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At least 685 records · Page 38

Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization

For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein–solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54 , e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.

59 BASIC BIOLOGICAL SCIENCES↗

Contributing to Sunny open source code

The Sunny package is an existing open source software to support the simulation of magnetic spin systems. It is available online under the MIT license here: https://github.com/SunnySuite/Sunny.jl The package aims to include the following features: - Analysis for symmetry-allowed interactions - Monte Carlo algorithms for simulating equilibrium configurations. - Schemes for integrating spin dynamics. - Inference of model Hamiltonians - Support for generalized SU(N) spins - Tools for interpreting experimental data, such as diffraction data, magnetization curves, and heat capacity data

Barros, Kipton↗

Multivariate regression modelling for gender prediction using volatile organic compounds from hand odor profiles via HS-SPME-GC-MS

The efficacy of using human volatile organic compounds (VOCs) as a form of forensic evidence has been well demonstrated with canines for crime scene response, suspect identification, and location checking. Although the use of human scent evidence in the field is well established, the laboratory evaluation of human VOC profiles has been limited. This study used Headspace-Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS) to analyze human hand odor samples collected from 60 individuals (30 Females and 30 Males). The human volatiles collected from the palm surfaces of each subject were interpreted for classification and prediction of gender. The volatile organic compound (VOC) signatures from subjects’ hand odor profiles were evaluated with supervised dimensional reduction techniques: Partial Least Squares-Discriminant Analysis (PLS-DA), Orthogonal-Projections to Latent Structures Discriminant Analysis (OPLS-DA), and Linear Discriminant Analysis (LDA). The PLS-DA 2D model demonstrated clustering amongst male and female subjects. The addition of a third component to the PLS-DA model revealed clustering and minimal separation of male and female subjects in the 3D PLS-DA model. The OPLS-DA model displayed discrimination and clustering amongst gender groups with leave one out cross validation (LOOCV) and 95% confidence regions surrounding clustered groups without overlap. The LDA had a 96.67% accuracy rate for female and male subjects. The culminating knowledge establishes a working model for the prediction of donor class characteristics using human scent hand odor profiles.

59 BASIC BIOLOGICAL SCIENCES↗

Phase-curve Pollution of Exoplanet Transit Depths

The next generation of space telescopes will enable transformative science to understand the nature and origin of exoplanets. In particular, transit spectroscopy will reveal the chemical composition of the exoplanet atmospheres with unprecedented detail thanks to precise measurements of the visible-to-infrared transit depths down to 10 parts per million. Such a level of instrumental precision raises the challenge to obtain even more precise astrophysical models so as not to significantly influence the interpretation of the observed data. We must therefore critically revisit some of the commonly accepted assumptions that were adequate for analyzing past and current observations. A common approximation in the analysis of exoplanetary primary transits is that the planet does not contribute to the recorded flux, so-called dark planet hypothesis. In this paper, we investigate the impact of the dark planet hypothesis on the parameters obtained from the analysis of transits with particular attention to the transit depth. We develop mathematical formulae and release new software to estimate the magnitude of the potential bias. These tools will be useful in the preparation of observing proposals, as well as within the scientific consortia of the James Webb Space Telescope (JWST) and the Atmospheric Remote-sensing Infrared Exoplanet Large-survey (ARIEL) missions. We probe the accuracy of the mathematical formulae through the analysis of synthetic observations with the JWST Mid-InfraRed Instrument. We find that self-blending from nightside emission attenuates the transit depth by >3σ for some of the known exoplanet systems, in agreement with previous work. An additional unreported effect caused by the nightside rotating into view can also impart a significant effect, but in the opposite direction (increasing the transit depth); this effect can largely be removed with conventional detrending practices, at the expense of a slight increase in noise, and mixing astrophysical variations and instrumental drifts.

79 ASTRONOMY AND ASTROPHYSICS↗

An Interpretable Index of Social Vulnerability to Environmental Hazards

Index-based measures of social vulnerability to environmental hazards are commonly modeled from composites of population-level risk factors. These models overlook individual context in communities' experiences of environmental hazards, producing metrics that may hinder spatial decision support for mitigating and responding to hazards. This paper introduces an interpretable, high-resolution model for generating an individual-oriented social vulnerability index (IOSVI) for the United States built on synthetic populations that couples individual and social determinants of vulnerability. The IOSVI combines an individual vulnerability index (IVI) that ranks individuals in an area’s synthetic population based on intersecting risk factors, with a social vulnerability index (SVI) based on the population’s cumulative distribution of IVI scores. Interpretability of the IOSVI procedure is demonstrated through examples of national, metropolitan, and neighborhood (census tract) level spatial variation in index scores and IVI themes, as well as an exploratory analysis examining risk factors affecting a specific sub-population (military veterans) in areas of high social and environmental vulnerability.

