Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein
Abstract not provided
Ye, Qiaozhen↗
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Geometry and spatial distribution of lenticulae on Europa
The surface of Europa contains several types of roughly elliptical features, collectively called lenticulae. Lenticulae may have positive relief (domes) or negative relief (pits), may disrupt the crust (chaos), or discolor the surface (spots); some lenticulae have attributes of both domes and chaos (dome/chaos). In this study, we map the location, dimensions and shapes of all lenticulae and their interactions with other lenticulae and lineaments. We find that (1) pits and domes have similar sizes; (2) chaos are larger than the other lenticulae; (3) pits are clustered within the trailing antijovian quadrant and the leading subjovian quadrant whereas domes, dome/chaos, and chaos terrains are more uniformly distributed; (4) the areal density for all lenticulae is not uniform; (5) lenticulae do not divert the path of younger lineaments such as ridges. Taken together, these observations are consistent with conceptual models in which lenticulae are created by intrusion of liquid water bodies, or convection within, the ice shell. Additionally, the observations are consistent with the notion that each type of lenticula is a surface expression of dynamics within the ice shell at a different stage of lenticulae evolution. The similar size and shape of pits and domes suggests that one may evolve into the other. Because domes are more numerous and more uniformly distributed than pits, they are more likely to represent the end stage of this evolution, assuming the end-stage leaves a longer-lasting surface expression. Models also predict that larger features are more likely to disrupt the crust, which is consistent with dome/chaos and chaos being larger than pits and domes. We find no examples of lineaments offsetting pits but lineaments do cross some chaos. Pits also have a preferred northwest-southeast elongation, whereas domes, dome/chaos, and chaos do not have a preferred orientation. If lenticulae orientation is influenced by crustal stress, then pits may have formed during a shorter time interval than the other features. As a result, pits may sample a shorter, more recent time period than domes, dome/chaos, and chaos, consistent with pits being the earliest stage in the evolution of lenticulae. In conclusion, we find no strong evidence that lineaments are deflected by lenticulae, implying either that the stresses created by lenticulae are too small to influence lineaments, or that the complete evolution of lenticulae occurs on a time scale that is short compared to the time between the formation of lineaments at a given location.
58 GEOSCIENCES↗
Delineation of Supraclavicular Target Volumes in Breast Cancer Radiation Therapy
Purpose: To map the location of gross supraclavicular metastases in patients with breast cancer, in order to determine areas at highest risk of harboring subclinical disease. Methods and Materials: Patients with axial imaging of gross supraclavicular disease were identified from an institutional breast cancer registry. Locations of the metastatic lymph nodes were transferred onto representative axial computed tomography images of the supraclavicular region and compared with the Radiation Therapy Oncology Group (RTOG) breast cancer atlas for radiation therapy planning. Results: Sixty-two patients with 161 supraclavicular nodal metastases were eligible for study inclusion. At the time of diagnosis, 117 nodal metastases were present in 44 patients. Forty-four nodal metastases in 18 patients were detected at disease recurrence, 4 of whom had received prior radiation to the supraclavicular fossa. Of the 161 nodal metastases, 95 (59%) were within the RTOG consensus volume, 4 nodal metastases (2%) in 3 patients were marginally within the volume, and 62 nodal metastases (39%) in 30 patients were outside the volume. Supraclavicular disease outside the RTOG consensus volume was located in 3 regions: at the level of the cricoid and thyroid cartilage (superior to the RTOG volume), in the posterolateral supraclavicular fossa (posterolateral to the RTOG volume), and in the lateral low supraclavicular fossa (lateral to the RTOG volume). Only women with multiple supraclavicular metastases had nodal disease that extended superiorly to the level of the thyroid cartilage. Conclusions: For women with risk of harboring subclinical supraclavicular disease warranting the addition of supraclavicular radiation, coverage of the posterior triangle and the lateral low supraclavicular region should be considered. For women with known supraclavicular disease, extension of neck coverage superior to the cricoid cartilage may be warranted.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Testing Hidden Assumptions of Representativeness in Reach-Scale Studies of Hyporheic Exchange
Field studies of hyporheic exchange in mountain systems are often conducted using short study reaches and a limited number of observations. It is common practice to assume these study reaches represent hyporheic exchange at larger scales or different sites and to infer general relationships among potential causal mechanisms from the limited number of observations. However, these assumptions of representativeness are rarely tested. In this study, we develop numerical models from four segments of mountain streams in different geomorphologic settings and extract shorter reaches to test how representative exchange metrics are in shorter reaches compared to their reference segments. We also map the locations of the representative reaches to determine if a pattern exists based on location. Finally, we compare variance of these shorter within-site reaches to 29 additional reaches across the same basin to understand the impacts of inferring causal mechanisms, for example, the expectation that wide and narrow valley bottoms will yield different hyporheic exchange patterns. Our results show that the location and length strategy of the study reach must be considered before assuming an exchange metric to be representative of anything other than the exact segment studied. Further, it is necessary to quantify within and between site variations before making causal inferences based on observable characteristics, such as valley width or stream morphology. Our findings have implications for future field practices and how those practices are translated into models.
