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DOE OSTI2022

Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells

Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. Patterning within cells can extend down to the level of individual proteins and mRNA. But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning - the giant ciliate Stentor coeruleus. Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning. A Stentor cell is roughly 2mmlong, allowing a ‘‘proteomic dissection’’ in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell’s anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Pollen Cell Wall Patterns Form from Modulated Phases

The ornately geometric walls of pollen grains have inspired scientists for decades. Here, we show that the evolved diversity of these patterns is entirely recapitulated by a biophysical model in which an initially uniform polysaccharide layer in the extracellular space, mechanically coupled to the cell membrane, phase separates to a spatially modulated state. Experiments reveal this process occurring in living cells. We observe that in ~10% of extant species, this phase separation reaches equilibrium during development such that individual pollen grains are identical and perfectly reproducible. About 90% of species undergo an arrest of this process prior to equilibrium such that individual grains are similar but inexact copies. Equilibrium patterns have appeared multiple times during the evolution of seed plants, but selection does not favor these states. This framework for pattern development provides a route to rationalizing the surface textures of other secreted structures, such as cell walls and insect cuticle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

PERIODIC STRUCTURE IN THE MEGAPARSEC-SCALE JET OF PKS 0637-752

We present 18 GHz Australia Telescope Compact Array imaging of the megaparsec-scale quasar jet PKS 0637-752 with angular resolution {approx}0.''58. We draw attention to a spectacular train of quasi-periodic knots along the inner 11'' of the jet, with average separation {approx}1.1 arcsec (7.6 kpc projected). We consider two classes of model to explain the periodic knots: those that involve a static pattern through which the jet plasma travels (e.g., stationary shocks) and those that involve modulation of the jet engine. Interpreting the knots as re-confinement shocks implies the jet kinetic power Q{sub jet} {approx} 10{sup 46} erg s{sup -1}, but the constant knot separation along the jet is not expected in a realistic external density profile. For models involving modulation of the jet engine, we find that the required modulation period is 2 Multiplication-Sign 10{sup 3} yr < {tau} < 3 Multiplication-Sign 10{sup 5} yr. The lower end of this range is applicable if the jet remains highly relativistic on kiloparsec scales, as implied by the IC/CMB model of jet X-ray emission. We suggest that the periodic jet structure in PKS 0637-752 may be analogous to the quasi-periodic jet modulation seen in the microquasar GRS 1915+105, believed to result from limit cycle behavior in an unstable accretion disk. If variations in the accretion rate are driven by a binary black hole, the predicted orbital radius is 0.7 pc {approx}< a {approx}< 30 pc, which corresponds to a maximum angular separation of {approx}0.1-5 mas.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1987

Optical strain measurement system development, phase 1

A laser speckle, differential strain measurement system was built and tested for future applications in hostile environments. One dimensional electronic correlation of speckle pattern movement allows a quasi-real time measure of strain. The system was used successfully to measure uniaxial strain reaching into plastic deformation of a test specimen, at temperatures ranging to 450 C. A resolution of 16 microstrain is given by the photodiode array sensor pitch and the specimen to sensor separation. The strain measurement limit of the gauge is determined by air density perturbations causing decorrelation of the reference and shifted speckle patterns, and may be improved by limiting convective flow in the immediate vicinity of the test specimen.

Lant, Christian T.↗

NASA NTRS1991

An investigation to determine the producibility of a 3-D braider and bias direction weaving loom

