High-Resolution Structural Proteomics of Mitochondria Using the ‘Build and Retrieve’ Methodology
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Recent advancement in scanning transmission electron microscopy (STEM) allows the use of 4D-STEM, a technique that captures an electron diffraction pattern at each scan point in STEM, to measure electrostatic and magnetic potential and field in materials. However, accurate measurement, separation of the magnetic and electric signals, and removal of artifacts remain challenging, especially in the presence of complex non-uniform diffraction contrast within the disks. In this work, based on dynamic simulations of 4D-STEM patterns built upon superstructures consisting of millions of atoms to account for different sample thickness and edge geometries, we show how the shape and intensity distribution of the central disk are affected by multiple scattering. We propose a robust refinement procedure through iteration of the spin-sensitive peak position of the disk-center in the circular Hough transform filtered images from experimental Lorentz 4D-STEM dataset after minimizing the possible artifacts, such as those due to the change of thickness, dynamic scattering, and scanning process. We verify that caution must be taken as in practice the rigid-disk-shift model used to reconstruct induction maps can easily break down due to disk-protrusion when there exists a nonconstant phase gradient or thickness within the width of the probe. Through quantitative analysis and comparing experiment with calculation the effect of the non-spin-related intensity distribution inside the disk as well as that causes the disk shift due to the intensity-protrusion can be removed, and high-quality magnetic field mapping is possible.
Abstract Optical space‐based lightning sensors such as the Geostationary Lightning Mapper (GLM) detect and geolocate lightning by recording rapid changes in cloud top illumination. While lightning locations can be determined to within a pixel on the GLM imaging array, these instruments are not individually able to natively report lightning altitude. It has previously been shown that thunderclouds are illuminated differently based on the altitude of the optical source. In this study, we examine how altitude information can be extracted from the spatial distributions of GLM energy recorded from each optical pulse. We match GLM “groups” with Lightning Mapping Array (LMA) source data that accurately report the 3‐D positions of coincident Radio‐Frequency (RF) emitters. We then use machine learning methods to predict the mean LMA source altitudes matched to GLM groups using metrics from the optical data that describe the amplitude, breadth, and texture of the group spatial energy distribution. The resulting model can predict the LMA mean source altitude from GLM group data with a median absolute error of <1.5 km, which is sufficient to determine the location of the charge layer where the optical energy originated. This model is able to capture changes to the source altitude distribution in response to convective processes in the thunderstorm, and the GLM predictions can reveal the vertical structure of individual flashes ‐ enabling 3‐D flash geolocation with GLM for the first time. Future work will account for differences in thunderstorm charge/precipitation structures and viewing angle across the GLM Field of View.
Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
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Complex systems frequently exhibit multi-way, rather than pairwise, interactions. These group interactions can- not be faithfully modeled as collections of pairwise interactions using graphs and instead require hypergraphs. However, methods that analyze hypergraphs directly, rather than via lossy graph reductions, remain limited. Hypergraph motifs hold promise in this regard, as motif patterns serve as building blocks for larger group interactions which are inexpressible by graphs. Recent work has focused on categorizing and counting hypergraph motifs based on the existence of nodes in hyperedge intersection regions. Here, we argue that the relative sizes of hyperedge inter- sections within motifs contain varied and valuable information. We propose a suite of efficient algorithms for finding top-k triplets of hyperedges based on optimizing the sizes of these intersection patterns. This formulation uncovers interesting local patterns of interaction, finding hyperedge triplets that either (1) are the least similar with each other, (2) have the highest pairwise but not groupwise correlation, or (3) are the most similar with each other. We formalize this as a combinatorial optimization problem and design efficient algorithms based on filtering hyperedges. Our comprehensive experimental evaluation shows that the resulting hyperedge triplets yield insightful information on real-world hypergraphs. Our approach is also orders of magnitude faster than a naive baseline implementation.
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The Echo Classification from COnvectivity (ECCO) algorithm identifies convective and stratiform types of radar echo in three dimensions. It is based on the calculation of reflectivity texture—a combination of the intensity and the heterogeneity of the radar echoes on each horizontal plane in a 3D Cartesian volume. Reflectivity texture is translated into convectivity, which is designed to be a quantitative measure of the convective nature of each 3D radar grid point. It ranges from 0 (100% stratiform) to 1 (100% convective). By thresholding convectivity, a more traditional qualitative categorization is obtained, which classifies radar echoes as convective, mixed, or stratiform. In contrast to previous algorithms, these echo-type classifications are provided on the full 3D grid of the reflectivity field. The vertically resolved classifications, in combination with temperature data, allow for subclassifications into shallow, mid-, deep, and elevated convective features, and low, mid-, and high stratiform regions—again in three dimensions. The algorithm was validated using datasets collected over the U.S. Great Plains during the PECAN field campaign. An analysis of lightning counts shows ~90% of lightning occurring in regions classified as convective by ECCO. A statistical comparison of ECCO echo types with the well-established GPM radar precipitation-type categories show 84% (88%) of GPM stratiform (convective) echo being classified as stratiform (convective) or mixed by ECCO. ECCO was applied to radar grids for the continental United States, the United Arab Emirates, Australia, and Europe, illustrating its robustness and adaptability to different radar grid characteristics and climatic regions.