54 ENVIRONMENTAL SCIENCES↗
A multi-omic future for microbiome studies
Microbes constitute about a third of the Earth’s biomass and play critical roles in sustaining life. While results from multiple sequence-based studies have illustrated the importance of microbial communities for human health and the environment, additional technological developments are still needed to gain more insight into their functions [1]. To date, the majority of sequencing studies have focused on the 16S rRNA gene as a phylogenetic marker. This approach has enabled exploration of microbial compositions in a range of sample types, while bypassing the need for cultivation. 16S rRNA gene sequencing has also enabled a vast majority of microorganisms never previously isolated in culture to be identified and placed into a phylogenetic context [2]. These technologies have been utilized to map the locations of microbes inhabiting various locations of the body [3]. Similarly, sequencing has been used to determine the identities and distributions of microorganisms inhabiting different ecosystems [4, 5], and efforts in single cell sequencing of the microbiome have helped fill in missing branches of the phylogenetic tree [6].
Environmental Molecular Sciences Laboratory↗
Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants
Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.
3-D reconstruction↗
Dewetting and spreading transitions for active matter on random pinning substrates
Here, we show that sterically interacting self-propelled disks in the presence of random pinning substrates exhibit transitions among a variety of different states. In particular, from a phase separated cluster state, the disks can spread out and homogeneously cover the substrate in what can be viewed as an example of an active matter wetting transition. We map the location of this transition as a function of activity, disk density, and substrate strength, and we also identify other phases including a cluster state, coexistence between a cluster and a labyrinth wetted phase, and a pinned liquid. Convenient measures of these phases include the cluster size, which dips at the wetting-dewetting transition, and the fraction of sixfold coordinated particles, which drops when dewetting occurs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Non-radiative recombination at dislocations in InAs quantum dots grown on silicon
We study the impact of misfit dislocations on the luminescence from InAs quantum dots (QDs) grown on Si substrates. Electron channeling contrast imaging is used together with cathodoluminescence mapping to locate misfit dislocations and characterize the resulting nonradiative recombination of carriers via near-infrared light emission profiles. With a 5 kV electron beam probe, the dark line defect width due to a typical misfit dislocation in a shallow QD active layer is found to be approximately 1 μ m, with a 40%–50% peak emission intensity loss at room temperature. Importantly, we find that at cryogenic temperatures, the dislocations affect the QD ground state and the first excited state emission significantly less than the second excited state emission. At the same time, the dark line defect width, which partially relates to carrier diffusion in the system, is relatively constant across the temperature range of 10 K–300 K. Our results suggest that carrier dynamics in the QD wetting layer control emission intensity loss at dislocations, and that these defects reduce luminescence only at those temperatures where the probability of carriers thermalizing from the dots into the wetting layer becomes significant. We discuss the implications of these findings toward growing dislocation-tolerant, reliable quantum dot lasers on silicon.
Electron beams↗
GIANT MOLECULAR CLOUDS AND STAR FORMATION IN THE NON-GRAND DESIGN SPIRAL GALAXY NGC 6946
We present high spatial resolution observations of giant molecular clouds (GMCs) in the eastern part of the nearby spiral galaxy NGC 6946 obtained with the Combined Array for Research in Millimeter-wave Astronomy (CARMA). We have observed CO(1 {yields} 0), CO(2 {yields} 1) and {sup 13}CO(1 {yields} 0), achieving spatial resolutions of 5.''4 Multiplication-Sign 5.''0, 2.''5 Multiplication-Sign 2.''0, and 5.''6 Multiplication-Sign 5.''4, respectively, over a region of 6 Multiplication-Sign 6 kpc. This region extends from 1.5 kpc to 8 kpc galactocentric radius, thus avoiding the intense star formation in the central kpc. We have recovered short-spacing u-v components by using single dish observations from the Nobeyama 45 m and IRAM 30 m telescopes. Using the automated CPROPS algorithm, we identified 45 CO cloud complexes in the CO(1 {yields} 0) map and 64 GMCs in the CO(2 {yields} 1) maps. The sizes, line widths, and luminosities of the GMCs are similar to values found in other extragalactic studies. We have classified the clouds into on-arm and inter-arm clouds based on the stellar mass density traced by the 3.6 {mu}m map. Clouds located on-arm present in general higher star formation rates than clouds located in inter-arm regions. Although the star formation efficiency shows no systematic trend with galactocentric radius, some on-arm clouds-which are more luminous and more massive compared to inter-arm GMCs-are also forming stars more efficiently than the rest of the identified GMCs. We find that these structures appear to be located in two specific regions in the spiral arms. One of them shows a strong velocity gradient, suggesting that this region of high star formation efficiency may be the result of gas flow convergence.
