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At least 1,261 records · Page 70

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

59 BASIC BIOLOGICAL SCIENCES↗

Refining Jets for CMS Run 3 using Fast Simulation

As the LHC moves into its high-luminosity phase, the CMS experiment must handle more complex data collected at much higher rates. While the Geant4-based simulation application (FullSim) provides highly accurate simulation to complement real data, FullSim’s intensive consumption of computing resources becomes an increasing liability as the rates increase, while faster tools offer an advantage. The fast MC production application (FastSim) delivers a complete simulation with a factor of 10 speedup over FullSim, but introduces inaccuracies in some observables. A specialized refinement method, Fast Perfekt, employs machine learning to improve the accuracy of FastSim. An initial report of this work focused on the refinement of jet flavor tagging observables. This article presents an update on the refinement, focusing on PUPPI jets with Run 3 data-taking conditions. Refinement is extended to include jet transverse momentum as well as its propagation to missing transverse momentum. A gridbased framework and real-time monitoring system have been developed to facilitate optimization and scaling of the refinement to a large number of target variables.

Güngördü, Açelya Deniz [Istanbul Tech. U.]↗

Volcanic arc rigidity variations illuminated by coseismic deformation of the 2011 Tohoku-oki M9

Rock strength has long been linked to lithospheric deformation and seismicity. However, independent constraints on the related elastic heterogeneity are missing, yet could provide key information for solid Earth dynamics. Using coseismic Global Navigation Satellite Systems (GNSS) data for the 2011 M9 Tohoku-oki earthquake in Japan, we apply an inverse method to infer elastic structure and fault slip simultaneously. We find compliant material beneath the volcanic arc and in the mantle wedge within the partial melt generation zone inferred to lie above ~100 km slab depth. We also identify low-rigidity material closer to the trench matching seismicity patterns, likely associated with accretionary wedge structure. Along with traditional seismic and electromagnetic methods, our approach opens up avenues for multiphysics inversions. Those have the potential to advance earthquake and volcano science, and in particular once expanded to InSAR type constraints, may lead to a better understanding of transient lithospheric deformation across scales.

58 GEOSCIENCES↗

Search for new phenomena in final states with large jet multiplicities and missing transverse momentum at s =8 TeV proton-proton collisions using the ATLAS experiment

CERN-LHC. Results are presented of a search that looks for new particles decaying to large numbers (7 to greater or equal to 10) of jets, missing transverse momentum and no isolated electrons or muons. This analysis uses 20.3/fb of pp collision data at sqrt(s)=8 TeV collected by the ATLAS experiment at the Large Hadron Collider. The sensitivity of the search is enhanced by considering the number of b-tagged jets and the scalar sum of masses of large-radius jets in an event. No evidence is found for physics beyond the Standard Model. The results are interpreted in the context of various simplified supersymmetry-inspired models where gluinos are pair produced, as well as a mSUGRA/CMSSM model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Faint and Fading Tails: The Fate of Stripped H i Gas in Virgo Cluster Galaxies

Although many galaxies in the Virgo cluster are known to have lost significant amounts of H i gas, only about a dozen features are known where the H i extends significantly outside its parent galaxy. Previous numerical simulations have predicted that H i removed by ram pressure stripping should have column densities far in excess of the sensitivity limits of observational surveys. We construct a simple model to try and quantify how many streams we might expect to detect. This accounts for the expected random orientation of the streams in position and velocity space as well as the expected stream length and mass of stripped H i. Using archival data from the Arecibo Galaxy Environment Survey, we search for any streams that might previously have been missed in earlier analyses. We report the confident detection of 10 streams as well as 16 other less-certain detections. We show that these well match our analytic predictions for which galaxies should be actively losing gas; however, the mass of the streams is typically far below the amount of missing H i in their parent galaxies, implying that a phase change and/or dispersal renders the gas undetectable. By estimating the orbital timescales, we estimate that dissolution rates of 1–10 M {sub ⊙} yr{sup −1} are able to explain both the presence of a few long, massive streams and the greater number of shorter, less-massive features.

79 ASTRONOMY AND ASTROPHYSICS↗

Neutrino masses, neutrino oscillations, and cosmological implications

Theoretical concepts and motivations for considering neutrinos having finite masses are discussed and the experimental situation on searches for neutrino masses and oscillations is summarized. The solar neutrino problem, reactor, deep mine and accelerator data, tri decay experiments and double beta-decay data are considered and cosmological implications and astrophysical data relating to neutrino masses are reviewed. The neutrino oscillation solution to the solar neutrino problem, the missing mass problem in galaxy halos and galaxy cluster galaxy formation and clustering, and radiative neutrino decay and the cosmic ultraviolet background radiation are examined.

