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At least 91 records · Page 5

Machine learning-driven descriptions of protein dynamics at solid-liquid interfaces

This chapter has described how ML has enabled quantitative analysis of HS-AFM data to discover the physical phenomena governing protein dynamics and ordering at solid-liquid interfaces. The research detailed in this chapter modeled the rotation models of protein nanorods, the discovery of which would otherwise not be possible. By tracking the trajectories of individual protein rods from frame to frame, it was possible to model Brownian type motion and behaviors and Levy-flight dynamics that had not previously been shown. We also described the application of the Python package AtomAI, which has been developed specifically to analyze and extract physical phenomena, providing exemplar code for training an ensemble of deep neural networks to produce the semantic segmentation of AFM data and functions for encoding and decoding local environments. We last described a combinatorial approach to analyze very noisy data with a densely covered substrate where the emergence of order for the protein liquid crystals could be elucidated. By combining the methods from Case 1 and 2, it was possible to obtain the center of mass and angle for each rod in the images and track the assembly of the rods over time into a 2D liquid crystal array on the surface of mica.

protein dynamics, solid-liquid interfaces, atomic ↗

STExNMF: Spatio-Temporally Exclusive Topic Discovery for Anomalous Event Detection

Understanding newly emerging events or topics associated with a particular region of a given day can provide deep insight on the critical events occurring in highly evolving metropolitan cities. We propose herein a novel topic modeling approach on text documents with spatio-temporal information (e.g., when and where a document was published) such as location-based social media data to discover prevalent topics or newly emerging events with respect to an area and a time point. We consider a map view composed of regular grids or tiles with each showing topic keywords from documents of the corresponding region. To this end, we present a tilebased spatio-temporally exclusive topic modeling approach called STExNMF, based on a novel nonnegative matrix factorization (NMF) technique. STExNMF mainly works based on the two following stages: (1) first running a standard NMF of each tile to obtain general topics of the tile and (2) running a spatiotemporally exclusive NMF on a weighted residual matrix. These topics likely reveal information on newly emerging events or topics of interest within a region. We demonstrate the advantages of our approach using the geo-tagged Twitter data of New York City. We also provide quantitative comparisons in terms of the topic quality, spatio-temporal exclusiveness, topic variation, and qualitative evaluations of our method using several usage scenarios. In addition, we present a fast topic modeling technique of our model by leveraging parallel computing.

Shin, Sungbok↗

Relationship Between Column-Density and Surface Mixing Ratio: Statistical Analysis of O3 and NO2 Data from the July 2011 Maryland DISCOVER-AQ Mission

To investigate the ability of column (or partial column) information to represent surface air quality, results of linear regression analyses between surface mixing ratio data and column abundances for O3 and NO2 are presented for the July 2011 Maryland deployment of the DISCOVER-AQ mission. Data collected by the P-3B aircraft, ground-based Pandora spectrometers, Aura/OMI satellite instrument, and simulations for July 2011 from the CMAQ air quality model during this deployment provide a large and varied data set, allowing this problem to be approached from multiple perspectives. O3 columns typically exhibited a statistically significant and high degree of correlation with surface data (R(sup 2) > 0.64) in the P- 3B data set, a moderate degree of correlation (0.16 < R(sup 2) < 0.64) in the CMAQ data set, and a low degree of correlation (R(sup 2) < 0.16) in the Pandora and OMI data sets. NO2 columns typically exhibited a low to moderate degree of correlation with surface data in each data set. The results of linear regression analyses for O3 exhibited smaller errors relative to the observations than NO2 regressions. These results suggest that O3 partial column observations from future satellite instruments with sufficient sensitivity to the lower troposphere can be meaningful for surface air quality analysis.

