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At least 253 records · Page 14

Accurate prediction of protein structures and interactions using a three-track neural network

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. Here, we make the method available to the scientific community to speed biological research.

59 BASIC BIOLOGICAL SCIENCES↗

The perception of three-dimensionality across continuous surfaces

The apparent three-dimensionality of a viewed surface presumably corresponds to several internal preceptual quantities, such as surface curvature, local surface orientation, and depth. These quantities are mathematically related for points within the silhouette bounds of a smooth, continuous surface. For instance, surface curvature is related to the rate of change of local surface orientation, and surface orientation is related to the local gradient of distance. It is not clear to what extent these 3D quantities are determined directly from image information rather than indirectly from mathematically related forms, by differentiation or by integration within boundary constraints. An open empirical question, for example, is to what extent surface curvature is perceived directly, and to what extent it is quantitative rather than qualitative. In addition to surface orientation and curvature, one derives an impression of depth, i.e., variations in apparent egocentric distance. A static orthographic image is essentially devoid of depth information, and any quantitative depth impression must be inferred from surface orientation and other sources. Such conversion of orientation to depth does appear to occur, and even to prevail over stereoscopic depth information under some circumstances.

Stevens, Kent A.↗

Reliable Devices Yield Stable Quantum Computations

Stable quantum computation requires noisy results to remain bounded even in the presence of noise fluctuations. Yet non-stationary noise processes lead to drift in the varying characteristics of a quantum device that can greatly influence the circuit outcomes. Here we address how temporal and spatial variations in noise relate device reliability to quantum computing stability. First, our approach quantifies the differences in statistical distributions of characterization metrics collected at different times and locations using Hellinger distance. We then validate an analytical bound that relates this distance directly to the stability of a computed expectation value. Our demonstration uses numerical simulations with models informed by the washington superconducting transmon device. We find that the stability metric is consistently bounded from above by the corresponding Hellinger distance, which can be cast as a specified tolerance level. These results underscore the significance of reliable quantum computing devices and the impact for stable quantum computation.

Dasgupta, Samudra↗

Software Tool for Tracking & Mapping the NASA Orion AA-2 Test Flight Ejectable Data Recorders in Real Time

On 2 July 2019, the NASA Ascent Abort 2 flight took place off the Florida coast to test the emergency systems to separate the Orion Crew Module (CM) from the future Space Launch System rocket in the event of a malfunction. During this high-altitude test, instrumentation data was recorded on twelve customized buoyant Ejectable Data Recorders (EDRs) and subsequently jettisoned from the CM in mid-air. Upon release, the EDRs activated their GPS-Iridium beacon systems and began transmitting Short Burst Data (SBD) messages via the Iridium satellite network to relay their individual location and system health information. To locate, track and retrieve each EDR from the ocean surface in real-time, multiple open-source programming tools (Python and Linux shells) were developed for parsing the incoming Iridium binary SBD messages. For this, a Linux laptop was used to receive the Iridium-generated emails containing the SBD messages and autonomously execute the parsing tools. The received SBD data contained location, timestamp and health status information that was translated, saved, and subsequently used for simultaneously generating a continuously updated color-coded tabular display summary and unique KML files used with Google Earth to track their locations. Once their locations were known, dedicated recovery vessels retrieved all EDRs from the ocean. An additional tool was also developed in order to generate 5- and 10-minute geolocation predictions for each EDR by deriving the displacement distance, elapsed time, displacement heading and velocity based on the latest known information available. The recovery vessels were also tracked with the use of a separate commercial GPS beacon system. After jettison, 67% of the EDRs transmitted valid data by the time they were retrieved from the ocean. However, the real-time information presented by the plotting tool allowed for the ready depiction of EDR dispersal patterns and reference drift trajectories, which contributed to the recovery of all twelve EDRs and the AA-2 flight data. Lastly, the available data showed that the distance between the software’s reported drift/predicted locations and the recovery locations did not exceed 38 meters, therefore demonstrating the advantages of this software tool for supporting real-time tracking and recovery efforts of beacon devices.

Moxey, Lucas↗

Ice in space: An experimental and theoretical investigation

Basic knowledge is provided on the behavior of ice and ice particles under a wide variety of conditions including those of interplanetary space. This information and, in particular, the lifetime of ice particles as a function of solar distance is an absolute requirement for a proper interpretation of photometric profiles in comets. Because fundamental properties of ice and ice particles are developed in this report, the applicability of this information extends beyond the realm of comets into any area where volatile particles exist, be it in space or in the earth's atmosphere.

