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At least 145 records · Page 8

Ionization induced dynamic alignment of water

Two-body dissociation resulting from strong-field double ionization of water is investigated. Two distinct features are seen in the alignment of the fragment momenta with respect to the laser polarization. One feature shows alignment of the H–OH axis with the laser polarization, while the other indicates polarization alignment normal to the H–OH axis. By analyzing kinematic differences between the OH + /D + and OD + /H + channels of HOD, these two alignment features are shown to result from dissociation from different states in the dication. Only dissociation from one of these states has an alignment dependence consistent with predictions of sequential strong-field tunneling ionization models. Finally, the alignment dependence of dissociation from the other state can only be explained by dynamic alignment launched by the unbending of the molecule during ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The alignment between brightest cluster galaxies and host clusters

The alignment between the brightest cluster galaxies (BCGs) and host clusters can reveal the mystery of the formation and evolution of galaxy clusters. We measure cluster orientations in optical based on the projected distribution of member galaxies and in X-ray by fitting the morphology of intracluster medium (ICM). Cluster orientations determined in the two wavelengths are generally consistent. The orientation alignment between BCGs and host clusters is confirmed and more significant than in previous works. We find that BCGs are more aligned with cluster orientations measured in X-ray than those from optical data. Clusters with a brighter BCG generally show a stronger alignment. We argue that the detected redshift evolution of the alignment is probably caused by observational bias rather than intrinsic evolution. The alignment is not related to the ellipticity of BCGs, and the richness, ellipticity, and dynamical state of host clusters. As a result, the strong alignment between BCGs and the morphology of ICMs may be the consequence of the co-evolution between the central massive galaxy and host clusters.

79 ASTRONOMY AND ASTROPHYSICS↗

Increasing the power of weak lensing data with multipole-based intrinsic alignment estimators

ABSTRACT It has long been known that galaxy shapes align coherently with the large-scale density field. Characterizing this effect is essential to interpreting measurements of weak gravitational lensing, the deflection of light from distant galaxies by matter overdensities along the line of sight, as it also produces coherent galaxy alignments that we wish to interpret in terms of a cosmological model. Existing direct measurements of intrinsic alignments using galaxy samples with high-quality shape and redshift measurements typically use well-understood but sub-optimal projected estimators, which do not make good use of the information in the data when comparing those estimators to theoretical models. We demonstrate a more optimal estimator, based on a multipole expansion of the correlation functions or power spectra, for direct measurements of galaxy intrinsic alignments. We show that even using the lowest order multipole alone increases the significance of inferred model parameters using simulated and real data, without any additional modelling complexity. We apply this estimator to measurements of parameters of the non-linear alignment model using data from the Sloan Digital Sky survey, demonstrating consistent results with a factor of ∼2 greater precision in parameter fits to intrinsic alignments models. This result is functionally equivalent to quadrupling the survey area, but without the attendant costs – thereby demonstrating the value in using this new estimator in current and future intrinsic alignments measurements using spectroscopic galaxy samples.

Astronomy & Astrophysics↗

Observing neutron alignment at high angular momenta in heavy deformed actinides

An outstanding puzzle in the structure of very heavy nuclei lies in the rotation response of deformed transuranic isotopes. While the rotation alignment of pairs of 𝑖 13/2 protons is ubiquitous and well understood, observing the analogous alignment of the 𝑗 15/2 neutrons has been elusive. In this work we present a new quantitative analysis approach: from their moments of inertia as a function of frequency, we compare the alignments of rotational bands with both “low” and high-𝑗 intrinsic structures in the 𝑁 = 151 isotones of Pu, Cm, Cf, and No, thereby distinguishing between the alignments of neutron versus proton pairs through “blocking” effects. In this way, the alignment of 𝑗 15/2 neutrons can be clearly identified for the first time. The protons and neutrons begin aligning at a very similar frequency. The contribution of 𝑗 15/2 neutrons to the total alignment is found to grow with increasing 𝑍 compared to 𝑖 13/2 protons. To explain these observations, it is necessary to adopt a self-consistent set of single-particle energies corresponding to the nuclear shape that minimizes the mass. The shape description needs to include high-order deformations up to at least 𝛽 6 .