Stecker, F. W.↗

Intelligent, Self-Diagnostic Thermal Protection System for Future Spacecraft

The goal of this project is to provide self-diagnostic capabilities to the thermal protection systems (TPS) of future spacecraft. Self-diagnosis is especially important in thermal protection systems (TPS), where large numbers of parts must survive extreme conditions after weeks or years in space. In-service inspections of these systems are difficult or impossible, yet their reliability must be ensured before atmospheric entry. In fact, TPS represents the greatest risk factor after propulsion for any transatmospheric mission. The concepts and much of the technology would be applicable not only to the Crew Exploration Vehicle (CEV), but also to ablative thermal protection for aerocapture and planetary exploration. Monitoring a thermal protection system on a Shuttle-sized vehicle is a daunting task: there are more than 26,000 components whose integrity must be verified with very low rates of both missed faults and false positives. The large number of monitored components precludes conventional approaches based on centralized data collection over separate wires; a distributed approach is necessary to limit the power, mass, and volume of the health monitoring system. Distributed intelligence with self-diagnosis further improves capability, scalability, robustness, and reliability of the monitoring subsystem. A distributed system of intelligent sensors can provide an assurance of the integrity of the system, diagnosis of faults, and condition-based maintenance, all with provable bounds on errors.

Hyers, Robert W.↗

Binomial Test Method for Determining Probability of Detection Capability for Fracture Critical Applications

The capability of an inspection system is established by applications of various methodologies to determine the probability of detection (POD). One accepted metric of an adequate inspection system is that for a minimum flaw size and all greater flaw sizes, there is 0.90 probability of detection with 95% confidence (90/95 POD). Directed design of experiments for probability of detection (DOEPOD) has been developed to provide an efficient and accurate methodology that yields estimates of POD and confidence bounds for both Hit-Miss or signal amplitude testing, where signal amplitudes are reduced to Hit-Miss by using a signal threshold Directed DOEPOD uses a nonparametric approach for the analysis or inspection data that does require any assumptions about the particular functional form of a POD function. The DOEPOD procedure identifies, for a given sample set whether or not the minimum requirement of 0.90 probability of detection with 95% confidence is demonstrated for a minimum flaw size and for all greater flaw sizes (90/95 POD). The DOEPOD procedures are sequentially executed in order to minimize the number of samples needed to demonstrate that there is a 90/95 POD lower confidence bound at a given flaw size and that the POD is monotonic for flaw sizes exceeding that 90/95 POD flaw size. The conservativeness of the DOEPOD methodology results is discussed. Validated guidelines for binomial estimation of POD for fracture critical inspection are established.

Generazio, Edward R.↗

sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing

The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).

59 BASIC BIOLOGICAL SCIENCES↗

Methodology and Software for Gross Defect Detection of Spent Nuclear Fuel at the Atucha-I Reactor [Novel Methodology and Software for Spent Fuel Gross Defect Detection at the Atucha-I Reactor]

Here, fuel assemblies in the spent fuel pool are stored by suspending them in two vertically stacked layers at the Atucha Unit 1 nuclear power plant (Atucha-I). This introduces the unique problem of verifying the presence of fuel in either layer without physically moving the fuel assemblies. Given that the facility uses both natural uranium and slightly enriched uranium at 0.85 wt% 235 U and has been in operation since 1974, a wide range of burnups and cooling times can exist in any given pool. A gross defect detection tool, the spent fuel neutron counter (SFNC), has been used at the site to verify the presence of fuel up to burnups of 8000 MWd/t. At higher discharge burnups, the existing signal processing software of the tool was found to fail due to nonlinearity of the source term with burnup.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Search for dark matter produced in association with a single top quark and an energetic W boson in $\sqrt{s}=$ 13 TeV $pp$ collisions with the ATLAS detector

This paper presents a search for dark matter, $χ$, using events with a single top quark and an energetic W boson. The analysis is based on proton–proton collision data collected with the ATLAS experiment at $\sqrt{s}=$ 13 TeV during LHC Run 2 (2015–2018), corresponding to an integrated luminosity of 139 fb -1 . The search considers final states with zero or one charged lepton (electron or muon), at least one $b$-jet and large missing transverse momentum. In addition, a result from a previous search considering two-charged-lepton final states is included in the interpretation of the results. The data are found to be in good agreement with the Standard Model predictions and the results are interpreted in terms of 95% confidence-level exclusion limits in the context of a class of dark matter models involving an extended two Higgs-doublet sector together with a pseudoscalar mediator particle. The search is particularly sensitive to on-shell pro duction of the charged Higgs boson state, $H$ ± , arising from the two-Higgs-doublet mixing, and its semi-invisible decays via the mediator particle, $a$: $H$ ± → $W$ ± $a$(→ $χ$ $χ$). Signal models with $H$ ± masses up to 1.5 TeV and a masses up to 350 GeV are excluded assuming a tan $β$ value of 1. For masses of a of 150 (250) GeV, tan $β$ values up to 2 are excluded for $H$ ± masses between 200 (400) GeV and 1.5 TeV. Signals with tan $β$ values between 20 and 30 are excluded for $H$ ± masses between 500 and 800 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Atomic Oxygen Erosion Yield Prediction for Spacecraft Polymers in Low Earth Orbit