nitrogen dioxide↗

197 candidates and 104 validated planets in K2's first five fields

We present 197 planet candidates discovered using data from the first year of the NASA K2 mission (Campaigns 0–4), along with the results of an intensive program of photometric analyses, stellar spectroscopy, high-resolution imaging, and statistical validation. We distill these candidates into sets of 104 validated planets (57 in multi-planet systems), 30 false positives, and 63 remaining candidates. Our validated systems span a range of properties, with median values of R {sub P} = 2.3 R{sub ⊕}, P = 8.6 days, T{sub eff} = 5300 K, and Kp = 12.7 mag. Stellar spectroscopy provides precise stellar and planetary parameters for most of these systems. We show that K2 has increased by 30% the number of small planets known to orbit moderately bright stars (1–4 R {sub ⊕}, Kp = 9–13 mag). Of particular interest are 76 planets smaller than 2 R {sub ⊕}, 15 orbiting stars brighter than Kp = 11.5 mag, 5 receiving Earth-like irradiation levels, and several multi-planet systems—including 4 planets orbiting the M dwarf K2–72 near mean-motion resonances. By quantifying the likelihood that each candidate is a planet we demonstrate that our candidate sample has an overall false positive rate of 15%–30%, with rates substantially lower for small candidates (<2R{sub ⊕}) and larger for candidates with radii >8R{sub ⊕} and/or with P<3 days. Extrapolation of the current planetary yield suggests that K2 will discover between 500 and 1000 planets in its planned four-year mission, assuming sufficient follow-up resources are available. Efficient observing and analysis, together with an organized and coherent follow-up strategy, are essential for maximizing the efficacy of planet-validation efforts for K2, TESS, and future large-scale surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Derivative-based SINDy (DSINDy): Addressing the challenge of discovering governing equations from noisy data

Recent advances in the field of data-driven dynamics allow for the discovery of ODE systems using state measurements. One approach, known as Sparse Identification of Nonlinear Dynamics (SINDy), assumes the dynamics are sparse within a predetermined basis in the states and finds the expansion coefficients through linear regression with sparsity constraints. This approach requires an accurate estimation of the state time derivatives, which is not necessarily possible in the high-noise regime without additional constraints. We present an approach called Derivative-based SINDy (DSINDy) that combines two novel methods to improve ODE recovery at high-noise levels. First, we denoise the state variables by applying a projection operator that leverages the assumed basis for the system dynamics. Second, we use a second order cone program (SOCP) to find the derivative and governing equations simultaneously. We derive theoretical results for the projection-based denoising step, which allow us to estimate the values of hyperparameters used in the SOCP formulation. This underlying theory helps limit the number of required user-specified parameters. Finally, we present results demonstrating that our approach leads to improved system recovery for the Van der Pol oscillator, the Duffing oscillator, the Rössler attractor, and the Lorenz 96 model.

97 MATHEMATICS AND COMPUTING↗

Comprehensive Computational Study of Partial Lead Substitution in Methylammonium Lead Bromide

Impurities in semiconductors, for example, lead-based hybrid perovskites, have a major influence on their performance as photovoltaic (PV) light absorbers. While impurities could create harmful trap states that lead to nonradiative recombination of charge carriers and adversely affect PV efficiency, they could also potentially increase absorption via midgap energy levels that act as stepping stones for subgap photons or introduce charge carriers via doping. To unearth trends in impurity energy states, we use first principles density functional theory calculations to extensively study partial substitution of Pb in methylammonium lead bromide (MAPbBr 3 ), a representative lead-halide perovskite. Investigation of the density of states and energy levels related to the transition of the substitutional defect from one charge state to another reveals that several elements create midgap energy states in MAPbBr 3 . We machine learned trends and design rules from the computational data and discovered that a few easily computed properties of the bromide compounds of any element can be used to predict the energetics and energy levels of the substitutional defect related to that element. The calculated Fermi level-dependent defect formation energies lead to the observation that substitution by transition metals, Zr, Hf, Nb, and Sc, and group V element Sb can shift the equilibrium Fermi level and change the perovskite conductivity, as determined by the dominant intrinsic point defects. Finally, metal-substituted MAPbBr 3 compounds of Bi, Sc, Ni, and Zr were experimentally investigated, and while there was an improvement in the thin-film morphology and an enhancement in charge carrier lifetimes, no clear evidence of subgap absorption features owing to the substituent being incorporated in the MAPbBr 3 lattice could be seen.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atmospheric wind energization of ocean weather