79 ASTRONOMY AND ASTROPHYSICS↗
Observational constraints on warm natural inflation
Warm natural inflation is studied for the case of the original cosine potential. The radiation bath during inflation induces a dissipation (friction) rate in the equation of motion for the inflation field, which can potentially reduce the field excursion needed for an observationally viable period of inflation. Here we examine if the dissipation thus provides a mechanism to avoid the large decay constant f ≳ M pl of cold cosine natural inflation. Whereas temperature independent dissipation has previously been shown to alleviate the need for a trans-Planckian decay constant f, we illustrate here the difficulties of accommodating a significantly sub-Planckian decay constant (f < 10 -1 M pl ) for the case of a temperature dependent dissipation rate in the form Γ ∝ T c , with c = {1,3}. Such dissipation rates represent physically well-motivated constructions in the literature. For each model, we map its location in the r-n s plane and compare with cosmic microwave background (CMB) data. For c = 1 (c = 3), we find that agreement with CMB data requires that dissipation be in the weak (moderate) regime and that the minimum allowed value of the decay constant in the potential is f min = 0.3 (0.8) M pl , respectively.
79 ASTRONOMY AND ASTROPHYSICS↗
A measurement of material in the ATLAS tracker using secondary hadronic interactions in 7 TeV pp collisions
Knowledge of the material in the ATLAS inner tracking detector is crucial in understanding the reconstruction of charged-particle tracks, the performance of algorithms that identify jets containing b-hadrons and is also essential to reduce background in searches for exotic particles that can decay within the inner detector volume. Interactions of primary hadrons produced in pp collisions with the material in the inner detector are used to map the location and amount of this material. The hadronic interactions of primary particles may result in secondary vertices, which in this analysis are reconstructed by an inclusive vertex-finding algorithm. Data were collected using minimum-bias triggers by the ATLAS detector operating at the LHC during 2010 at centre-of-mass energy √s = 7 TeV, and correspond to an integrated luminosity of 19 nb -1 . Kinematic properties of these secondary vertices are used to study the validity of the modelling of hadronic interactions in simulation. Finally, secondary-vertex yields are compared between data and simulation over a volume of about 0.7 m 3 around the interaction point, and agreement is found within overall uncertainties.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum , at ~3 Å resolution is described using a combination of homology modeling with MODELLER , molecular-replacement phasing with Phaser , deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot . This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.
59 BASIC BIOLOGICAL SCIENCES↗
Localization and Mapping Platform Software (LAMP Software) v1
The Localization and Mapping Platform (LAMP) software fuses radiation and contextual data to produce 3-D maps that locate and identify gamma-ray emitting sources in complex environments. It enables data collection, fusion, and processing in near-real-time and on-board in several configurations, including handheld and unmanned aerial system (UAS) form factors.