Patashnick, H.↗

Predicting the Atmospheric Composition of Extrasolar Giant Planets

To date, approximately 120 planet-sized objects have been discovered around other stars, mostly through the radial-velocity technique. This technique can provide information about a planet s minimum mass and its orbital period and distance; however, few other planetary data can be obtained at this point in time unless we are fortunate enough to find an extrasolar giant planet that transits its parent star (i.e., the orbit is edge-on as seen from Earth). In that situation, many physical properties of the planet and its parent star can be determined, including some compositional information. Our prospects of directly obtaining spectra from extrasolar planets may improve in the near future, through missions like NASA's Terrestrial Planet Finder. Most of the extrasolar giant planets (EGPs) discovered so far have masses equal to or greater than Jupiter's mass, and roughly 16% have orbital radii less than 0.1 AU - extremely close to the parent star by our own Solar-System standards (note that Mercury is located at a mean distance of 0.39 AU and Jupiter at 5.2 AU from the Sun). Although all EGPs are expected to have hydrogen-dominated atmospheres similar to Jupiter, the orbital distance can strongly affect the planet's temperature, physical, chemical, and spectral properties, and the abundance of minor, detectable atmospheric constituents. Thermochemical equilibrium models can provide good zero-order predictions for the atmospheric composition of EGPs. However, both the composition and spectral properties will depend in large part on disequilibrium processes like photochemistry, chemical kinetics, atmospheric transport, and haze formation. We have developed a photochemical kinetics, radiative transfer, and 1-D vertical transport model to study the atmospheric composition of EGPs. The chemical reaction list contains H-, C-, O-, and N-bearing species and is designed to be valid for atmospheric temperatures ranging from 100-3000 K and pressures up to 50 bar. Here we examine the effect of stellar distance (e.g., incident ultraviolet flux, atmospheric temperature) on the chemical properties of EGPs. The model is applied to two generic Class II and III intermediate temperature EGPs located at 3.3 and 0.27 AU from a solar-like parent star, and the results are compared with a model for Jupiter at 5.2 AU.

Sharp, A. G.↗

Recommendations for harmonized reporting of radiation Dosimetry by adoption of Compatibility in Irradiation Research Protocols Expert Roundtable (CIRPER)

Here, in radiobiology, radiation physics, and related areas, there is growing interest in transitioning from cesium-based irradiators to X-ray technologies. Therefore, it makes it imperative for reproducibility purposes, for researchers to provide specifications regarding device parameters, machine calibration details, and experimental setup when innovative X-ray technology is being employed. Several groups have already identified a glaring lack in completeness of critical information on experimental setups, equipment, and physical parameters in published radiation biology studies. The Alternative Technologies Meta Study Report by Brookhaven National Laboratory (BNL) examined 456 manuscripts published between 2017-2021. Only 64 of the reviewed studies (14.0%) consistently reported methods that could allow for replication of their studies. However, 85% provided information on the manufacturer, the irradiator model and the absorbed radiation dose. Approximately 66% provided information on the energy spectra and the dose rate, but only one third disclosed the filter used. Less than 15% of the reviewed studies reported information on calibration and field geometry, specifically field size and distance from source, which are critical parameters in determining the absorbed radiation dose.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An electron diffraction study of alkali chloride vapors

A study of monomers and dimers of the four alkali chlorides NaCl, KCl, RbCl, and CsCl in the vapor phase using the counting method of high energy electron diffraction is reported. Nozzle temperatures from 850-960 K were required to achieve the necessary vapor pressures of approximately 0.01 torr. Using harmonic calculations for the monomer and dimer 1 values, a consistent set of structures for all four molecules was obained. The corrected monomer distances reproduce the microwave values very well. The experiment yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Mawhorter, R. J.↗

Probing the Interstellar Medium of External Galaxies Using Quasar Absorption Lines: the 3C 232/NGC 3067 System

Quasar absorption lines offer unique opportunities to probe the interstellar medium of external galaxies. Researchers present new optical and UV absorption line spectroscopy of the quasar 3C232 (z=0.55) revealing new detail in the foreground absorption system due to the bright, spiral galaxy NGC 3067 (cz=1420 km/s). Specifically, the spectra show evidence for two and possibly three separate absorption components in CaII and Na I spanning approx. 150 km/s. The original HI detection of Haschick and Burke (1975) corresponds to the strongest of these metal systems which exhibits doublet ratios consistent with saturation in both CaII and Na I. Due to the recent detection in HI emission of a tidal tail or finger of HI extending from the western edge of NGC 3067 through the position of 3C 232 (Carilli, van Gorkom and Stocke, 1989), the morphology of the HI absorber is now known and is not either a warped disk nor a spherical halo as had been proposed. New deep continuum and H alpha imaging provides a sensitive upper limit on the the ionizing continuum impinging upon this cloud (and thus a limit on the intensity of the extragalactic ionizing radiation field). Together with the observed UV spectrum of 3C 232, the optical emission line ratios and the deep H alpha imaging set a minimum distance between the quasar and the HI cloud disregarding redshift information. This limit strains the non-cosmological redshift interpretation for 3C 232 -- and this quasar is one of the original 5 3C quasars found to be too close to NGC galaxies as if by chance (Burbidge, Burbidge, Solomon and Strittmatter, 1972).

