Direct visualization of anionic electrons in an electride reveals inhomogeneities
Anionic electron within an electride was visualized with atomic resolution using differential phase-contrast imaging.
36 MATERIALS SCIENCE↗
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Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ
DNA double-strand breaks (DSBs), one of the most cytotoxic forms of DNA damage, can be repaired by the tightly regulated nonhomologous end joining (NHEJ) machinery (Stinson and Loparo and Zhao et al.). Core NHEJ factors form an initial long-range (LR) synaptic complex that transitions into a DNA-PKcs (DNA-dependent protein kinase, catalytic subunit)–free, short-range state to align the DSB ends (Chen et al.). Using single-particle cryo–electron microscopy, we have visualized three additional key NHEJ complexes representing different transition states, with DNA-PKcs adopting distinct dimeric conformations within each of them. Upon DNA-PKcs autophosphorylation, the LR complex undergoes a substantial conformational change, with both Ku and DNA-PKcs rotating outward to promote DNA break exposure and DNA-PKcs dissociation. We also captured a dimeric state of catalytically inactive DNA-PKcs, which resembles structures of other PIKK (Phosphatidylinositol 3-kinase-related kinase) family kinases, revealing a model of the full regulatory cycle of DNA-PKcs during NHEJ.
59 BASIC BIOLOGICAL SCIENCES↗
Visualizing energy transfer between redox-active colloids
Redox-active colloids (RACs) represent a novel class of energy carriers that exchange electrical energy upon contact. Understanding contact-mediated electron transfer dynamics in RACs offers insights into physical contact events in colloidal suspensions and enables quantification of electrical energy transport in nonconjugated polymers. Redox-based electron transport was directly observed in monolayers of micron-sized RACs containing ethyl-viologen side groups via fluorescence microscopy through an unexpected nonlinear electrofluorochromism that is quantitatively coupled to the redox state of the colloid. Via imaging studies, using this electrofluorochromism, the apparent charge transfer diffusion coefficient D CT of the RAC was easily determined. The visualization of energy transport within suspensions of redox-active colloids was also demonstrated. Our work elucidates fundamental mechanisms of energy transport in colloidal systems, informs the development of next-generation redox flow batteries, and may inspire new designs of smart active soft matter including conductive polymers for applications ranging from electrochemical sensors and organic electronics to colloidal robotics.
Qu, Alan Subing [Univ. of Illinois at Urbana-Champ↗
Heterogeneous to homogeneous melting transition visualized with ultrafast electron diffraction
The ultrafast laser excitation of matters leads to nonequilibrium states with complex solid-liquid phase-transition dynamics. In this paper, we used electron diffraction at mega–electron volt energies to visualize the ultrafast melting of gold on the atomic scale length. For energy densities approaching the irreversible melting regime, we first observed heterogeneous melting on time scales of 100 to 1000 picoseconds, transitioning to homogeneous melting that occurs catastrophically within 10 to 20 picoseconds at higher energy densities. We showed evidence for the heterogeneous coexistence of solid and liquid. We determined the ion and electron temperature evolution and found superheated conditions. Finally, our results constrain the electron-ion coupling rate, determine the Debye temperature, and reveal the melting sensitivity to nucleation seeds.