Haefner, Andrew↗
Pauling’s rules for oxide-based minerals: A re-examination based on quantum mechanical constraints and modern applications of bond-valence theory to Earth materials
Since their introduction in 1929, Pauling’s five rules have been used by scientists from many disciplines to rationalize and predict stable arrangements of atoms and coordination polyhedra in crystalline solids; amorphous materials such as silicate glasses and melts; nanomaterials, poorly crystalline solids; aqueous cation and anion complexes; and sorption complexes at mineral-aqueous solution interfaces. The predictive power of these simple yet powerful rules was challenged recently by George et al. (2020), who performed a statistical analysis of the performance of Pauling’s five rules for about 5000 oxide crystal structures. They concluded that only 13% of the oxides satisfy the last four rules simultaneously and that the second rule has the most exceptions. They also found that Pauling’s first rule is satisfied for only 66% of the coordination environments tested and concluded that no simple rule linking ionic radius to coordination environment will be predictive due to the variable quality of univalent radii. We address these concerns and discuss quantum mechanical calculations that complement Pauling’s rules, particularly his first (radius sum and radius ratio rule) and second (electrostatic valence rule) rules. We also present a more realistic view of the bonded radii of atoms, derived by determining the local minimum in the electron density distribution measured along trajectories between bonded atoms known as bond paths, i.e., the bond critical point (rc). Electron density at the bond critical point is a quantum mechanical observable that correlates well with Pauling bond strength. Moreover, a metal atom in a polyhedron has as many bonded radii as it has bonded interactions, resulting in metal and O atoms that may not be spherical. O atoms, for example, are not spherical in many oxide-based crystal structures. Instead, the electron density of a bonded oxygen is often highly distorted or polarized, with its bonded radius decreasing systematically from ~1.38 Å when bonded to highly electropositive atoms like sodium to 0.64 Å when bonded to highly electronegative atoms like nitrogen. Bonded radii determined for metal atoms match the Shannon (1976) radii for more electropositive atoms, but the match decreases systematically as the electronegativities of the M atoms increase. As a result, significant departures from the radius ratio rule in the analysis by George et al. (2020) is not surprising. We offer a modified, more fundamental version of Pauling’s first rule and demonstrate that the second rule has a one-to-one connection between the electron density accumulated between the bonded atoms at the bond critical point and the Pauling bond strength of the bonded interaction. Pauling’s second rule implicitly assumes that bond strength is invariant with bond length for a given pair of bonded atoms. Many studies have since shown that this is not the case, and Brown and Shannon (1973) developed an equation and a set of parameters to describe the relation between bond length and bond strength, now redefined as bond valence to avoid confusion with Pauling bond-strength. Brown (1980) used the valence-sum rule, together with the path rule and the valence-matching principle, as the three axioms of bond-valence theory (BVT), a powerful method for understanding many otherwise elusive aspects of crystals and also their participation in dynamic processes. We show how a priori bond-valence calculations can predict unstrained bond-lengths and how bond-valence mapping can locate low-Z atoms in a crystal structure (e.g., Li) or examine possible diffusion pathways for atoms through crystal structures. In addition, we briefly discuss Pauling’s third, fourth, and fifth rules, the first two of which concern the sharing of polyhedron elements (edges and faces) and the common instability associated with structures in which a polyhedron shares an edge or face with another polyhedron and contains high-valence cations. The olivine [α-(MgxFe1–x)2SiO4] crystal structure is used to illustrate the distortions from hexagonal close-packing of O atoms caused by metal-metal repulsion across shared polyhedron edges. We conclude by discussing several applications of BVT to Earth materials, including the use of BVT to: (1) locate H+ ions in crystal structures, including the location of protons in the crystal structures of nominally anhydrous minerals in Earth’s mantle; (2) determine how strongly bonded (usually anionic) structural units interact with weakly bonded (usually cationic) interstitial complexes in complex uranyl-oxide and uranyl-oxysalt minerals using the valence-matching principle; (3) calculate Lewis acid strengths of cations and Lewis base strengths of anions; (4) determine how (H2O) groups can function as bond-valence transformers by dividing one bond into two bonds of half the bond valence; (5) help characterize products of sorption reactions of aqueous cations (e.g., Co2+ and Pb2+) and oxyanions [e.g., selenate (Se6+O4)2- and selenite (Se4+O3)2-] at mineral-aqueous solution interfaces and the important role of protons in these reactions; and (6) help characterize the local coordination environments of highly charged cations (e.g., Zr4+, Ti4+, U4+, U5+, and U6+) in silicate glasses and melts.
Geochemistry & Geophysics↗
Finding Large Aperture Fractures in Geothermal Resource Areas Using a Three-Component Long-Offset Surface Seismic Survey, PSInSAR and Kinematic Structural Analysis
The DOE cost-share program applied innovative and cutting edge seismic surveying and processing, permanent scatter interferometry-synthetic aperture radar (PSInSAR) and structural kinematics to the exploration problem of locating and mapping largeaperture fractures (LAFs) for the purpose of targeting geothermal production wells. The San Emidio geothermal resource area, which is under lease to USG, contains production wells that have encountered and currently produce from LAFs in the southern half of the resource area (Figure 2). The USG lease block, incorporating the northern extension of the San Emidio geothermal resource, extends 3 miles north of the operating wellfield. The northern lease block was known to contain shallow thermal waters but was previously unexplored by deep drilling. Results of the Phase 1 exploration program are described in detail in the Phase 1 Final Report (Teplow et al., 2011). The DOE cost shared program was completed as planned on September 30, 2014. This report summarizes results from all of Phase 1 and 2 activities.