Using data from the airborne HIAPER Cloud Radar (HCR), a partitioning algorithm (ECCO-V) that provides vertically resolved convectivity and convective versus stratiform radar-echo classification is developed for vertically pointing radars. The algorithm is based on the calculation of reflectivity and radial velocity texture fields that measure the horizontal homogeneity of cloud and precipitation features. The texture fields are translated into convectivity, a numerical measure of the convective or stratiform nature of each data point. The convective–stratiform classification is obtained by thresholding the convectivity field. Subcategories of low, mid-, and high stratiform, shallow, mid-, deep, and elevated convective, and mixed echoes are introduced, which are based on the melting-layer and divergence-level altitudes. As the algorithm provides vertically resolved classifications, it is capable of identifying different types of vertically layered echoes, and convective features that are embedded in stratiform cloud layers. Its robustness was tested on data from four HCR field campaigns that took place in different meteorological and climatological regimes. The algorithm was adapted for use in spaceborne and ground-based radars, proving its versatility, as it is adaptable not only to different radar types and wavelengths, but also different research applications.
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Atmospheric model systems, such as those used for weather forecast and reanalysis production, often have significant and systematic errors in their representation of the Arctic surface energy budget and its components. The newly available observation data of the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition (2019/2020) enable a range of model analyses and validation in order to advance our understanding of potential model deficiencies. In the present study, we analyze deficiencies in the surface radiative energy budget over Arctic sea ice in the ERA5 global atmospheric reanalysis by comparing against the winter MOSAiC campaign data, as well as, a pan-Arctic level-2 MODIS ice surface temperature remote sensing product. We find that ERA5 can simulate the timing of radiatively clear periods, though it is not able to distinguish the two observed radiative Arctic winter states, radiatively clear and opaquely cloudy, in the distribution of the net surface radiative budget. The ERA5 surface temperature over Arctic sea ice has a conditional error with a positive bias in radiatively clear conditions and a negative bias in opaquely cloudy conditions. The mean surface temperature error is 4°C for radiatively clear situations at MOSAiC and up to 15°C in some parts of the Arctic. The spatial variability of the surface temperature, given by 4 observation sites at MOSAiC, is not captured by ERA5 due to its spatial resolution but represented in the level-2 satellite product. The sensitivity analysis of possible error sources, using satellite products of snow depth and sea ice thickness, shows that the positive surface temperature errors during radiatively clear events are, to a large extent, caused by insufficient sea ice thickness and snow depth representation in the reanalysis system. A positive bias characterizes regions with ice thickness greater than 1.5 m, while the negative bias for thinner ice is partly compensated by the effect of snow.
Measuring interfacial electrostatic potentials is vital to understanding many fundamental materials properties. A variety of TEM methods exist for measuring electric potentials from the phase shift produced on an electron wave as it passes through a sample. However, most are either experimentally challenging or poorly suited to resolving nanoscale features. Here, we demonstrate the viability of a simple, automatic differentiation-based exit wave reconstruction from a focal series of images to accurately measure nanoscale electric potentials. Here, the analysis suggests that under optimal measurement conditions, electric potentials can be resolved to less than 0.06 V in magnitude and less than 1 nm in spatial extent.
Focal Area(s): This white paper responds to Focal Area #3: Insight gleaned from complex data (both observed and simulated) using AI, big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI. Science Challenge: This white paper addresses the water-cycle and data-model integration grand challenge. It leverages data from the Atmospheric Radiation Measurement (ARM) Climate Research Facility, and Next-Generation Ecosystem Experiment (NGEE), and Science Focus Area (SFA). The white paper focuses on controlling cloud, precipitation, and radiative properties as observed and simulated by the Earth System Models (ESM). The described framework can be readily applied to any other ensemble of instruments, including satellites and other ground-based networks.
In this report, we refer to a pair of cameras that capture synchronized pictures with overlapping fields of view (FOV) as a stereo pair. Each stereo pair independently performs a stereo reconstruction of cloud points. Currently, there are three U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility stereo pairs (six cameras in total) positioned around the Southern Great Plains (SGP) observatory’s Central Facility (CF; Romps and Oktem 2017). Time-synchronized pictures from the two cameras in a stereo pair can be paired together to obtain a three-dimensional (3D) reconstruction of feature points by triangulation. This document explains how we use ARM stereo cameras and stereophotogrammetric principles to generate the Point Cloud of Cloud Points (PCCP) Value-Added Product (VAP). The PCCP VAP is essentially a set of 3D positions representing the locations of cloud features in the sky. Thousands of cloud features can be reconstructed instantly in each stereo pair's FOV, which covers an area of tens of square kilometers. Cloud base and cloud top heights can be extracted from the PCCP product.