74 ATOMIC AND MOLECULAR PHYSICS↗
Directly visualizing the momentum-forbidden dark excitons and their dynamics in atomically thin semiconductors
Resolving momentum degrees of freedom of excitons, which are electron-hole pairs bound by the Coulomb attraction in a photoexcited semiconductor, has remained an elusive goal for decades. In atomically thin semiconductors, such a capability could probe the momentum-forbidden dark excitons, which critically affect proposed opto-electronic technologies but are not directly accessible using optical techniques. In this work, we probed the momentum state of excitons in a tungsten diselenide monolayer by photoemitting their constituent electrons and resolving them in time, momentum, and energy. We obtained a direct visual of the momentum-forbidden dark excitons and studied their properties, including their near degeneracy with bright excitons and their formation pathways in the energy-momentum landscape. These dark excitons dominated the excited-state distribution, a surprising finding that highlights their importance in atomically thin semiconductors.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Direct visualization of magnetic domains and moiré magnetism in twisted 2D magnets
Moiré superlattices of twisted nonmagnetic two-dimensional (2D) materials are highly controllable platforms for the engineering of exotic correlated and topological states. In this work, we report emerging magnetic textures in small-angle twisted 2D magnet chromium triiodide (CrI 3 ). Using single-spin quantum magnetometry, we directly visualized nanoscale magnetic domains and periodic patterns, a signature of moiré magnetism, and measured domain size and magnetization. In twisted bilayer CrI 3 , we observed the coexistence of antiferromagnetic (AFM) and ferromagnetic (FM) domains with disorder-like spatial patterns. In twisted double-trilayer CrI 3 , AFM and FM domains with periodic patterns appear, which is in good agreement with the calculated spatial magnetic structures that arise from the local stacking-dependent interlayer exchange interactions in CrI 3 moiré superlattices. Our results highlight magnetic moiré superlattices as a platform for exploring nanomagnetism.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Visualizing the atomic-scale origin of metallic behavior in Kondo insulators
A Kondo lattice is often electrically insulating at low temperatures. However, several recent experiments have detected signatures of bulk metallicity within this Kondo insulating phase. In this study, we visualized the real-space charge landscape within a Kondo lattice with atomic resolution using a scanning tunneling microscope. We discovered nanometer-scale puddles of metallic conduction electrons centered around uranium-site substitutions in the heavy-fermion compound uranium ruthenium silicide (URu 2 Si 2 ) and around samarium-site defects in the topological Kondo insulator samarium hexaboride (SmB 6 ). These defects disturbed the Kondo screening cloud, leaving behind a fingerprint of the metallic parent state. Our results suggest that the three-dimensional quantum oscillations measured in SmB 6 arise from Kondo-lattice defects, although we cannot exclude other explanations. Finally, our imaging technique could enable the development of atomic-scale charge sensors using heavy-fermion probes.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Genetic and Antigenic Characterization of an Expanding H3 Influenza A Virus Clade in U.S. Swine Visualized by Nextstrain
Defining factors that influence spatial and temporal patterns of influenza A virus (IAV) is essential to inform vaccine strain selection and strategies to reduce the spread of potentially zoonotic swine-origin IAV. The relative frequency of detection of the H3 phylogenetic clade 1990.4.a (colloquially known as C-IVA) in U.S. swine declined to 7% in 2017 but increased to 32% in 2019. We conducted phylogenetic and phenotypic analyses to determine putative mechanisms associated with increased detection. We created an implementation of Nextstrain to visualize the emergence, spatial spread, and genetic evolution of H3 IAV in swine, identifying two C-IVA clades that emerged in 2017 and cocirculated in multiple U.S. states. Phylodynamic analysis of the hemagglutinin (HA) gene documented low relative genetic diversity from 2017 to 2019, suggesting clonal expansion. The major H3 C-IVA clade contained an N156H amino acid substitution, but hemagglutination inhibition (HI) assays demonstrated no significant antigenic drift. The minor HA clade was paired with the neuraminidase (NA) clade N2-2002B prior to 2016 but acquired and maintained an N2-2002A in 2016, resulting in a loss of antigenic cross-reactivity between N2-2002B- and -2002A-containing H3N2 strains. The major C-IVA clade viruses acquired a nucleoprotein (NP) of the H1N1pdm09 lineage through reassortment in the replacement of the North American swine-lineage NP. Instead of genetic or antigenic diversity within the C-IVA HA, our data suggest that population immunity to H3 2010.1 along with the antigenic diversity of the NA and the acquisition of the H1N1pdm09 NP gene likely explain the reemergence and transmission of C-IVA H3N2 in swine.
59 BASIC BIOLOGICAL SCIENCES↗
Visualizing Microbial Community Dynamics via a Controllable Soil Environment
Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.