The ability to predict the atomic oxygen erosion yield of polymers based on their chemistry and physical properties has been only partially successful because of a lack of reliable low Earth orbit (LEO) erosion yield data. Unfortunately, many of the early experiments did not utilize dehydrated mass loss measurements for erosion yield determination, and the resulting mass loss due to atomic oxygen exposure may have been compromised because samples were often not in consistent states of dehydration during the pre-flight and post-flight mass measurements. This is a particular problem for short duration mission exposures or low erosion yield materials. However, as a result of the retrieval of the Polymer Erosion and Contamination Experiment (PEACE) flown as part of the Materials International Space Station Experiment 2 (MISSE 2), the erosion yields of 38 polymers and pyrolytic graphite were accurately measured. The experiment was exposed to the LEO environment for 3.95 years from August 16, 2001 to July 30, 2005 and was successfully retrieved during a space walk on July 30, 2005 during Discovery s STS-114 Return to Flight mission. The 40 different materials tested (including Kapton H fluence witness samples) were selected specifically to represent a variety of polymers used in space as well as a wide variety of polymer chemical structures. The MISSE 2 PEACE Polymers experiment used carefully dehydrated mass measurements, as well as accurate density measurements to obtain accurate erosion yield data for high-fluence (8.43 1021 atoms/sq cm). The resulting data was used to develop an erosion yield predictive tool with a correlation coefficient of 0.895 and uncertainty of +/-6.3 10(exp -25)cu cm/atom. The predictive tool utilizes the chemical structures and physical properties of polymers to predict in-space atomic oxygen erosion yields. A predictive tool concept (September 2009 version) is presented which represents an improvement over an earlier (December 2008) version.

Banks, Bruce A.↗

Measurement of the $W$ boson mass with the D0 detector

We give a detailed description of the measurement of the $W$ boson mass, $M_W$, performed on an integrated luminosity of 4.3 fb$^{-1}$, which is based on similar techniques as used for our previous measurement done on an independent data set of 1 fb$^{-1}$ of data. The data were collected using the D0 detector at the Fermilab Tevatron Collider. This data set yields $1.68\times 10^6$ $W\rightarrow e\nu$ candidate events. We measure the mass using the transverse mass, electron transverse momentum, and missing transverse energy distributions. The $M_W$ measurements using the transverse mass and the electron transverse momentum distributions are the most precise of these three and are combined to give $M_W$ = 80.367 $\pm$ 0.013 (stat) $\pm$ 0.022 (syst) GeV = 80.367 $\pm$ 0.026 GeV. When combined with our earlier measurement on 1 fb$^{-1}$ of data, we obtain $M_W$ = 80.375 $\pm$ 0.023 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Precise determination of α s from the C -parameter distribution

We present a global fit for α s (m Z ), analyzing the available C -parameter data measured at center-of-mass energies between Q = 35 and 207 GeV. The experimental data is compared to a N 3 LL' + $\mathscr{O}$ (α$3\atop{s}$) + Ω 1 theoretical prediction (up to the missing four-loop cusp anomalous dimension), which includes power corrections coming from a field-theoretical nonperturbative soft function. The dominant hadronic parameter is its first moment Ω 1 , which is defined in a scheme which eliminates the $\mathscr{O}$ (Λ QCD ) renormalon ambiguity. The resummation region plays a dominant role in the C -parameter spectrum, and in this region a fit for α s (m Z ) and Ω 1 is sufficient. We find α s (m Z ) = 0.1123 ± 0.0015 and Ω 1 = 0.421 ± 0.063 GeV with χ 2 /d . o . f . = 0.988 for 404 bins of data. These results agree with the prediction of universality for Ω 1 between thrust and C -parameter within 1- σ .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for gluino mediated bottom- and top-squark production in multijet final states in pp collisions at 8 TeV