Stocke, John T.↗

Microgravity cursor control device evaluation for Space Station Freedom workstations

This research addressed direct manipulation interface (curser-controlled device) usability in microgravity. The data discussed are from KC-135 flights. This included pointing and dragging movements over a variety of angles and distances. Detailed error and completion time data provided researchers with information regarding cursor control shape, selection button arrangement, sensitivity, selection modes, and considerations for future research.

Adam, Susan↗

Statistical properties of the solar wind

We now have spacecraft observations spanning more than a complete 22-year solar cycle. PVO at Venus, IMP 8 at Earth, and Voyager 2 and Pioneers 10 and 11 in the outer heliosphere provide many years of data from locations scattered through the heliosphere. These large data sets enable us to look at the solar wind velocity, density, temperature and flow angles on a statistical basis. Comparison of results at the different locations will provide information on the evolution of the solar wind with radial distance and variation with latitude.

Richardson, J. D.↗

Corotating and transient structures of IMF at Venus and Earth orbits

Magnetometer data obtained from the Pioneer Venus orbiter (PVO) provide a unique data base for studying interplanetary magnetic field (IMF) structures at 0.7 AU. Comparison of the same structure observed at 0.7 and 1 AU provides information about the effects of stream interactions between these two distances. Besides, the PVO observations provide solar wind conditions at various longitude separations from the Sun-Earth line, because the orbital motion of Venus is about 0.6 deg/day faster than that of Earth. Thus, it is possible to examine the effects of time variations in the coronal conditions on the solar wind conditions by comparing corotating structures observed at Earth and those from the PVO at different longitude separations. Some results obtained so far are as follows. We have found several transient structures observed at both 0.7 and 1 AU, when the Sun, Venus, and Earth are closely aligned. Each event exhibits magnetic field variations very similar to each other between Venus and Earth, implying that the effects of stream interactions are small. The IMF sector boundaries were compared between the Venus and Earth orbits as typical examples of corotating structures. We have found both well-correlated and poorly-correlated structures depending on the longitude separation between the Earth and Venus, and on the persistence of the sector structures.

Marubashi, K.↗

Trans-Pacific Astronomy Experiment Project Status

The Trans-Pacific Astronomy Experiment is Phase 2 of the Trans-Pacific High Data Rate Satcom Experiments following the Trans-Pacific High Definition Video Experiment. It is a part of the Global Information Infrastructure-Global Interoperability for Broadband Networks Project (GII-GIBN). Provides global information infrastructure involving broadband satellites and terrestrial networks and access to information by anyone, anywhere, at any time. Collaboration of government, industry, and academic organizations demonstrate the use of broadband satellite links in a global information infrastructure with emphasis on astronomical observations, collaborative discussions and distance learning.

Hsu, Eddie↗

Estimating Temperature Retrieval Accuracy Associated With Thermal Band Spatial Resolution Requirements for Center Pivot Irrigation Monitoring and Management

This study explores the use of synthetic thermal center pivot irrigation scenes to estimate temperature retrieval accuracy for thermal remote sensed data, such as data acquired from current and proposed Landsat-like thermal systems. Center pivot irrigation is a common practice in the western United States and in other parts of the world where water resources are scarce. Wide-area ET (evapotranspiration) estimates and reliable water management decisions depend on accurate temperature information retrieval from remotely sensed data. Spatial resolution, sensor noise, and the temperature step between a field and its surrounding area impose limits on the ability to retrieve temperature information. Spatial resolution is an interrelationship between GSD (ground sample distance) and a measure of image sharpness, such as edge response or edge slope. Edge response and edge slope are intuitive, and direct measures of spatial resolution are easier to visualize and estimate than the more common Modulation Transfer Function or Point Spread Function. For these reasons, recent data specifications, such as those for the LDCM (Landsat Data Continuity Mission), have used GSD and edge response to specify spatial resolution. For this study, we have defined a 400-800 m diameter center pivot irrigation area with a large 25 K temperature step associated with a 300 K well-watered field surrounded by an infinite 325 K dry area. In this context, we defined the benchmark problem as an easily modeled, highly common stressing case. By parametrically varying GSD (30-240 m) and edge slope, we determined the number of pixels and field area fraction that meet a given temperature accuracy estimate for 400-m, 600-m, and 800-m diameter field sizes. Results of this project will help assess the utility of proposed specifications for the LDCM and other future thermal remote sensing missions and for water resource management.