A ≥ 220↗

A Graphical Design Approach for Two-Input Single-Output Systems Exploiting Plant/Controller Alignment: Design and Application

Due to the unique structure of two-input single-output (TISO) feedback systems, several closed-loop properties can be characterized using the concepts of plant and controller “directions” and “alignment.” Poor plant/controller alignment indicates significant limitations in terms of closed-loop performance. In general, it is desirable to design a controller that is well aligned with the plant in order to minimize the size of the closed-loop sensitivity functions and closed-loop interactions. Although the concept of alignment can be a useful analysis tool for a given plant/controller pair, it is not obvious how a controller should be designed to achieve good alignment. We present a new controller design approach, based on the PQ method (Schroeck et al., 2001, “On Compensator Design for Linear Time invariant Dual-Input Single-Output Systems,” IEEE/ASME Trans. Mechatronics, 6(1), pp. 50–57), which explicitly incorporates knowledge of alignment into the design process. Here, this is accomplished by providing graphical information about the alignment angle on the Bode plot of the PQ frequency response. We show the utility of this approach through a design example.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Xavier: High-Performance X-Drop Adaptive Banded Pairwise Alignment (Xavier) v1.0

Pairwise sequence alignment is one of the most compute-intense challenges for the analysis of genomics data and it can account for more than 90% of the runtime depending on the application. Despite the effort to reduce the computational cost introducing heuristics such as banded and x-drop alignment, the performance of state-of-the-art software is often unsatisfactory for long sequences. Recent advances in single-molecule sequencing technologies keep increasing the length of the sequences to align at the cost of higher error rates b ranging from 5% to 15% b, emphasizing the need for fast and accurate software. Our long-read alignment software, named Xavier, computes high-performance x-drop adaptive banded pairwise alignment exploiting instruction-level parallelism via Single-Instruction-Multiple-Data (SIMD) operations. Xavier uses a narrow bandwidth that appreciably improves performance reducing the search space for the optimal alignment. In our experiment, the adaptive mechanism enables Xavier to find the optimal alignment between related sequences even when the error rate is as high as 50%. Xavier achieves speed-up up to 5X over competitor software when enabling the x-drop termination and up to 415X when disabling it, with negligible accuracy loss.

Guidi, Giulia↗

LOGAN: High-Performance X-Drop Pairwise Alignment on GPU (LOGAN) v1.0

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the run time for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational expense of analyzing these long read lengths (1Kb-1Mb). Given the quadratic overhead of exact pairwise algorithms such as Smith-Waterman, for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, named LOGAN. Results show that our high-performance multi-GPU LOGAN implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6x and 30.7x using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 threads, with equivalent accuracy. We also demonstrate a 2.3x LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2. To highlight the impact of our work on a real-world application, we couple the LOGAN aligner with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6x. Finally, we adapt the Roofline model for our optimized kernel and demonstrate that our implementation is near-optimal on the NVIDIA Tesla V100s.

Guidi, Giulia↗

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

59 BASIC BIOLOGICAL SCIENCES↗

Data-driven Alignment of the Tracker for the Mu2e Experiment

An alignment of the Mu2e Tracker is investigated using the Mu2e Offline Software and Millepede-II. Simulated misalignments of Tracker planes were inserted between Monte-Carlo event generation and before reconstruction using randomly generated $(x,y,z)$-translations and rotations of the rigid-body planes in the detector model. Cosmic ray muons, with no magnetic field present in the Detector Solenoid, will follow a straight-line trajectory. A maximum-likelihood fit is used to reconstruct a track and determine its parameters. Tracks traversing at least four planes, with ten registered straw hits, and a maximum time residual of $20$ ns are selected to be used in an alignment sample. The cuts were chosen to discard tracks with low information content, such as those with high levels of multiple scattering or those with low numbers of measurements contributing to a single track fit. Millepede-II produces the resulting alignment constants according to a simultaneous least-squares fit of the alignment parameters and the track parameters for all input tracks. The improved alignment constants are used to repeat the process and recover an increased number of suitable tracks, further improving the estimate of the alignment constants in subsequent iterations. A performance study of the process was conducted on a misaligned Tracker in the case of translation-only, and translation plus rotational misalignments. In both cases, the correct alignment constants were recovered to within statistical error after three global fit iterations. Additionally, a continuous integration system was developed for the \texttt{Mu2e/Offline} GitHub repository, introducing a convenient automated testing process for all proposed changes (``pull requests"). The tests developed included a full build of the software, followed by tests of the validation routines, geometry overlap checking, and multi-threading mode. Additionally, code quality checks and low-statistics physics comparison checks a re also available.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effect of Alignment on Polarized Infrared Emission from Polycyclic Aromatic Hydrocarbons