The development of prototype machines for the production of generalized braid patterns is described. Mechanical operating principles and control strategies are presented for two prototype machines which were fabricated and evaluated. Both machines represent advances over current techniques for forming composite material preforms by enabling near ideal control of fiber orientation. Furthermore, they overcome both the lack of general control of produced fiber architectures and the complexity of other weaving processes that were produced for the same purpose. One prototype, the modified Farley braider, consists of an array of turntables which can be rotated 90 degrees and returned; hence, they can form tracks in the x and y axis. Yarn ends are transported about the surface formed by the turntables using motorized tractors. These tractors are controlled using an optical link with a control circuit and host computer. The tractors are powered through electrical contact with the turntables. The necessary relative motions are produced by a series of linear tractor moves combined with a sequence of turntable rotations. The movement of the tractors about the surface causes the yarns to produce the desired braiding pattern. The second device, the shuttle plate braider, consists of a braiding surface formed by an array of square elements, each separated from its neighbor by a gap. Beneath this surface lies a shuttle plate, which reciprocates first in one axis and then in the other. As this movement takes place, yarn carrying shuttles engage and disengage the plate by means of solenoid activated pins. By selective engagement and disengagement, the shuttles can move the yarn ends in any desired pattern, forming the desired braid. Control power, and control signals, are transmitted from the electronic interface circuit and host computer, via the braiding surface through electrical contact with the shuttles. Motive power is proved to the shuttles by motion of the shuttle plate, which is passively driven using pneumatic rams. Each shuttle is a simple device that uses only a solenoid to engage the plate and is a simple device that uses only a solenoid to engage the plate and is independently controllable. When compared with each other, the modified Farley braider has the advantage of speed, and the shuttle plate braider the advantage of mechanical control and simplicity.

Huey, Cecil O., Jr.↗

DOE OSTI2014

Quantitative transmission electron microscopy analysis of multi-variant grains in present L1{sub 0}-FePt based heat assisted magnetic recording media

We present a study on atomic ordering within individual grains in granular L1{sub 0}-FePt thin films using transmission electron microscopy techniques. The film, used as a medium for heat assisted magnetic recording, consists of a single layer of FePt grains separated by non-magnetic grain boundaries and is grown on an MgO underlayer. Using convergent-beam techniques, diffraction patterns of individual grains are obtained for a large number of crystallites. The study found that although the majority of grains are ordered in the perpendicular direction, more than 15% of them are multi-variant, or of in-plane c-axis orientation, or disordered fcc. It was also found that these multi-variant and in-plane grains have always grown across MgO grain boundaries separating two or more MgO grains of the underlayer. The in-plane ordered portion within a multi-variant L1{sub 0}-FePt grain always lacks atomic coherence with the MgO directly underneath it, whereas, the perpendicularly ordered portion is always coherent with the underlying MgO grain. Since the existence of multi-variant and in-plane ordered grains are severely detrimental to high density data storage capability, the understanding of their formation mechanism obtained here should make a significant impact on the future development of hard disk drive technology.

36 MATERIALS SCIENCE↗

NASA NTRS1987

Component variations and their effects on bipolar nickel-hydrogen cell performance

A 50 cell bipolar nickel-hydrogen battery was assembled to demonstrate the feasibility of constructing a high voltage stack of cells. Various component combinations were tested in this battery. The battery had approximately 1 ampere-hour of capacity and was constructed from components with an active area of 2 x 2 inches. The components were parametrically varied to give a comparison of nickel electrodes, hydrogen electrodes, separators, fill procedures and electrolyte reservoir plate thicknesses. Groups of five cells were constructed using the same components; ten combinations were tested in all. The battery was thoroughly characterized at various change and discharge rates as well as with various pulse patterns and rates. Over a period of 1400 40-percent DOD LEO cycles some of the groups began to exhibit performance differences. In general, only separator variations had a significant effect on cell performance. It also appears that shunt currents may have been operating within the stack, resulting in electrolyte transfer from one cell to another, thus contributing to cell performance variations.

Manzo, Michelle A.↗

DOE OSTI2022

Wire-cell 3D pattern recognition techniques for neutrino event reconstruction in large LArTPCs: algorithm description and quantitative evaluation with MicroBooNE simulation

Wire-Cell is a 3D event reconstruction package for liquid argon time projection chambers. Through geometry, time, and drifted charge from multiple readout wire planes, 3D space points with associated charge are reconstructed prior to the pattern recognition stage. Pattern recognition techniques, including track trajectory and dQ/dx (ionization charge per unit length) fitting, 3D neutrino vertex fitting, track and shower separation, particle-level clustering, and particle identification are then applied on these 3D space points as well as the original 2D projection measurements. A deep neural network is developed to enhance the reconstruction of the neutrino interaction vertex. Compared to traditional algorithms, the deep neural network boosts the vertex efficiency by a relative 30% for charged-current ν e interactions. Therefore, this pattern recognition achieves 80–90% reconstruction efficiencies for primary leptons, after a 65.8% (72.9%) vertex efficiency for charged-current ν e (ν μ ) interactions. Based on the resulting reconstructed particles and their kinematics, we also achieve 15-20% energy reconstruction resolutions for charged-current neutrino interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1998