Ocean weather comprises vortical and straining mesoscale motions, which play fundamentally different roles in the ocean circulation and climate system. Vorticity determines the movement of major ocean currents and gyres. Strain contributes to frontogenesis and the deformation of water masses, driving much of the mixing and vertical transport in the upper ocean. While recent studies have shown that interactions with the atmosphere damp the ocean’s mesoscale vortices O(100) km in size, the effect of winds on straining motions remains unexplored. Here, we derive a theory for wind work on the ocean’s vorticity and strain. Using satellite and model data, we discover that wind damps strain and vorticity at an equal rate globally, and unveil striking asymmetries based on their polarity. Subtropical winds damp oceanic cyclones and energize anticyclones outside strong current regions, while subpolar winds have the opposite effect. A similar pattern emerges for oceanic strain, where subtropical convergent flow is damped along the west-equatorward east-poleward direction and energized along the east-equatorward west-poleward direction. These findings reveal energy pathways through which the atmosphere shapes ocean weather.

54 ENVIRONMENTAL SCIENCES↗

Single-cell quantification of ribosome occupancy in early mouse development

Translation regulation is critical for early mammalian embryonic development. However, previous studies had been restricted to bulk measurements, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N 6 -methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting the viscoplastic response of a crystallizing fluoropolymer using transient network theory

We employ a molecular theory of dynamic polymer networks to describe the viscoplastic response of rubbery FK-800, a thermoplastic copolymer of chlorotrifluoroethylene and vinylidene fluoride, over a broad range of thermal histories. The kinetics of crystallization at different annealing temperatures was modeled using a modified Avrami equation, whose parameters were found to evolve through simple relationships over the full temperature range of the rubbery state. By fitting experimental compression data, we discovered predictable trends for the physical parameters in our mechanical model over its full range of crystallinities (up to ≈20%) and provided insights based on molecular-level physics to justify them. Using this, an end-to-end model was developed to predict the yielding and post-yield behavior of rubbery FK-800 for arbitrary thermal histories. The model successfully predicted the highly nonlinear evolution of characteristic mechanical signatures (stiffness, yield point, post-yield drop) throughout the crystallization process. A statistical analysis of variance test was employed to determine that the measured variations in the mechanical behavior of rubbery FK-800 are primarily dictated by its fractional crystallinity, regardless of its exact thermal history.

36 MATERIALS SCIENCE↗

VERY-LOW-MASS STELLAR AND SUBSTELLAR COMPANIONS TO SOLAR-LIKE STARS FROM MARVELS. III. A SHORT-PERIOD BROWN DWARF CANDIDATE AROUND AN ACTIVE G0IV SUBGIANT

We present an eccentric, short-period brown dwarf candidate orbiting the active, slightly evolved subgiant star TYC 2087-00255-1, which has effective temperature T{sub eff} = 5903 {+-} 42 K, surface gravity log (g) = 4.07 {+-} 0.16 (cgs), and metallicity [Fe/H] = -0.23 {+-} 0.07. This candidate was discovered using data from the first two years of the Multi-object APO Radial Velocity Exoplanets Large-area Survey, which is part of the third phase of Sloan Digital Sky Survey. From our 38 radial velocity measurements spread over a two-year time baseline, we derive a Keplerian orbital fit with semi-amplitude K = 3.571 {+-} 0.041 km s{sup -1}, period P = 9.0090 {+-} 0.0004 days, and eccentricity e = 0.226 {+-} 0.011. Adopting a mass of 1.16 {+-} 0.11 M{sub Sun} for the subgiant host star, we infer that the companion has a minimum mass of 40.0 {+-} 2.5 M{sub Jup}. Assuming an edge-on orbit, the semimajor axis is 0.090 {+-} 0.003 AU. The host star is photometrically variable at the {approx}1% level with a period of {approx}13.16 {+-} 0.01 days, indicating that the host star spin and companion orbit are not synchronized. Through adaptive optics imaging we also found a point source 643 {+-} 10 mas away from TYC 2087-00255-1, which would have a mass of 0.13 M{sub Sun} if it is physically associated with TYC 2087-00255-1 and has the same age. Future proper motion observation should be able to resolve if this tertiary object is physically associated with TYC 2087-00255-1 and make TYC 2087-00255-1 a triple body system. Core Ca II H and K line emission indicate that the host is chromospherically active, at a level that is consistent with the inferred spin period and measured v{sub rot}sin i, but unusual for a subgiant of this T{sub eff}. This activity could be explained by ongoing tidal spin-up of the host star by the companion.

