorithmic techniques, which reduce the need for precise alignment of the sensors on the segments or scripted functional calibration procedures. The ASIK system was tested in a 7-subject pilot study. Each subject donned NASA’s new prototype exploration spacesuit in the Active Response Gravity Offload System (ARGOS) facility at the NASA Johnson Space Center. The subjects were outfitted with a set of 14 APDM (Portland, OR, USA) Opal IMUs, 12 of which were used in the ASIK model to estimate lower body and trunk kinematics. The subjects were also outfitted with a set of reflective OMC markers and traditional OMC data was collected and processed. Presented results will include characterization of ASIK-derived suit joint angles accuracy against an optical motion capture datum. Discussion of these results, as well as discussion of system calibration and nuances of mathematical observability, will be included.If successful, IMU-based motion capture will enable testing and validation of spacesuits more frequently, with less overhead, in more extreme environments. Future work will apply these techniques to common spacesuit testing tasks, such as gait, mobility, and balance assessment, physical workload characterization, and ergonomics evaluations.

Timothy Mcgrath↗

Matrix converter operating in current control mode using feed forward signals

A matrix converter system having a current control mode operation is provided. The system includes a matrix converter having a switching matrix. The matrix converter is coupled at its low-voltage side to a generator and at its output load side to a load. A controller having a pulse width modulation (PWM) control circuit is configured to control the matrix converter via its switching matrix to increase energy within the internal inductances of the generator when the switching matrix causes a short circuit. A feed forward calculator is configured to calculate a feed forward output phase angle. The feed forward output phase angle is an estimation of an angle between an output current vector and an output voltage vector that represent feedback signals of current and voltage output by the matrix converter. The angular position of the voltage output vector is adjusted as a function of the feed forward output phase angle to align angular position or phase angle of the voltage output vector that represents the voltage output with a selected angular position or phase angle.

42 ENGINEERING↗

On-Orbit Lunar Modulation Transfer Function Measurements for the Moderate Resolution Imaging Spectroradiometer

Spatial quality of an imaging sensor can be estimated by evaluating its modulation transfer function (MTF) from many different sources such as a sharp edge, a pulse target, or bar patterns with different spatial frequencies. These well-defined targets are frequently used for prelaunch laboratory tests, providing very reliable and accurate MTF measurements. A laboratory-quality edge input source was included in the spatial-mode operation of the Spectroradiometric Calibration Assembly (SRCA), which is one of the onboard calibrators of the Moderate Resolution Imaging Spectroradiometer (MODIS). Since not all imaging satellites have such an instrument, SRCA MTF estimations can be used as a reference for an on-orbit lunar MTF algorithm and results. In this paper, the prelaunch spatial quality characterization process from the Integrated Alignment Collimator and SRCA is briefly discussed. Based on prelaunch MTF calibration using the SRCA, a lunar MTF algorithm is developed and applied to the lifetime on-orbit Terra and Aqua MODIS lunar collections. In each lunar collection, multiple scan-directionMoon-to-background transition profiles are aligned by the subpixel edge locations from a parametric Fermi function fit. Corresponding accumulated edge profiles are filtered and interpolated to obtain the edge spread function (ESF). The MTF is calculated by applying a Fourier transformation on the line spread function through a simple differentiation of the ESF. The lifetime lunar MTF results are analyzed and filtered by a relationship with the Sun-Earth-MODIS angle. Finally, the filtered lunarMTF values are compared to the SRCA MTF results. This comparison provides the level of accuracy for on-orbit MTF estimations validated through prelaunch SRCA measurements. The lunar MTF values had larger uncertainty than the SRCA MTF results; however, the ratio mean of lunarMTF fit and SRCA MTF values is within 2% in the 250- and 500-m bands. Based on the MTF measurement uncertainty range, the suggested lunar MTF algorithm can be applied to any on-orbit imaging sensor with lunar calibration capability.

Choi, Taeyong↗

Cosmological constraints using Minkowski functionals from the first year data of the Hyper Suprime-Cam

We use Minkowski functionals to analyse weak lensing convergence maps from the first-year data release of the Subaru Hyper Suprime-Cam (HSC-Y1) survey. Minkowski functionals provide a description of the morphological properties of a field, capturing the non-Gaussian features of the Universe matter-density distribution. Using simulated catalogues that reproduce survey conditions and encode cosmological information, we emulate Minkowski functionals predictions across a range of cosmological parameters to derive the best-fit from the data. By applying multiple scales cuts, we rigorously mitigate systematic effects, including baryonic feedback and intrinsic alignments. From the analysis, combining constraints of the angular power spectrum and Minkowski functionals, we obtain S8≡σ8Ωm/0.3=0.808−0.046+0.033 and Ωm=0.293−0.043+0.157⁠. These results represent a 40 per cent improvement on the S8 constraints compared to using power spectrum only. Minkowski functionals results are consistent with other two-point, and higher order statistics constraints using the same data, being in agreement with CMB results from the Planck S8 measurements. Our study demonstrates the power of Minkowski functionals beyond two-point statistics to constrain and break the degeneracy between Ωm and σ8⁠.

79 ASTRONOMY AND ASTROPHYSICS↗

Multifunctional Metal–Oxide Nanocomposite Thin Film with Plasmonic Au Nanopillars Embedded in Magnetic La 0.67 Sr 0.33 MnO 3 Matrix

Searching for multifunctional materials with tunable magnetic and optical properties has been a critical task toward the implementation of future integrated optical devices. Vertically aligned nanocomposite (VAN) thin films provide a unique platform for multifunctional material designs. In this work, a new metal–oxide VAN has been designed with plasmonic Au nanopillars embedded in a ferromagnetic La 0.67 Sr 0.33 MnO 3 (LSMO) matrix. Such Au–LSMO nanocomposite presents intriguing plasmon resonance in the visible range and magnetic anisotropy property, which are functionalized by the Au and LSMO phase, respectively. Furthermore, the vertically aligned nanostructure of metal and dielectric oxide results in the hyperbolic property for near-field electromagnetic wave manipulation. Such optical and magnetic response could be further tailored by tuning the composition of Au and LSMO phases.