A Search for Giant Convection Cells on the Sun

Giant convection cells (slow, long-lived cellular flows in the Sun's convection zone with typical diameters greater than about 100,000 km) have been the subject of many searches over the last 30 years. If such flows exist, they should play a key role in structuring the Sun's large scale magnetic field and in driving the large scale axisymmetric flows: the differential rotation and meridional circulation. Detailed observations of the flows in these cells may also allow us to better predict future magnetic field configurations and the solar activity associated with them. Line-of-sight velocity data from the Michelson Doppler Interferometer on the ESA/NASA Solar and Heliospheric Observatory provides us with new opportunities to search for giant cells. This data is free of any atmospheric distortion and has been obtained continuously without any day/night gaps for more than two months at a time. These two-month datasets are important because giant cells are expected to have lifetimes somewhat longer that the Sun's 27 day rotation period. Any reappearance of a flow pattern after 27 days would be an important confirmation of the existence of these cells. The approach taken in this search is to separate the giant cell velocity signal from the other, stronger velocity signals by using a spherical harmonic representation of the spatial structures and a fourier decomposition of the temporal behavior. Any giant cell signal should be characterized by low spatial wavenumbers with temporal frequencies appropriate to the solar rotation of these patterns.

Hathaway, David H.↗

DOE OSTI2020

Estimating region-specific fuel economy in the United States from real-world driving cycles

Here we describe a method for estimating region-specific real-world light-duty vehicle fuel economy in the United States that is unique in both the size and representativeness of real-world driving that was considered, and for its ability to model regional variations in driving patterns. Over one million miles of national driving data were used to select real-world cycles representative of observed trip categories. The six cycles were compared to U.S. legislative cycles, revealing some key differences. Finally, a set of cycle weighting factors for 533 separate U.S. regions was derived from annual traffic statistics. Applying this method, it was found that regional fuel economy varies due to differences in driving patterns alone and that rural driving patterns lead to improved fuel economy (for conventional vehicles). The driving cycles and regional weighting factors described here are useful for testing and simulation studies, specifically those sensitive to regional variations in driving patterns.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

Trends in extreme temperature over Nigeria from percentile‐based threshold indices

ABSTRACT This study analyses spatial and temporal trends in extreme temperature indices over Nigeria. The percentile indices were calculated from newly homogenized daily minimum and maximum temperature data for the period 1971–2012 for 21 stations in Nigeria. Indices describing the characteristics of hot extremes and cold extremes are calculated with the RClimDex software. The annual and seasonal trends in these indices are obtained using the ordinary least square fit and the statistical significance tested using the R‐based modified Mann–Kendall test. We examine characteristics of these indices for the entire country and separately for the three geographical zones in Nigeria: Guinea, Savanna, and Sahel. The spatial and temporal patterns of trends in the indices indicate that Nigeria has experienced statistically significant increase in the frequency of hot extreme and decrease in cold extreme events. Although majority of the stations have significant trends in warm days and warm nights, the annual trend is greatest in warm nights. In addition, the rate of warming in minimum temperature (‘warm nights’) is stronger in June, July, August ( JJA ) and September, October, November ( SON ) compare with December, January, February ( DJF ) and March, April, May ( MAM ). As for the trends in cold days and cold nights, the trends in cold nights are larger than for cold days at both the annual and seasonal scales. The regional analysis indicates that trends in warm nights and cold nights are most pronounced in Guinea and Sahel regions.