Ryan, Robert E.↗

High-Speed Schlieren Analysis of Retropropulsion Jet in Mach 10 Flow

High-speed schlieren imaging of a 5-in.-diam, 70° sphere-cone model with a single centerline 15° half-angle nozzle was performed in a Mach 10 flow. Image sequences captured at 100 kHz were obtained with the nozzle plugged (fully blunted model), no nozzle flow, and with nozzle flow over a range of supply pressures. The freestream unit Reynolds number was kept constant for all runs at3.38×106m−1. Time-average information pertaining to the location, width, and stand-off distance of the bow shock, interface, terminal shock, and triple point as a function of jet pressure ratio are presented based on analysis of covariance images from each run. Measurement of jet plume boundary shape as a function of jet pressure ratio is also presented. Analyses of frequency content associated with the jet structure are shown, as are results of the proper orthogonal decomposition of these data. For all runs with nozzle flow, a dominant fundamental frequency of 2 kHz was observed. Finally, a discussion of bow shock unsteadiness resulting from interaction with freestream disturbances for the blunted and no nozzle flow is provided, as is a discussion on the formation of weak waves emanating from the bow shock resulting from this interaction.

Brett F Bathel↗

Multiple Coulomb scattering for muon energy reconstruction in SBND Monte Carlo simulations

The Short Baseline Near Detector (SBND) is a liquid argon time projection chamber (LArTPC) located 110 meters downstream of the Booster Neutrino Beam target at Fermilab \cite{SBN}. The LArTPC is a detector technology with unprecedented position and calorimetric resolution for precise neutrino studies. The most dominant neutrino interaction topology in SBND is charged-current quasi-elastic muon neutrino-argon interactions, where the final state consists of a muon and a proton. Here, muons often travel long distances, sometimes exiting the detector before stopping. This loss of information creates a challenge for accurate energy estimation. There have been efforts in the MicroBooNE and ICARUS collaborations to improve energy estimation using a phenomenon known as Multiple Coulomb Scattering (MCS), which describes the jagged path taken by muons through a detector due to continuous Coulomb interactions with argon atoms. Building on these efforts, my project aims to improve an MCS-based approach to estimating the energies of exiting muons in SBND.

Puig, Xilonem Angeles [Mt. Holyoke Coll.; Fermilab↗

Information content of higher order galaxy correlation functions

The shapes of galaxy N-point correlation functions can be used as standard rulers to constrain the distance–redshift relationship. The cosmological density fields traced by late-time galaxy formation are initially nearly Gaussian, and hence, all the cosmological information can be extracted from their two-point correlation function. Subsequent non-linear evolution under gravity, as well as halo and then galaxy formation, generates higher order correlation functions. Since the mapping of the initial to the final density field is, on large scales, invertible, it is often claimed that the information content of the initial field’s power spectrum is equal to that of all the higher order functions of the final, non-linear field. This claim implies that reconstruction of the initial density field from the non-linear field renders analysis of higher order correlation functions of the latter superfluous. We show that this claim is false when the N-point functions are used as standard rulers. Constraints available from joint analysis of the two and three-point correlation functions can, in some cases, exceed those offered by the initial power spectrum. We provide a mathematical justification for this claim and demonstrate it using a large suite of N-body simulations. In particular, we show that for the z = 0 real-space matter field in the limit of vanishing shot-noise, taking modes up to k max = 0.2 h Mpc −1 , using the bispectrum alone offers a factor of 2 reduction in the variance on the cosmic distance scale relative to that available from the linear power spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

Determination of depth-viewing volumes for stereo three-dimensional graphic displays

Real-world, 3-D, pictorial displays incorporating true depth cues via stereopsis techniques offer a potential means of displaying complex information in a natural way to prevent loss of situational awareness and provide increases in pilot/vehicle performance in advanced flight display concepts. Optimal use of stereopsis requires an understanding of the depth viewing volume available to the display designer. Suggested guidelines are presented for the depth viewing volume from an empirical determination of the effective region of stereopsis cueing (at several viewer-CRT screen distances) for a time multiplexed stereopsis display system. The results provide the display designer with information that will allow more effective placement of depth information to enable the full exploitation of stereopsis cueing. Increasing viewer-CRT screen distances provides increasing amounts of usable depth, but with decreasing fields-of-view. A stereopsis hardware system that permits an increased viewer-screen distance by incorporating larger screen sizes or collimation optics to maintain the field-of-view at required levels would provide a much larger stereo depth-viewing volume.

Parrish, Russell V.↗