59 BASIC BIOLOGICAL SCIENCES↗
Visualizing and quantifying biomineralization in a wellbore analog reactor
Visualizing and quantifying biomineralization in a wellbore analog reactor
Norton, Drew↗
Visualization of Dynamic Vortex Structures in Magnetic Films with Uniaxial Anisotropy (Micromagnetic Simulation)
Three-dimensional computer simulation of dynamic processes in a moving domain boundary separating domains in a soft magnetic uniaxial film with planar anisotropy is performed by numerical solution of Landau-Lifshitz-Gilbert equations. The developed visualization methods are used to establish the connection between the motion of surface vortices and antivortices, singular (Bloch) points, and core lines of intrafilm vortex structures. A relation between the character of magnetization dynamics and the film thickness is found. The analytical models of spatial vortex structures for imitation of topological properties of the structures observed in micromagnetic simulation are constructed.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Determination of the Thicknesses and Visualization of Ion-Exchange Waveguides in Glasses by Scanning Electron Microscopy
The formation of a surface layer with silver and sodium concentration gradients in K8-grade glasses as a result of ion exchange is demonstrated by scanning electron microscopy (SEM) and electron probe X-ray microanalysis. The silver ions enriched layers with different thicknesses, depending on the duration of the ion exchange from the silver melt, are visualized in the secondary electrons mode. SEM data on the thickness of the silver enriched layer are in good agreement with the results of calculation from the diffusion equation for silver in glass. The dependence of the silver concentration on the diffusion depth is obtained using elemental composition mapping over the glass cross section. The presence of a layer with a silver concentration gradient leads to formation of a gradient waveguide. Discrete peaks in silver concentration profiles, caused by specific features of mutual diffusion of sodium and silver ions in glasses, are found.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Mixed Presence Collaboration using Scalable Visualizations in Heterogeneous Display Spaces
Mixed presence collaboration involves remote collaboration between multiple collocated groups. This paper presents the design and results of a user study that focused on mixed presence collaboration using large-scale tiled display walls. The research was conducted in order to compare data synchronization schemes for multi-user visualization applications. Our study compared three techniques for sharing data between display spaces with varying constraints and affordances. The results provide empirical evidence that using data sharing techniques with continuous synchronization between the sites lead to improved collaboration for a search and analysis task between remotely located groups. We have also identified aspects of synchronized sessions that result in increased remote collaborator awareness and parallel task coordination. It is believed that this research will lead to better utilization of large-scale tiled display walls for distributed group work.
data-conferencing↗
Interpreting Black-Box Classifiers Using Instance-Level Visual Explanations
To realize the full potential of machine learning in diverse real- world domains, it is necessary for model predictions to be readily interpretable and actionable for the human in the loop. Analysts, who are the users but not the developers of machine learning models, often do not trust a model because of the lack of transparency in associating predictions with the underlying data space. To address this problem, we propose Rivelo, a visual analytic interface that enables analysts to understand the causes behind predictions of binary classifiers by interactively exploring a set of instance-level explanations. These explanations are model-agnostic, treating a model as a black box, and they help analysts in interactively probing the high-dimensional binary data space for detecting features relevant to predictions. We demonstrate the utility of the interface with a case study analyzing a random forest model on the sentiment of Yelp reviews about doctors.