Abatan, Abayomi A.↗

DOE OSTI2011

Retrospective Analysis of Outcome Differences in Preoperative Concurrent Chemoradiation With or Without Elective Nodal Irradiation for Esophageal Squamous Cell Carcinoma

Purpose: To evaluate the efficacy and patterns of failure of elective nodal irradiation (ENI) in patients with esophageal squamous cell carcinoma (SCC) undergoing preoperative concurrent chemoradiation (CCRT) followed by radical surgery. Methods and Materials: We retrospectively studied 118 patients with AJCC Stage II to III esophageal SCC undergoing preoperative CCRT (median, 36 Gy), followed by radical esophagectomy. Of them, 73 patients (62%) had ENI and 45 patients (38%) had no ENI. Patients with ENI received radiotherapy to either supraclavicular (n = 54) or celiac (n = 19) lymphatics. Fifty-six patients (57%) received chemotherapy with paclitaxel plus cisplatin. The 3-year progression-free survival, overall survival, and patterns of failure were analyzed. Distant nodal recurrence was classified into M1a and M1b regions. A separate analysis using matched cases was conducted. Results: The median follow-up was 38 months. There were no differences in pathological complete response rate (p = 0.12), perioperative mortality rate (p = 0.48), or delayed Grade 3 or greater cardiopulmonary toxicities (p = 0.44), between the groups. More patients in the non-ENI group had M1a failure than in the ENI group, with 3-year rates of 11% and 3%, respectively (p = 0.05). However, the 3-year isolated distant nodal (M1a + M1b) failure rates were not different (ENI, 10%; non-ENI, 14%; p = 0.29). In multivariate analysis, pathological nodal status was the only independent prognostic factor associated with overall survival (hazard ratio = 1.78, p = 0.045). The 3-year overall survival and progression-free survival were 45% and 45%, respectively, in the ENI group, and 52% and 43%, respectively, in the non-ENI group (p = 0.31 and 0.89, respectively). Matched cases analysis did not show a statistical difference in outcomes between the groups. Conclusions: ENI reduced the M1a failure rate but was not associated with improved outcomes in patients undergoing preoperative CCRT for esophageal SCC. Pathological nodal metastasis predicted poor outcome.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2018

Notified access in coarray-based hydrodynamics applications on many-core architectures: Design and performance

With the increasing availability of the Remote Direct Memory Access (RDMA) support in computer networks, the so called Partitioned Global Address Space (PGAS) model has evolved in the last few years. Although there are several cases where a PGAS approach can easily solve difficult message passing situations, like in particle tracking and adaptive mesh refinement applications, the producer-consumer pattern, usually adopted in task-based parallelism, can only be implemented inefficiently because of the separation between data transfer and synchronization (which is usually unified in message passing programming models). Here, in this paper, we provide two contributions: (1) we propose an extension for the Fortran language that provides the concept of Notified Access by associating regular coarray variables with event variables. (2) We demonstrate that the MPI extension proposed by foMPI for Notified Access can be used effectively to implement the same concept in a PGAS run-time library like OpenCoarrays. Moreover, for a hydrodynamics mini-application, we found that Fortran 2018 events perform always better than Fortran 2008 sync statements on many-core processors. We finally show how the proposed Notified Access can improve the performance even more.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2011

Surface Detection in a STXM Microscope

We have modified scanning transmission x-ray microscopes (STXM) at the Canadian Light Source and the Advanced Light Source with total electron yield (TEY) detection (TEY-STXM). This provides improved surface-sensitive detection, simultaneous with existing bulk-sensitive transmission detection in the STXM microscopes. We have explored sample-current and channeltron-based electron yield detection. Both approaches provide improved surface sensitive imaging and spectroscopy, although channeltron-based detection is superior. TEY-STXM provides surface sensitive imaging of ultrathin films such as phase-separated Langmuir-Blodgett monolayer films, as well as differentiation of surface and bulk oxides of patterned metallic thin films. This paper will outline the experimental challenges of this method and the opportunities for correlative surface and bulk measurements of complex samples.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2015

Exchange coupling in hybrid anisotropy magnetic multilayers quantified by vector magnetometry

Hybrid anisotropy thin film heterostructures, where layers with perpendicular and in-plane anisotropy are separated by a thin spacer, are novel materials for zero/low field spin torque oscillators and bit patterned media. Here, we report on magnetization reversal and exchange coupling in a archetypal Co/Pd (perpendicular)-NiFe (in-plane) hybrid anisotropy system studied using vector vibrating sample magnetometry. This technique allows us to quantify the magnetization reversal in each individual magnetic layer, and measure of the interlayer exchange as a function of non-magnetic spacer thickness. At large (>1 nm) spacer thicknesses Ruderman-Kittel-Kasuya-Yosida-like exchange dominates, with orange-peel coupling providing a significant contribution only for sub-nm spacer thickness.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Principal component analysis of computed emission lines from protostellar jets

