Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how ...the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below ...subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.
Lead Iodide (PbI
) is a large bandgap 2D layered material that has potential for semiconductor applications. However, atomic level study of PbI
monolayer has been limited due to challenges in ...obtaining thin crystals. Here, we use liquid exfoliation to produce monolayer PbI
nanodisks (30-40 nm in diameter and > 99% monolayer purity) and deposit them onto suspended graphene supports to enable atomic structure study of PbI
. Strong epitaxial alignment of PbI
monolayers with the underlying graphene lattice occurs, leading to a phase shift from the 1 T to 1 H structure to increase the level of commensuration in the two lattice spacings. The fundamental point vacancy and nanopore structures in PbI
monolayers are directly imaged, showing rapid vacancy migration and self-healing. These results provide a detailed insight into the atomic structure of monolayer PbI
, and the impact of the strong van der Waals interaction with graphene, which has importance for future applications in optoelectronics.
The solid progress in the study of a single two-dimensional (2D) material underpins the development for creating 2D material assemblies with various electronic and optoelectronic properties. We ...introduce an asymmetric structure by stacking monolayer semiconducting tungsten disulfide, metallic graphene, and insulating boron nitride to fabricate numerous red channel light-emitting devices (LEDs). All the 2D crystals were grown by chemical vapor deposition (CVD), which has great potential for future industrial scale-up. Our LEDs exhibit visibly observable electroluminescence (EL) at both 5.5 V forward and 7.0 V backward biasing, which correlates well with our asymmetric design. The red emission can last for at least several minutes, and the success rate of the working device that can emit detectable EL is up to 80%. In addition, we show that sample degradation is prone to happen when a continuing bias, much higher than the threshold voltage, is applied. Our success of using high-quality CVD-grown 2D materials for red light emitters is expected to provide the basis for flexible and transparent displays.
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We show how an oxide passivating layer on the Cu surface before the growth of h-BN by chemical vapor deposition (CVD) can lead to increased domain sizes from 1 to 20 μm by reducing the nucleation ...density from 106 to 103 mm–2. The h-BN domains within each Cu grain are well-oriented, indicating an epitaxial relationship between the h-BN crystals and the Cu growth substrates that leads to larger crystal domains within the film of ∼100 μm. Continuous films are grown and show a high degree of monolayer uniformity. This CVD approach removes the need for low pressures, electrochemical polishing, and expensive substrates for large-area continuous films of h-BN monolayers, which is beneficial for industrial applications that require scalable synthesis.
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Heterophase homojunction formation in atomically thin 2D layers is of great importance for next-generation nanoelectronics and optoelectronics applications. Technologically challenging, controllable ...transformation between the semiconducting and metallic phases of transition metal chalcogenides is of particular importance. Here, we demonstrate that controlled laser irradiation can be used to directly ablate PdSe2 thin films using high power or trigger the local transformation of PdSe2 into a metallic phase PdSe2–x using lower laser power. Such transformations are possible due to the low decomposition temperature of PdSe2 and a variety of stable phases compared to other 2D transition metal dichalcogenides. Scanning transmission electron microscopy is used to reveal the laser-induced Se-deficient phases of PdSe2 material. The process sensitivity to the laser power allows patterning flexibility for resist-free device fabrication. The laser-patterned devices demonstrate that a laser-induced metallic phase PdSe2–x is stable with increased conductivity by a factor of about 20 compared to PdSe2. These findings contribute to the development of nanoscale devices with homojunctions and scalable methods to achieve structural transformations in 2D materials.
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The influence of nanostructuring and quantum confinement on the thermoelectric properties of materials has been extensively studied. While this has made possible multiple breakthroughs in the ...achievable figure of merit, classical confinement, and its effect on the local Seebeck coefficient has mostly been neglected, as has the Peltier effect in general due to the complexity of measuring small temperature gradients locally. Here we report that reducing the width of a graphene channel to 100 nm changes the Seebeck coefficient by orders of magnitude. Using a scanning thermal microscope allows us to probe the local temperature of electrically contacted graphene two-terminal devices or to locally heat the sample. We show that constrictions in mono- and bilayer graphene facilitate a spatially correlated gradient in the Seebeck and Peltier coefficient, as evidenced by the pronounced thermovoltage V th and heating/cooling response ΔT Peltier, respectively. This geometry dependent effect, which has not been reported previously in 2D materials, has important implications for measurements of patterned nanostructures in graphene and points to novel solutions for effective thermal management in electronic graphene devices or concepts for single material thermocouples.
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Understanding the stability of monolayer transition metal dichalcogenides in atmospheric conditions has important consequences for their handling, life-span, and utilization in applications. We show ...that cryogenic photoluminescence spectroscopy (PL) is a highly sensitive technique to the detection of oxidation induced degradation of monolayer tungsten disulfide (WS2) caused by exposure to ambient conditions. Although long-term exposure to atmospheric conditions causes massive degradation from oxidation that is optically visible, short-term exposure produces no obvious changes to the PL or Raman spectra measured at either room temperature or even cryogenic environment. Laser processing was employed to remove the surface adsorbents, which enables the defect states to be detected via cryogenic PL spectroscopy. Thermal cycling to room temperature and back down to 77 K shows the process is reversible. We also monitor the degradation process of WS2 using this method, which shows that the defect related peak can be observed after one month aging in ambient conditions.
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Here we study the layer-dependent photoconductivity in Gr/WS2/Gr vertical stacked tunneling (VST) cross-bar devices made using two-dimensional (2D) materials all grown by chemical vapor deposition. ...The larger number of devices (>100) enables a statistically robust analysis on the comparative differences in the photovoltaic response of monolayer and bilayer WS2, which cannot be achieved in small batch devices made using mechanically exfoliated materials. We show a dramatic increase in photovoltaic response for Gr/WS2(2L)/Gr compared to monolayers because of the long inter- and intralayer exciton lifetimes and the small exciton binding energy (both interlayer and intralayer excitons) of bilayer WS2 compared with that of monolayer WS2. Different doping levels and dielectric environments of top and bottom graphene electrodes result in a potential difference across a ∼1 nm vertical device, which gives rise to large electric fields perpendicular to the WS2 layers that cause band structure modification. Our results show how precise control over layer number in all 2D VST devices dictates the photophysics and performance for photosensing applications.
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Graphene provides a two-dimensional platform for contacting individual molecules, which enables transport spectroscopy of molecular orbital, spin, and vibrational states. Here we report ...single-electron tunneling through a molecule that has been anchored to two graphene leads. Quantum interference within the graphene leads gives rise to an energy-dependent transmission and fluctuations in the sequential tunnel-rates. The lead states are electrostatically tuned by a global back-gate, resulting in a distinct pattern of varying intensity in the measured conductance maps. This pattern could potentially obscure transport features that are intrinsic to the molecule under investigation. Using ensemble averaged magneto-conductance measurements, lead and molecule states are disentangled, enabling spectroscopic investigation of the single molecule.
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