36 MATERIALS SCIENCE↗

Self-assembled vertically aligned nanocomposite systems integrated on silicon substrate: Progress and future perspectives

Silicon (Si) integration is a critical step for implementing functional oxides into Si-based electronic devices, considering the advantages of low-cost and scalability of Si substrates. In the past decade, self-assembled vertically aligned nanocomposites (VANs) have attracted enormous research interest owing to their unique multifunctionalities and highly tunable physical properties as well as their one-step self-assembly process. Most of the VAN thin films have been reported to grow epitaxially on single crystalline oxide substrates, however, with limited systems reported on Si substrates due to the very large lattice mismatch between oxides and Si lattices. In this review, the current progress for self-assembled VAN systems integrated on a Si substrate is summarized. Buffer layered enabled VAN growth has been proven to be an effective approach for improving the epitaxial quality of oxide-oxide and oxide-metal VAN systems, while direct growth is preferred in nitride-metal VAN systems. Furthermore, the material versatility enables the Si-integrated VAN thin films to exhibit distinct physical properties such as ferromagnetism, ferroelectricity, magnetoresistance, as well as unique optical properties. The review also summarizes the various parameters for tuning the growth morphologies and corresponding properties for the VAN systems, including phase molar ratio, deposition frequency, buffer layers, background pressure, etc. Finally, future perspectives are discussed including new VAN system exploration, physical properties tuning, as well as design and fabrication of Si-based nanoelectronics and nanophotonic devices applications.

36 MATERIALS SCIENCE↗

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↗

Anisotropic optical and magnetic response in self-assembled TiN–CoFe 2 nanocomposites

Transition metal nitrides (e.g., TiN) have shown tremendous promise in optical metamaterials for nanophotonic devices due to their plasmonic properties comparable to noble metals and superior high temperature stability. Vertically aligned nanocomposites (VANs) offer a great platform for combining two dissimilar functional materials with a one-step deposition technique toward multifunctionality integration and strong structural/property anisotropy. Here, we report a two-phase nanocomposite design combining ferromagnetic CoFe 2 nanosheets in the plasmonic TiN matrix as a new hybrid plasmonic metamaterial. The hybrid metamaterials exhibit anisotropic optical and magnetic responses, as well as a pronounced magneto-optical coupling response evidenced by Magneto-optic Kerr Effect measurement, owing to the novel vertically aligned structure. This work demonstrates a new TiN-based metamaterial with anisotropic properties and multifunctionality toward light polarization modulation, optical switching, and integrated optics.

36 MATERIALS SCIENCE↗

The Damper Spring Unit of the Sentinel 1 Solar Array

The Damper Spring Unit (DSU, see Figure 1) has been designed to provide the damping required to control the deployment speed of the spring driven solar array deployment in an ARA Mk3 or FRED based Solar Array in situations where the standard application of a damper at the root-hinge is not feasible. The unit consists of four major parts: a main bracket, an eddy current damper, a spring unit, an actuation pulley which is coupled via Kevlar cables to a synchro-pulley of a hinge. The damper slows down the deployment speed and prevents deployment shocks at deployment completion. The spring unit includes 4 springs which overcome the resistances of the damper and the specific DSU control cable loop. This means it can be added to any spring driven deployment system without major modifications of that system. Engineering models of the Sentinel 1 solar array wing have been built to identify the deployment behavior, and to help to determine the optimal pulley ratios of the solar array and to finalize the DSU design. During the functional tests, the behavior proved to be very sensitive for the alignment of the DSU. This was therefore monitored carefully during the qualification program, especially prior to the TV cold testing. During TV "Cold" testing the measured retarding torque exceeded the max. required value: 284 N-mm versus the required 247 N-mm. Although this requirement was not met, the torque balance analysis shows that the 284 N-mm can be accepted, because the spring unit can provide 1.5 times more torque than required. Some functional tests of the DSU have been performed without the eddy current damper attached. It provided input data for the ADAMS solar array wing model. Simulation of the Sentinel-1 deployment (including DSU) in ADAMS allowed the actual wing deployment tests to be limited in both complexity and number of tests. The DSU for the Sentinel-1 solar array was successfully qualified and the flight models are in production.

Doejaaren, Frans↗

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↗

An Innovative Infrastructure with a Universal Geo-Spatiotemporal Data Representation Supporting Cost-Effective Integration of Diverse Earth Science Data

The SpatioTemporal Adaptive Resolution Encoding (STARE) is a unifying scheme encoding geospatial and temporal information for organizing data on scalable computing/storage resources, minimizing expensive data transfers. STARE provides a compact representation that turns set-logic functions into integer operations, e.g. conditional sub-setting, taking into account representative spatiotemporal resolutions of the data in the datasets. STARE geo-spatiotemporally aligns data placements of diverse data on massive parallel resources to maximize performance. Automating important scientific functions (e.g. regridding) and computational functions (e.g. data placement) allows scientists to focus on domain-specific questions instead of expending their efforts and expertise on data processing. With STARE-enabled automation, SciDB (Scientific Database) plus STARE provides a database interface, reducing costly data preparation, increasing the volume and variety of interoperable data, and easing result sharing. Using SciDB plus STARE as part of an integrated analysis infrastructure dramatically eases combining diametrically different datasets.

Rilee, Michael Lee↗