79 ASTRONOMY AND ASTROPHYSICS↗

Probing topological relations between high-density and low-density regions of 2MASS with hexagon cells

We introduced a new two-dimensional (2D) hexagon technique for probing the topological structure of the universe in which we mapped regions of the sky with high and low galaxy densities onto a 2D lattice of hexagonal unit cells. We defined filled cells as corresponding to high-density regions and empty cells as corresponding to low-density regions. The numbers of filled cells and empty cells were kept the same by controlling the size of the cells. By analyzing the six sides of each hexagon, we could obtain and compare the statistical topological properties of high-density and low-density regions of the universe in order to have a better understanding of the evolution of the universe. We applied this hexagonal method to Two Micron All Sky Survey data and discovered significant topological differences between the high-density and low-density regions. Both regions had significant (>5σ) topological shifts from both the binomial distribution and the random distribution.

79 ASTRONOMY AND ASTROPHYSICS↗

Distinguishing between extra natural inflation and natural inflation after BICEP2

In this paper, we carefully calculated the tensor-to-scalar ratio, the running spectral index, and the running of running spectrum for (extra) natural inflation in order to compare with recent BICEP2 data, PLANCK satellite data and future 21 cm data. We discovered that the prediction for running spectral index and the running of running spectrum in natural inflation is different from that in the case of extra natural inflation. Near future observation for the running spectral index can only provide marginal accuracy which may not allow us distinguishing between extra natural inflation from natural inflation clearly unless the experimental accuracy can be further improved.

79 ASTRONOMY AND ASTROPHYSICS↗

THE MASSIVE DISTANT CLUSTERS OF WISE SURVEY: THE FIRST DISTANT GALAXY CLUSTER DISCOVERED BY WISE

We present spectroscopic confirmation of a z = 0.99 galaxy cluster discovered using data from the Wide-field Infrared Survey Explorer (WISE). This is the first z {approx} 1 cluster candidate from the Massive Distant Clusters of WISE Survey to be confirmed. It was selected as an overdensity of probable z {approx}> 1 sources using a combination of WISE and Sloan Digital Sky Survey DR8 photometric catalogs. Deeper follow-up imaging data from Subaru and WIYN reveal the cluster to be a rich system of galaxies, and multi-object spectroscopic observations from Keck confirm five cluster members at z = 0.99. The detection and confirmation of this cluster represents a first step toward constructing a uniformly selected sample of distant, high-mass galaxy clusters over the full extragalactic sky using WISE data.

79 ASTRONOMY AND ASTROPHYSICS↗

Plutonium-238 Loadout Calorimeter Return To Service

The calorimeter in the transfer area in Building 7920 at the US Department of Energy’s Oak Ridge National Laboratory is used to measure the amount of 238 Pu in the Plutonium Heat Source Oxide. The calorimetry measurement is taken after the oxide is packaged in an ORISC (Oak Ridge Inner Shipping Capsule)/FSO (Fuel Storage Outer) assembly before loading into the Containment Vessel and shipping container. The equipment is used in three specific configurations: zero measurement (nothing in the sample cup), FSO measurement (actual measurement of 238 Pu), and reference calibration measurement (using the reference FSO as a known heat source). System checks were performed in July 2023 in preparation for scheduled material loadout. During these checks, personnel discovered that the reference FSO had experienced an electrical short in the heater cable and was no longer functional. The calorimeter was in the reference calibration measurement configuration at this time. Facility management was notified when the damage was discovered. The data from the Yokogawa recorder were pulled and analyzed for a span of time between September 2022 and July 2023. An unusual spike was found in the sample cup temperature data that started on October 19, 2022, and ended on October 20, 2022. The sample cup reached a temperature of 191.1°C. The maximum allowable temperature for the calorimeter thermopile to reach is 220°C based on the manufacturer statement provided in Appendix B of this report [1]. The calorimeter thermopile and the sample cup thermocouple are physically close to each other; therefore, the data suggest that the calorimeter itself never saw a temperature in excess of 191.1°C. Physical damage present on the cable, tape, and insulation suggests that the temperature reached a higher value in some locations within the sample cup than the data shows. Because of this discrepancy, testing of the calorimeter was required to confirm that the calorimeter is functioning the same as it was before the electrical short. The intent of this report is to assess the functionality of the calorimeter and determine if it is acceptable to use for 238 Pu loadout material measurement. Testing showed that the calorimeter is functionally equivalent to the initial calibration that was performed in the summer of 2021, and thus, the calorimeter was cleared to be used for its intended purposes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Discovery of a longitudinal asymmetry in the H Lyman-alpha brightness of Jupiter