A very important issue concerning protostellar jets is the mechanism behind their formation. Obtaining information on the region at the base of a jet can shed light on the subject, and some years ago this was done through a search for a rotational signature in the jet line spectrum. The existence of such signatures, however, remains controversial. In order to contribute to the clarification of this issue, in this paper we show that principal component analysis (PCA) can potentially help to distinguish between rotation and precession effects in protostellar jet images. This method reduces the dimensions of the data, facilitating the efficient extraction of information from large data sets such as those arising from integral field spectroscopy. PCA transforms the system of correlated coordinates into a system of uncorrelated coordinates, the eigenvectors, ordered by principal components of decreasing variance. The projection of the data on these coordinates produces images called tomograms, while eigenvectors can be displayed as eigenspectra. The combined analysis of both can allow the identification of patterns correlated to a particular physical property that would otherwise remain hidden, and can help to separate the effects of physically uncorrelated phenomena in the data. These are, for example, rotation and precession in the kinematics of a stellar jet. In order to show the potential of PCA analysis, we apply it to synthetic spectro-imaging datacubes generated as an output of numerical simulations of protostellar jets. In this way we generate a benchmark with which a PCA diagnostics of real observations can be confronted. Using the computed emission line profiles for [O i]λ6300 and [S ii]λ6716, we recover and analyze the effects of rotation and precession in tomograms generated by PCA. We show that different combinations of the eigenvectors can be used to enhance and to identify the rotation features present in the data. Our results indicate that PCA can be useful for disentangling rotation from precession in jets with an inclination of the jet with respect to the plane of the sky as high as 45°. We have been able to recover the initially imposed rotation jet profile for models at a moderate inclination angle (&straightphi;&NestedLessLess;15°) and without precession.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Decays of the Three Top Contributors to the Reactor ν ¯ e High-Energy Spectrum, Rb 92 , Y 96 gs , and Cs 142 , Studied with Total Absorption Spectroscopy

Here, we report total absorption spectroscopy measurements of 92 Rb, 96 gs Y, and 142 Cs β decays, which are the most important contributors to the high energy ν¯ e spectral shape in nuclear reactors. These three β decays contribute 43% of the ¯νe flux near 5.5 MeV emitted by nuclear reactors. This ν¯ e energy is particularly interesting due to spectral features recently observed in several experiments including the Daya Bay, Double Chooz, and RENO Collaborations. Measurements were conducted at Oak Ridge National Laboratory by means of proton-induced fission of 238 U with on-line mass separation of fission fragments and the Modular Total Absorption Spectrometer. We observe a β-decay pattern that is similar to recent measurements of 92 Rb, with a ground-state to ground-state β feeding of 91(3)%. We verify the 96gs Y ground-state to ground-state β feeding of 95.5(20)%. Our measurements substantially modify the β-decay feedings of 142 Cs, reducing the β feeding to 142 Ba states below 2 MeV by 32% when compared with the latest evaluations. Our results increase the discrepancy between the observed and the expected reactor ν¯ e flux between 5 and 7 MeV, the maximum excess increases from ~10% to ~12%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Orthotropic Viscoelastic Modeling of Polymeric Battery Separator

The separator is one of the most important components for battery safety since its failure can cause short-circuit that may lead to thermal runaway. As such, understanding the mechanical behaviors of separators is critical to improve battery safety. Nevertheless, modeling the mechanical behaviors of separators is challenging since they usually depend on multiple factors such as orientation, temperature and strain rate due to the microstructure of separators. Here we develop an orthotropic linear viscoelastic model for separators, which takes both anisotropy and strain rate effects into account. This model is the first step of a future model that considers more factors such as temperature and large deformation. The model has been implemented as a user material model in a finite element package, where a discretization algorithm is developed to evaluate the stiffness-based hereditary integral with a kernel of Prony series. The user model has been applied to a polypropylene (PP) separator Celgard ® 2400. The simulation results agree well with experimental data, which include the rate dependent uniaxial tensile behavior of the separator in the two in-plane material directions and in shear, and the strain contour patterns of every strain component during biaxial tension.

25 ENERGY STORAGE↗