Polarized emission from polycyclic aromatic hydrocarbons (PAHs) potentially provides a new way to test the basic physics of the alignment of ultrasmall grains. In this paper, we present a new model of polarized PAH emission that takes into account the effect of PAH alignment with the magnetic field. We first generate a large sample of the grain angular momentum J by simulating the alignment of PAHs due to resonance paramagnetic relaxation that accounts for various interaction processes. We then calculate the polarization level of the PAH emission features for the different phases of the interstellar medium, including the cold neutral medium (CNM), reflection nebulae (RNe), and photodissociation regions. We find that a moderate degree of PAH alignment can significantly enhance the polarization degree of the PAH emission compared to the previous results obtained with randomly oriented angular momentum. In particular, we find that the smallest negatively charged PAHs in RNe can be excited to slightly suprathermal rotation due to enhanced ion collisional excitation, resulting in an increase of the polarization with the ionization fraction. Our results suggest that an RN is the most favorable environment in which to observe polarized PAH emission and to test the alignment physics of nanoparticles. Finally, we present an explicit relationship between the polarization level of PAH emission and the degree of external alignment for the CNM and RNe. The obtained relationship will be particularly useful for testing the alignment physics of PAHs in future observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Orbit Alignment in Triple Stars

The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ∼50 au, where the average Φ is about 20{sup ∘}. In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have Φ<70{sup ∘} and the remaining ones are randomly aligned.

79 ASTRONOMY AND ASTROPHYSICS↗

Galaxy Alignments with Surrounding Structure in the Sloan Digital Sky Survey

Using data from the Sloan Digital Sky Survey Legacy Survey, we study the alignment of luminous galaxies with spectroscopic data with the surrounding larger-scale structure as defined by galaxies with only photometric data. We find that galaxies from the red sequence have a statistically significant tendency for their apparent long axes to align parallel to the projected surrounding structure. Red galaxies more luminous than the median of our sample (M r < –21.78) have a mean alignment angle $\langle$Φ$\rangle$ < 45°, indicating preferred parallel alignment, at a significance level >4.5σ on projected scales 0.1 Mpc < r p ≤ 7.5 Mpc. Fainter red galaxies have $\langle$Φ$\rangle$ < 45° at a significance level >4.3σ at scales 1 Mpc < r p < 3 Mpc. At a projected scale r p = 3.0 Mpc, the mean alignment angle decreases steadily with increasing luminosity for red galaxies with M r ≲ –22.5, reaching $\langle$Φ$\rangle$ = 40$^{°}_{.}$49 ± 0$^{°}_{.}$56 for the most luminous 1% (M r ~ –23.57). Galaxies from the blue sequence show no statistically significant tendency for their axes to align with larger-scale structure, regardless of galaxy luminosity. Galaxies in higher-density regions do not show a statistically significant difference in the mean alignment angle from galaxies in lower-density regions; this holds true for the faint blue, luminous blue, faint red, and luminous red subsets.

79 ASTRONOMY AND ASTROPHYSICS↗

Comparison of two on-orbit attitude sensor alignment methods

Compared here are two methods of on-orbit alignment of vector attitude sensors. The first method uses the angular difference between simultaneous measurements from two or more sensors. These angles are compared to the angular differences between the respective reference positions of the sensed objects. The alignments of the sensors are adjusted to minimize the difference between the two sets of angles. In the second method, the sensor alignment is part of a state vector that includes the attitude. The alignments are adjusted along with the attitude to minimize all observation residuals. It is shown that the latter method can result in much less alignment uncertainty when gyroscopes are used for attitude propagation during the alignment estimation. The additional information for this increased accuracy comes from knowledge of relative attitude obtained from the spacecraft gyroscopes. The theoretical calculations of this difference in accuracy are presented. Also presented are numerical estimates of the alignment uncertainties of the fixed-head star trackers on the Extreme Ultraviolet Explorer spacecraft using both methods.

Krack, Kenneth↗

Automatic array alignment in data-parallel programs

FORTRAN 90 and other data-parallel languages express parallelism in the form of operations on data aggregates such as arrays. Misalignment of the operands of an array operation can reduce program performance on a distributed-memory parallel machine by requiring nonlocal data accesses. Determining array alignments that reduce communication is therefore a key issue in compiling such languages. We present a framework for the automatic determination of array alignments in array-based, data-parallel languages. Our language model handles array sectioning, reductions, spreads, transpositions, and masked operations. We decompose alignment functions into three constituents: axis, stride, and offset. For each of these subproblems, we show how to solve the alignment problem for a basic block of code, possibly containing common subexpressions. Alignments are generated for all array objects in the code, both named program variables and intermediate results. We assign computation to processors by virtue of explicit alignment of all temporaries; the resulting work assignment is in general better than that provided by the 'owner-computes' rule. Finally, we present some ideas for dealing with control flow, replication, and dynamic alignments that depend on loop induction variables.