Tuccillo, Joe↗

XPS analysis of molecular contamination and sp 2 amorphous carbon on oxidized (100) diamond

The efficacy of oxygen (O) surface terminations on diamond is an important factor for the performance and stability for diamond-based quantum sensors and electronics. Given the wide breadth of O-termination techniques, it can be difficult to discern which method would yield the highest and most consistent O coverage. Furthermore, the interpretation of surface characterization techniques is complicated by surface morphology and purity, which if not accounted for will yield inconsistent determination of the oxygen coverage. We present a comprehensive approach to consistently prepare and analyze oxygen termination of surfaces on (100) single-crystalline diamond. We report on x-ray photoelectron spectroscopy (XPS) characterization of diamond surfaces treated with six oxidation methods that include various wet chemical oxidation techniques, photochemical oxidation with UV illumination, and steam oxidation using atomic layer deposition (ALD). Our analysis entails a rigorous XPS peak-fitting procedure for measuring the functionalization of O-terminated diamond. The findings herein have provided molecular-level insights on oxidized surfaces in (100) diamond, including the demonstration of clear correlation between the measured oxygen atomic percentage and the presence of molecular contaminants containing nitrogen, silicon, and sulfur. We also provide a comparison of the sp 2 carbon content with the O1s atomic percentage and discern a correlation with the diamond samples treated with dry oxidation which eventually tapers off at a max O1s atomic percentage value of 7.09 ± 0.40%. Given these results, we conclude that the dry oxidation methods yield some of the highest oxygen amounts, with the ALD water vapor technique proving to be the cleanest technique out of all the oxidation methods explored in this work.

XPS↗

Analysis of Hybrid Gas–Dust Outbursts Observed at 67P/Churyumov–Gerasimenko

Cometary outbursts offer a valuable window into the composition of comet nuclei with their forceful ejection of dust and volatiles in explosive events, revealing the interior components of the comet. Understanding how different types of outbursts influence the dust properties and volatile abundances, to better interpret what signatures can be attributed to primordial composition and what features are the result of processing, is an important task best undertaken with a multi-instrument approach. The European Space Agency Rosetta mission to 67P/Churyumov–Gerasimenko carried a suite of instruments capable of carrying out this task in the near-nucleus coma with unprecedented spatial and spectral resolution. In this work, we discuss two outbursts that occurred 2015 November 7 and were observed by three instruments on board: the Alice ultraviolet spectrograph, the Visual Infrared and Thermal Imaging Spectrometer, and the Optical, Spectroscopic, and Infrared Remote Imaging System. Together, the observations show that mixed gas and dust outbursts can have different spectral signatures representative of their initiating mechanisms, with the first outburst showing indicators of a cliff collapse origin and the second more representative of fresh volatiles being exposed via a deepening fracture. This analysis opens up the possibility of remote spectral classification of cometary outbursts with future work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Exploring Transport Behavior in Hybrid Perovskites Solar Cells via Machine Learning Analysis of Environmental-Dependent Impedance Spectroscopy

Hybrid organic–inorganic perovskites are one of the promising candidates for the next-generation semiconductors due to their superlative optoelectronic properties. However, one of the limiting factors for potential applications is their chemical and structural instability in different environments. Herein, the stability of (FAPbI3)0.85(MAPbBr3)0.15 perovskite solar cell is explored in different atmospheres using impedance spectroscopy. An equivalent circuit model and distribution of relaxation times (DRTs) are used to effectively analyze impedance spectra. DRT is further analyzed via machine learning workflow based on the non-negative matrix factorization of reconstructed relaxation time spectra. This exploration provides the interplay of charge transport dynamics and recombination processes under environment stimuli and illumination. The results reveal that in the dark, oxygen atmosphere induces an increased hole concentration with less ionic character while ionic motion is dominant under ambient air. Under 1 Sun illumination, the environment-dependent impedance responses show a more striking effect compared with dark conditions. In this case, the increased transport resistance observed under oxygen atmosphere in equivalent circuit analysis arises due to interruption of photogenerated hole carriers. The results not only shed light on elucidating transport mechanisms of perovskite solar cells in different environments but also offer an effective interpretation of impedance responses.