Tamagnini, Paolo↗
Evaluating the Effects of Missing Values and Mixed Data Types on Social Sequence Clustering Using t-SNE Visualization
© 2019 Association for Computing Machinery. The goal of this work is to investigate the impact of missing values in clustering joint categorical social sequences. Identifying patterns in sociodemographic longitudinal data is important in a number of social science settings. However, performing analytical operations, such as clustering on life course trajectories, is challenging due to the categorical and multidimensional nature of the data, their mixed data types, and corruption by missing and inconsistent values. Data quality issues were investigated previously on single variable sequences. To understand their effects on multivariate sequence analysis, we employ a dataset of mixed data types and missing values, a dissimilarity measure designed for joint categorical sequence data, together with dimensionality reduction methodologies in a systematic design of sequence clustering experiments. Given the categorical nature of our data, we employ an “edit” distance using optimal matching. Because each data record has multiple variables of different types, we investigate the impact of mixing these variables in a single dissimilarity measure. Between variables with binary values and those with multiple nominal values, we find that the ability to overcome missing data problems is more difficult in the nominal domain than in the binary domain. Additionally, alignment of leading missing values can result in systematic biases in dissimilarity matrices and subsequently introduce both artificial clusters and unrealistic interpretations of associated data domains. We demonstrate the usage of t-distributed stochastic neighborhood embedding to visually guide mitigation of such biases by tuning the missing value substitution cost parameter or determining an optimal sequence span.
Lazar, Alina↗
Spatiotemporal Visualization and Chemical Identification of the Metal Diffusion Layer at the Electrochemical Interface
The diffusion layer created by transition metal dissolution is ubiquitous at the electrochemical solid-liquid interface and plays a key role in determining electrochemical performance. Tracking the spatiotemporal dynamics of the diffusion layer has remained an unresolved challenge. With spatially resolved synchrotron X-ray fluorescence microscopy and micro-X-ray absorption spectroscopy, we demonstrate the in situ visualization and chemical identification of the dynamic diffusion layer near the electrode surface under electrochemical operating conditions. Finally, our method allows for direct mapping of the reactive electrochemical interface and provides insights into engineering the diffusion layer for improving electrochemical performance.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Understanding the Dynamics of Primary Zn-MnO 2 Alkaline Battery Gassing with Operando Visualization and Pressure Cells
The leading cause for safety vent rupture in alkaline batteries is the intrinsic instability of Zn in the highly alkaline reacting environment. Zn and aqueous KOH react in a parasitic process to generate hydrogen gas, which can rupture the seal and vent the hydrogen along with small amounts of electrolyte, and thus, damage consumer devices. Abusive conditions, particularly deep discharge, are known to accelerate this “gassing” phenomena. In order to understand the fundamental drivers and mechanisms for such gassing behavior, the results from multiphysics modeling, ex-situ microscopy and operando measurements of cell potential, pressure and visualization have been combined. Operando measurements were enabled by the development a new research platform that enables a cross-sectional view of a cylindrical Zn-MnO 2 primary alkaline battery throughout its discharge and recovery. A second version of this cell can actively measure the in-cell pressure during the discharge. It is shown that steep concentration gradients emerge during the cell discharge through a redox electrolyte mechanism, leading to the formation of high surface area Zn deposits that experience rapid corrosion when the cell rests to its open circuit voltage. Such corrosion is paired with the release of hydrogen and high cell pressure – eventually leading to cell rupture.
25 ENERGY STORAGE↗
Quantifying High-Performance Material Microstructure Using Nanomechanical Tools with Visual and Frequency Analysis
High-performance materials like ballistic fibers have remarkable mechanical properties owing to specific patterns of organization ranging from the molecular scale, to the micro scale and macro scale. Understanding these strategies for material organization is critical to improving the mechanical properties of these high-performance materials. In this work, atomic force microscopy (AFM) was used to detect changes in material composition at an extremely high resolution with transverse-stiffness scanning. New methods for direct quantification of material morphology were developed, and applied as an example to these AFM scans, although these methods can be applied to any spatially-resolved scans. These techniques were used to delineate between subtle morphological differences in commercial ultra-high-molecular-weight polyethylene (UHMWPE) fibers that have different processing conditions and mechanical properties as well as quantify morphology in commercial Kevlar®, a high-performance material with an entirely different organization strategy. Both frequency analysis and visual processing methods were used to systematically quantify the microstructure of the fiber samples in this study. These techniques are the first step in establishing structure-property relationships that can be used to inform synthesis and processing techniques to achieve desired morphologies, and thus superior mechanical performance.
Sandoz-Rosado, Emil↗