Chatterjee, Siddhartha↗

Radio-Optical Alignments in a Low Radio Luminosity Sample

We present an optically-based study of the alignment between the radio axes and the optical major axes of eight z approximately 0.7 radio galaxies in a 7C sample. The radio galaxies in this sample are approximately 20-times less radio luminous than 3C galaxies at the same redshift, and are significantly less radio-luminous than any other well-defined samples studied to date. Using Nordic Optical Telescope images taken in good seeing conditions at rest-frame wavelengths just longward of the 4000A break, we find a statistically significant alignment effect in the 7C sample. Furthermore, in two cases where the aligned components are well separated from the host we have been able to confirm spectroscopically that they are indeed at the same redshift as the radio galaxy. However, a quantitative analysis of the alignment in this sample and in a corresponding 3C sample from HST (Hubble Space Telescope) archival data indicates that the percentage of aligned flux may be lower and of smaller spatial scale in the 7C sample. Our study suggests that alignments on the 50-kpc scale are probably closely related to the radio luminosity, whereas those on the 15 kpc scale are not. We discuss these results in the context of popular models for the alignment effect.

Lacy, Mark↗

Modeling of Field-Aligned Guided Echoes in the Plasmasphere

The conditions under which high frequency (f>>f(sub uh)) long-range extraordinary-mode discrete field-aligned echoes observed by the Radio Plasma Imager (RPI) on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite in the plasmasphere are investigated by ray tracing modeling. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and less than 10 wavelengths wide can guide nearly field-aligned propagating high frequency X mode waves. Effective guidance of wave at a given frequency and wave normal angle (Psi) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

Fung, Shing F.↗

Wavefront Aberrations Due to Alignment and Figure Compensation of the NASA James Webb Space Telescope

This viewgraph presentation describes wavefront aberrations due to the alignment and improper compensation of the NASA James Webb Space Telescope. The contents include: 1) James Webb Space Telescope (JWST); 2) Optical design of JWST; 3) Alignment Observables for JWST; 4) Low order Zernike Polynomials; 5) PM SM Ability to Target Low Order Aberrations; 6) Compensator definitions and Modes; 7) Field impact from compensation; 8) PM align error compensated by PM figure; 9) PM align error compensated by SM alignment; 10) SM align error compensated by PM figure; 11) SM figure error compensated by SM alignment; 12) Worst Case Pupil Maps; 13) Worst Case Pupil Maps at BEST FOCUS; 14) Field impact from compensation (+/- 1 arcmin FOV); and 15) Concluding Remarks.

Howard, Joseph↗

Fabrication of Single, Vertically Aligned Carbon Nanotubes in 3D Nanoscale Architectures

Plasma-enhanced chemical vapor deposition (PECVD) and high-throughput manufacturing techniques for integrating single, aligned carbon nanotubes (CNTs) into novel 3D nanoscale architectures have been developed. First, the PECVD growth technique ensures excellent alignment of the tubes, since the tubes align in the direction of the electric field in the plasma as they are growing. Second, the tubes generated with this technique are all metallic, so their chirality is predetermined, which is important for electronic applications. Third, a wafer-scale manufacturing process was developed that is high-throughput and low-cost, and yet enables the integration of just single, aligned tubes with nanoscale 3D architectures with unprecedented placement accuracy and does not rely on e-beam lithography. Such techniques should lend themselves to the integration of PECVD grown tubes for applications ranging from interconnects, nanoelectromechanical systems (NEMS), sensors, bioprobes, or other 3D electronic devices. Chemically amplified polyhydroxystyrene-resin-based deep UV resists were used in conjunction with excimer laser-based (lambda = 248 nm) step-and-repeat lithography to form Ni catalyst dots = 300 nm in diameter that nucleated single, vertically aligned tubes with high yield using dc PECVD growth. This is the first time such chemically amplified resists have been used, resulting in the nucleation of single, vertically aligned tubes. In addition, novel 3D nanoscale architectures have been created using topdown techniques that integrate single, vertically aligned tubes. These were enabled by implementing techniques that use deep-UV chemically amplified resists for small-feature-size resolution; optical lithography units that allow unprecedented control over layer-to-layer registration; and ICP (inductively coupled plasma) etching techniques that result in near-vertical, high-aspect-ratio, 3D nanoscale architectures, in conjunction with the use of materials that are structurally and chemically compatible with the high-temperature synthesis of the PECVD-grown tubes. The techniques offer a wafer-scale process solution for integrating single PECVD-grown nanotubes into novel architectures that should accelerate their integration in 3D electronics in general. NASA can directly benefit from this technology for its extreme-environment planetary missions. Current Si transistors are inherently more susceptible to high radiation, and do not tolerate extremes in temperature. These novel 3D nanoscale architectures can form the basis for NEMS switches that are inherently less susceptible to radiation or to thermal extremes.

Kaul, Anupama B.↗