36 MATERIALS SCIENCE↗

GeoSoilEnviroCARS (Sector 13) at the Advanced Photon Source: a comprehensive synchrotron radiation facility for Earth science research at ambient and extreme conditions

GeoSoilEnviroCARS (GSECARS) is a comprehensive analytical laboratory for Earth and environmental science research using X-ray beams from the Advanced Photon Source, Argonne National Laboratory. State-of-the-art instruments are available for (1) high-pressure/high- or low-temperature diffraction, total scattering, and spectroscopy (Brillouin, Raman, and VIS-IR) using the laser heated diamond anvil cell (DAC); (2) high-pressure/high-temperature diffraction, scattering, and imaging as well as acoustic emission (AE) and ultrasonics using the large-volume press (LVP); (3) powder, single crystal, and surface/interface diffraction; (4) X-ray absorption fine structure spectroscopy; (5) X-ray fluorescence microprobe analysis; and (6) microtomography. As shown here, experiments are facilitated by senior level staff who collaborate on all aspects of the analytical work including experiment design, sample preparation, data collection, data interpretation, and publication preparation. Both technical and scientific synergies occur as a result of the intimate association of the various techniques and scientists experienced in the applications of synchrotron radiation to Earth, environmental, and planetary science problems. The facility includes state-of-the-art instrumentation designed and built in-house, including custom X-ray optics, online and offline laser-based systems, specialized sample environments and positioning systems, as well as pixel-array and multi-crystal energy dispersive X-ray detectors, which are available to be shared among the experimental stations.

36 MATERIALS SCIENCE↗

Influence of physical and chemical hydrology on bioremediation of a U-contaminated aquifer informed by reactive transport modeling incorporating 238 U/ 235 U ratios

Microbially-catalyzed reductive immobilization of aqueous uranium (U) as a solid phase has been proposed as a U remediation technique. Both laboratory and field experiments have demonstrated that this reduction reaction alters the 238 U/ 235 U ratio, producing a 238 U-enriched U(IV) solid. In contrast, other major U reactive transport processes fractionate these isotopes much less. This suggests the potential to quantify the extent of bioreduction occurring in groundwater containing U using the 238 U/ 235 U ratio, which would substantially improve upon current practices largely relying on U concentration measurements alone. Current reactive transport models for uranium dynamics include only concentration measurements, which are strongly influenced by highly coupled reactive transformation and aqueous transport processes. The complex physical and chemical behavior of U potentially compromises such quantitative analysis of U storage and release. Here we report the first numerical reactive transport model which explicitly incorporates variations in the 238 U/ 235 U ratio of U and demonstrates improved interpretation of the principal chemical reactions and groundwater transport processes affecting the subsurface mobility and distribution of this widespread contaminant. Recent U bioreduction studies performed in a contaminated aquifer in Rifle, Colorado, USA applied Rayleigh distillation models to interpret U stable isotope fractionation observed as a result of acetate amendment. These simplified models were unable to resolve the spatiotemporal pattern of U isotope fractionation recorded in the aqueous solutes. Here, we employ the multi-component, isotope-enabled CrunchTope reactive transport software to interpret these measured U isotope ratios, and demonstrate accurate reproduction of observed trends in both geochemistry and 238 U/ 235 U ratios for two consecutive years of field experiments. Overall, our results indicate that accurately modeling both the U concentration and isotope ratio distributions greatly constrains the parameter space of the model. We find that the transport properties of U in the Rifle aquifer are governed by the presence of low-permeability regions, which the isotopes are uniquely sensitive to. When U reduction is spatially constrained by these low-permeability regions, the shift in the 238 U/ 235 U ratio becomes more muted. Accurate modeling of observed U isotope ratios thus provides a powerful means to better understand bioremediation, and the current study serves to advance the application of this novel method.