A strong longitude variation in the midlatitude Lyman-alpha brightness of Jupiter has been discovered using data from the Voyager ultraviolet spectrometers. A minimum brightness of 14.4 kR was observed in the System III (1965) west longitude range 200-300 deg. The intensity rises to a broad peak of 19.6 kR near a longitude of 110 deg, a 36% increase over the minimum. This intensity 'bulge' was observed to rotate with the planet and appeared at the same longitude during both Voyager encounters, four months apart. This is a surprising discovery; no other planet studied to date has such a characteristic and the upper levels of the Jovian atmosphere were expected to be uniform in longitude. It is likely that a longitudinal asymmetry in charged particle precipitation leads to selective heating of the upper atmosphere and increased dissociation of H2, increasing the hydrogen column abundance. The resulting increase in resonant scattering could produce the observed intensity bulge.

Sandel, B. R.↗

New advances in thermal plasma research

Recent measurements obtained of the cold or thermal plasma of the earth's magnetosphere, which is believed to originate in the ionosphere, are reviewed. Consideration is given to the results of ATS 6 measurements which indicated unexpectedly high plasma temperatures and varied pitch-angle distributions, and the data from the low-energy plasma experiments on board GEOS 1 and 2 and ISEE 1, which were intended to clarify the ATS 6 results. These later measurements of ion composition, plasma energy and plasma distribution are noted to have confirmed earlier data and discovered new plasma components (D(+) or He(+2)), an intermixing of cold ionospheric plasma and hot magnetospheric plasma, the ordering of the plasma by the magnetic field rather than the ram direction in the outer magnetosphere, and wave phenomena. Questions remaining concerning the temperature and composition distributions of the plasmasphere and plasma trough, the relative densities of the cold and warmer components of the magnetosphere, plasma energization mechanisms, and the relative mix of the various plasma distributions are indicated.

Chappell, C. R.↗

Prospecting for planets in circumstellar dust - Sifting the evidence from Beta Pictoris

IRAS and near-IR coronographic data for the A5V star Beta Pic are analyzed for evidence of planetary formation. The light scattered from the central star in the system is integrated along the distance to the star to determine the disk magnitude at various distances from the star. A modified gamma distribution is applied to evaluate the scattering coefficient to test a hypothesis that the inner 30 AU of the disk has been swept out by planets. The scattering from the region around Beta Pic is compared with scattering around other A5V stars. Finally, the IR data at 0.89 micron is compared with scattering at the coronograph wavelengths. No evidence is found to support the hypothesis of clearing in the inner disk, although large particle densities can be found very close to Beta Pic. The study illustrates the effectiveness of using scattered light and IR data to discover and characterize matter distributions circumstellar disks.

Diner, D. J.↗

Does Lafayette = Nakhla? Not necessarily so, based on 4.2K Mossbauer spectra of all of the SNC meteorites

In previous Mossbauer spectral studies of many of the Shergotite Nakhlite Chassignite (SNC) meteorites, attention was drawn to the close similarities of spectrum profiles between Lafayette and Nakhla, which were once suggested to be identical meteorites. These observations led to the acquisition of Governador Valadares and another specimen of Nakhla, as well as Zagami and Shergotty, for Mossbauer spectral measurements at 4.2K. Results reported here demonstrate that there are subtle differences between the three nakhlites (Nakhla, Lafayette, and Governador Valadares), as there are for three of the shergottites (Shergotty, Zagami, EETA 79001/lithologies A and B) and olivine-dominated Chassigny and ALHA 77005, indicating that all eight of the SNC meteorites discovered to data fell independently to Earth.

Burns, Roger G.↗