15 GEOTHERMAL ENERGY↗
Shallow Water Imaging Sonar System for Environmental Surveying Final Report CRADA No. TC-1130-95
The scope of this research is to develop a shallow water sonar system designed to detect and map the location of objects such as hazardous wastes or discarded ordnance in coastal waters. The system will use high frequency wide-bandwidth imaging sonar, mounted on a moving platform towed behind a boat, to detect and identify objects on the sea bottom. Resolved images can be obtained even if the targets are buried in an overlayer of silt. Reference 1 ( also attached) summarized the statement of work and the scope of collaboration.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Experimental Study of the Fundamental Properties of Warm Dense Mixtures
The aim of the proposed research was to provide a multi-scale study of the properties of warm dense hydrocarbons, by studying the thermodynamic properties through the equation of state and the microscopic properties by x-ray scattering. Understanding the fundamental properties of warm dense mixtures is an intellectual challenge due to the complexity of the system. Unlike liquids or gases, where constituent particle interactions occur through collisions or bonding between valence electrons, in these strongly coupled systems the atoms will be partially ionized and compressed so tightly together that interactions between the inner core electrons can play a role in the systems chemistry. Advances in computational capabilities and development of new theoretical models have been used to predict the properties of mixtures but there is currently no experimental data of the fundamental interaction between the particles in mixtures to test these predictions against. The proposed research was to experimentally investigate the interaction of the different species in hydrocarbons by measuring the compressibility of substances with different carbon and hydrogen ratios and the complexity of the microscopic interactions through elastic and inelastic x-ray scattering. To study the bulk properties of warm dense hydrocarbons we established the Warm Dense Matter Research Laboratory (WDMRL) in the Institute for Shock Physics at Washington State University. The goal was for experiments in the WDMRL to determine shock loading conditions of interest in the hydrocarbon mixtures. We planned on using Hugoniot EOS measurements and a range of carbon and hydrogen concentrations to determine conditions when the EOS of the mixture varied significantly from that of the classical mixing model. Even though shock transit measurements through aluminum foils suggested pressures upto 400GPa, the experiments in the WDMRL were unsuccessful in getting usable shockwave compression data above 100GPa in polystyrene which was below the pressure of interest for hydrocarbon mixtures (>200GPa). To complete the project, we tested a technique using x-ray phase contrast imaging to map the location of tracer layers in a test sample of polycarbonate to record the material motion in dynamically compressed samples. A technique that will be useful for future warm dense matter experiments. These experiments used <200nm gold layers in polycarbonate samples to measure the material velocity and shock speed using x-ray phase contrast imaging. These results were compared to continuum surface measurements performed at ISP and show that the tracer layer technique can measure hydrodynamic properties accurately in dynamically compressed materials.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Quantifying Impacts of Renewable Electricity Deployment on Air Quality and Human Health in Southeast Asia Based on AIMS III Scenarios
This study augments the ASEAN Interconnection Masterplan Study III (AIMS III) by quantifying changes to air quality and human health that result from its renewable integration and transmission interconnection scenarios. Performing this analysis requires translation of the changes in projected generation from different power sector fuel sources in the AIMS III scenarios to changes in air pollutant emissions, developing what is known as an emissions inventory for each scenario and year evaluated. An emissions inventory represents who emits air pollutants, from where the pollutants are emitted, when, and how much of which air pollutants are emitted. With the assistance of the ASEAN Centre for Energy and leveraging the best available in-region public data sources, the National Renewable Energy Laboratory (NREL) team compiled a detailed inventory of power plants in the ASEAN region, mapping their PM 2.5 , sulfur oxides (SOx), and nitrogen oxides (NOx) emissions. A new, first-of-its-kind, and user-friendly global air quality model, Global InMAP (Thakrar et al. 2022), is then used to transform the inventory of changes in emissions to changes in concentration of fine particulate matter. Global InMAP then maps the location of human populations in ASEAN countries to calculate humans' exposure to PM 2.5 and estimate excess PM 2.5 -caused mortality attributable to thermal generation sources, as modeled in the AIMS III scenarios.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