238U/235U↗

Past fires and post-fire impacts reconstructed from a southwest Australian stalagmite

Speleothem records of past environmental change provide an important opportunity to explore fire frequency and intensity in the past, and the antecedent climatic conditions leading to fire events. Here, fire sensitive geochemical signals in a stalagmite from Yonderup Cave, a shallow cave in Western Australia, are compared to well-documented wildfire events that occurred in recent decades. The results are extended to identify wildfires during the growth interval of the speleothem (1760 CE–2005 CE). Principal component analysis of the stalagmite time-series revealed distinct peaks in a combination of phosphorus and metal (aluminium, zinc, copper and lead) concentrations in response to known fire events, which are interpreted to have come from ash. Varying responses in the geochemical signal in the pre- and post-European colonisation period are likely linked to changes in land management, fire frequency and fire intensities. Of note is what we infer to be a particularly intense fire event concluded to have occurred in 1897 ± 5 CE, which climate sensitive proxies (δ18O and bedrock-derived elements) indicate was preceded by a multi-decadal dry period that began in the late 1860s. The intensity of the deduced fire event is supported by a peak in P that is 6.3 times higher than elsewhere in the speleothem, accompanied by a peak in Zn. It was also inferred that changes to the surface-cave hydrology occurred as a result of this event, indicated by increased input of colloidal organic material onto the stalagmite that was interpreted to be caused by shallow karst bedrock fracturing from the heat-induced deformation that is observed after intense fires. These findings show the potential for speleothems to provide dated records of fire intensity and recurrence intervals. Further development could lead to a better understanding of the climate-fire relationship and the effects of land-management practices on wildfire frequency and intensity.

58 GEOSCIENCES↗

Structure-preserving neural networks for the regularized entropy-based closure of a linear, kinetic, radiative transport equation

The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy-based closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy-based closure as a two-stage approximation to the original entropy-based closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy. The code and all trained networks are provided on GitHub.

entropy closure↗

The exit-wave power-cepstrum transform for scanning nanobeam electron diffraction: robust strain mapping at subnanometer resolution and subpicometer precision

Scanning nanobeam electron diffraction (NBED) with fast pixelated detectors is a valuable technique for rapid, spatially resolved mapping of lattice structure over a wide range of length scales. However, intensity variations caused by dynamical diffraction and sample mistilts can hinder the measurement of diffracted disk centers as necessary for quantification. Robust data processing techniques are needed to provide accurate and precise measurements for complex samples and non-ideal conditions. Here we present an approach to address these challenges using a transform, called the exit wave power cepstrum (EWPC), inspired by cepstral analysis in audio signal processing. The EWPC transforms NBED patterns into real-space patterns with sharp peaks corresponding to inter-atomic spacings. We describe a simple analytical model for interpretation of these patterns that cleanly decouples lattice information from the intensity variations in NBED patterns caused by tilt and thickness. With tracking the inter-atomic spacing peaks in EWPC patterns, strain mapping is demonstrated for two practical applications: mapping of ferroelectric domains in epitaxially strained PbTiO 3 films and mapping of strain profiles in arbitrarily oriented core-shell Pt-Co nanoparticle fuel-cell catalysts. The EWPC transform enables lattice structure measurement at sub-pm precision and sub-nm resolution that is robust to small sample mistilts and random orientations.

42 ENGINEERING↗

Clustering analysis of medium-band selected high-redshift galaxies

Next-generation large-scale structure spectroscopic surveys will probe cosmology at high redshifts (2.3 < z < 3.5), relying on abundant galaxy tracers such as Lyα emitters (LAEs) and Lyman break galaxies (LBGs). Medium-band photometry has emerged as a potential technique for efficiently selecting these high-redshift galaxies. In this work, we present clustering analysis of medium-band selected galaxies at high redshift, utilizing photometric data from the Intermediate Band Imaging Survey (IBIS) and spectroscopic data from the Dark Energy Spectroscopic Instrument (DESI). We interpret the clustering of such samples using both Halo Occupation Distribution (HOD) modeling and a perturbation theory description of large-scale structure. Our modeling indicates that the current target sample is composed from an overlapping mixture of LAEs and LBGs with emission lines. Despite differences in target selection, we find that the clustering properties are consistent with previous studies, with correlation lengths r 0 ≃ 3-4 h -1 Mpc and a linear bias of b ∼ 1.8-2.5. Finally, we discuss the simulation requirements implied by these measurements and demonstrate that the properties of the samples would make them excellent targets to enhance our understanding of the high-z universe.