A search for supersymmetry is presented based on events with large missing transverse energy, no isolated electron or muon, and at least three jets with one or more identified as a bottom-quark jet. A simultaneous examination is performed of the numbers of events in exclusive bins of the scalar sum of jet transverse momentum values, missing transverse energy, and bottom-quark jet multiplicity. The sample, corresponding to an integrated luminosity of 19.4 inverse femtobarns, consists of proton-proton collision data recorded at a center-of-mass energy of 8 TeV with the CMS detector at the LHC in 2012. The observed numbers of events are found to be consistent with the standard model expectation, which is evaluated with control samples in data. The results are interpreted in the context of two simplified supersymmetric scenarios in which gluino pair production is followed by the decay of each gluino to an undetected lightest supersymmetric particle and either a bottom or top quark-antiquark pair, characteristic of gluino mediated bottom- or top-squark production. Using the production cross section calculated to next-to-leading-order plus next-to-leading-logarithm accuracy, and in the limit of a massless lightest supersymmetric particle, we exclude gluinos with masses below 1170 GeV and 1020 GeV for the two scenarios, respectively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Volumetric Properties and Fluid Phase Equilibria of CO2 + H2O

The need for accurate modeling of fluid-mineral processes over wide ranges of temperature, pressure and composition highlighted considerable uncertainties of available property data and equations of state, even for the CO2 + H2O binary system. In particular, the solubility, activity, and ionic dissociation equilibrium data for the CO2-rich phase, which are essential for understanding dissolution/precipitation, fluid-matrix reactions, and solute transport, are uncertain or missing. In this paper we report the results of a new experimental study of volumetric and phase equilibrium properties of CO2 + H2O, to be followed by measurements for bulk and confined multicomponent fluid mixtures. Mixture densities were measured by vibrating tube densimetry (VTD) over the entire composition range at T = 200 and 250 C and P = 20, 40, 60, and 80 MPa. Initial analysis of the mutual solubilities, determined from volumetric data, shows good agreement with earlier results for the aqueous phase, but finds that the data of Takenouchi and Kennedy (1964) significantly overestimated the solubility of water in supercritical CO2 (by a factor of more than two at 200 C). Resolving this well-known discrepancy will have a direct impact on the accuracy of predictive modeling of CO2 injection in geothermal reservoirs and geological carbon sequestration through improved equations of state, needed for calibration of predictive molecular-scale models and large-scale reactive transport simulations.

Capobianco, Ryan↗

Space-qualified Chalcogenide Materials through ISS MISSE Exposure —From Property to Application

In March 2021, twenty-four samples of various phase change materials (PCMs - Ge2Sb2Te5, Ge2Sb2Se4Te1, and Sb2Se3) along with metasurface optical components comprised of these PCMs, were delivered to the International Space Station (ISS) as part of the Materials International Space Station Experiment (MISSE-14) test campaign [1]. Although PCMs have previously been noted for their resilience to various forms of radiation [2], they had not been tested in a realistic space environment until this exposure campaign with joint NASA and MIT collaboration. During the six-month total open exposure time in low earth orbit (LEO), high-resolution cameras scanned and captured photographs of the samples to detect changes as a function of time along with on-orbit measured temperature, UV radiation, total atomic oxygen fluence, and total ionizing radiation doses. The samples were returned to NASA Langley Research Center in March 2022 for post-flight characterization. This duplicated the preflight characterization (i.e., material composition and crystallinity that limits switching speed, index contrast, loss, etc.) conducted before launch. The space sector has witnessed tremendous growth within the past decade—not only from government agencies but also entrants from the private sector. Future growth in the capabilities of Earth observation, deep space, and planetary surface missions using miniaturized spacecraft platforms can only be sustained by innovations in the design of remote sensors and other sub-systems. Active metasurface optics with enhanced tunability and reconfigurability continues to redefine the boundaries of optical science [3]. The introduction of PCM technology and associated optical devices will help to accelerate the adoption of new architectures for reduced size, weight, power, and cost (SWaP-C) platforms in space.Here we introduce results obtained from the MISSE-14 mission related to space qualification of PCM-based optic devices and constituent materials. We then discuss our recent work developing active integrated photonic devices and metasurface optics based on PCMs for space applications. This includes tunable and reconfigurable optical metasurface devices to support NASA space communication and LIDAR applications. PCMs are quickly becoming interesting photonics materials but questions related to mission suitability remain, particularly in regard to key properties like figures-of-merit (FOM, Δn/Δk), glass forming temperatures, and phase transition speeds. This talk will describe efforts to afford researchers the ability to have access to cost-effective data on exposure-induced changes to PCM fundamental physical and optical properties to assess their utility for space applications. The MISSE-14 sample exposure campaign allows a complete understanding of the limitations of the PCMs for various space-based electronic and optoelectronic applications.

Chalcogenide Phase change material↗