79 ASTRONOMY AND ASTROPHYSICS↗

On data set tensions and signatures of new cosmological physics

ABSTRACT Can new cosmic physics be uncovered through tensions amongst data sets? Tensions in parameter determinations amongst different types of cosmological observation, especially the ‘Hubble tension’ between probes of the expansion rate, have been invoked as possible indicators of new physics, requiring extension of the ΛCDM paradigm to resolve. Within a fully Bayesian framework, we show that the standard tension metric gives only part of the updating of model probabilities, supplying a data co-dependence term that must be combined with the Bayes factors of individual data sets. This shows that, on its own, a reduction of data set tension under an extension to ΛCDM is insufficient to demonstrate that the extended model is favoured. Any analysis that claims evidence for new physics solely on the basis of alleviating data set tensions should be considered incomplete and suspect. We describe the implications of our results for the interpretation of the Hubble tension.

Cortês, Marina (ORCID:0000000304853767)↗

Selected 3D Flash-X Checkpoints for the Long-Time Evolution of a 9.6 Solar-Mass Core-Collapse Supernova Model

This dataset contains selected 3D Flash-X checkpoint files from the long-time evolution of a low-energy core-collapse supernova explosion of a 9.6 Msun zero-metallicity, low-mass iron-core progenitor. The checkpoints span the shock-breakout phase through the young-remnant phase, ending at approximately 3 yr after core bounce. The dataset is intended for follow-up analysis and post-processing, especially radiation-transport calculations using the hydrodynamic and compositional structure of the ejecta. For a full description of the numerical setup, physical assumptions, limitations, and interpretation of the simulation, users should refer to the associated paper.

79 ASTRONOMY AND ASTROPHYSICS↗

DEEPEN: Final 3D PFA Favorability Models and 2D Favorability Maps at Newberry Volcano

Part of the DEEPEN (DE-risking Exploration of geothermal Plays in magmatic ENvironments) project involved developing and testing a methodology for a 3D play fairway analysis (PFA) for multiple play types (conventional hydrothermal, superhot EGS, and supercritical). This was tested using new and existing geoscientific exploration datasets at Newberry Volcano. This GDR submission includes images, data, and models related to the 3D favorability and uncertainty models and the 2D favorability and uncertainty maps. The DEEPEN PFA Methodology, detailed in the journal article below, is based on the method proposed by Poux & O'brien (2020), which uses the Leapfrog Geothermal software with the Edge extension to conduct PFA in 3D. This method uses all available data to build a 3D geodata model which can be broken down into smaller blocks and analyzed with advanced geostatistical methods. Each data set is imported into a 3D model in Leapfrog and divided into smaller blocks. Conditional queries can then be used to assign each block an index value which conditionally ranks each block's favorability, from 0-5 with 5 being most favorable, for each model (e.g., lithologic, seismic, magnetic, structural). The values between 0-5 assigned to each block are referred to as index values. The final step of the process is to combine all the index models to create a favorability index. This involves multiplying each index model by a given weight and then summing the resulting values. The DEEPEN PFA Methodology follows this approach, but split up by the specific geologic components of each play type. These components are defined as follows for each magmatic play type: 1. Conventional hydrothermal plays in magmatic environments: Heat, fluid, and permeability 2. Superhot EGS plays: Heat, thermal insulation, and producibility (the ability to create and sustain fractures suitable for and EGS reservoir) 3. Supercritical plays: Heat, supercritical fluid, pressure seal, and producibility (the proper permeability and pressure conditions to allow production of supercritical fluid) More information on these components and their development can be found in Kolker et al., (2022). For the purposes of subsurface imaging, it is easier to detect a permeable fluid-filled reservoir than it is to detect separate fluid and permeability components. Therefore, in this analysis, we combine fluid and permeability for conventional hydrothermal plays, and supercritical fluid and producibility for supercritical plays. We also project the 3D favorability volumes onto 2D surfaces for simplified joint interpretation, and we incorporate an uncertainty component. Uncertainty was modeled using the best approach for the dataset in question, for the datasets where we had enough information to do so. Identifying which subsurface parameters are the least resolved can help qualify current PFA results and focus future efforts in data collection. Where possible, the resulting uncertainty models/indices were weighted using the same weights applied to the respective datasets, and summed, following the PFA methodology above, but for uncertainty.

15 GEOTHERMAL ENERGY↗