Deciphering chemical order/disorder and material properties at the single-atom level.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Facile bottom-up synthesis of partially oxidized black phosphorus nanosheets as metal-free photocatalyst for hydrogen evolution.

Few-layer black phosphorus (BP) nanosheets were first reported as a 2D material for the application of field-effect transistors in 2014 and have stimulated intense activity among physicists, chemists, and material and biomedical scientists, driving research into novel synthetic techniques to produce BP nanosheets. At present, exfoliation is the main route toward few-layer BP nanosheets via employing bulk BP as raw material. However, this is a complicated and time-consuming process, which is difficult for the large-scale synthesis of BP nanosheets. Moreover, BP degrades rapidly when exfoliated to nanoscale dimensions, resulting in the rapid loss of semiconducting properties. Here, we report the direct wet-chemical synthesis of few-layer BP nanosheets in gram-scale quantities in a bottom-up approach based on common laboratory reagents at low temperature, showing excellent stability due to partial oxidation of surface. Solvent and temperature are two critical factors, controlling not only the formation of BP nanosheets but also the thickness. The as-prepared BP nanosheets can extract hydrogen from pure water (pH = 6.8), exhibiting more than 24-fold higher activity than the well-known C3N4 nanosheets. Our results reporting the ability to prepare few-layer BP nanosheets with a facile, scalable, low-cost approach take us a step closer to real-world applications of phosphorene including next-generation metal-free photocatalysts for photosynthesis.

Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution.

Dislocations and their interactions strongly influence many material properties, ranging from the strength of metals and alloys to the efficiency of light-emitting diodes and laser diodes. Several experimental methods can be used to visualize dislocations. Transmission electron microscopy (TEM) has long been used to image dislocations in materials, and high-resolution electron microscopy can reveal dislocation core structures in high detail, particularly in annular dark-field mode. A TEM image, however, represents a two-dimensional projection of a three-dimensional (3D) object (although stereo TEM provides limited information about 3D dislocations). X-ray topography can image dislocations in three dimensions, but with reduced resolution. Using weak-beam dark-field TEM and scanning TEM, electron tomography has been used to image 3D dislocations at a resolution of about five nanometres (refs 15, 16). Atom probe tomography can offer higher-resolution 3D characterization of dislocations, but requires needle-shaped samples and can detect only about 60 per cent of the atoms in a sample. Here we report 3D imaging of dislocations in materials at atomic resolution by electron tomography. By applying 3D Fourier filtering together with equal-slope tomographic reconstruction, we observe nearly all the atoms in a multiply twinned platinum nanoparticle. We observed atomic steps at 3D twin boundaries and imaged the 3D core structure of edge and screw dislocations at atomic resolution. These dislocations and the atomic steps at the twin boundaries, which appear to be stress-relief mechanisms, are not visible in conventional two-dimensional projections. The ability to image 3D disordered structures such as dislocations at atomic resolution is expected to find applications in materials science, nanoscience, solid-state physics and chemistry.

Electron tomography at 2.4-ångström resolution.

Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved and resolution below 0.5 ångströms has been demonstrated. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice, with cubic-nanometre resolution currently achievable. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter, but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-ångström resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution, but also to improve the spatial resolution and image quality in other tomography fields.

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography.

Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. Here, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ∼19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field and the full strain tensor with a 3D resolution of ∼1 nm(3) and a precision of ∼10(-3), which are further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.

Comparison of fluorescence in-situ hybridisation with dual-colour in-situ hybridisation for assessment of HER2 gene amplification of breast cancer in Hong Kong.

OBJECTIVES: To compare the PathVysion fluorescence in-situ hybridisation assay with the INFORM HER2 Dual in-situ hybridisation assay on 104 invasive breast cancers with a broad spectrum of immunohistochemistry scores. METHODS: This case series involved consecutive patients diagnosed with invasive breast carcinoma with equivocal immunohistochemistry score and referred for further HER2 assessment from the departments of Surgery and/or Clinical Oncology of the two hospitals between January 2013 and February 2014. An additional 10 cases with negative HER2 immunohistochemistry and 11 cases with positive HER2 immunohistochemistry were further included. RESULTS: The results of both fluorescence in-situ hybridisation and dual in-situ hybridisation were available in 99 of 104 cases, respectively. Student'st test showed no statistically significant difference in the mean number of HER2 count, CEP17 copies, or HER2/CEP17 ratio between that obtained by fluorescence in-situ hybridisation and that obtained by dual in-situ hybridisation. Pearson's correlation of results for the two assays was strong for HER2/CEP17 signal ratio (R=0.963, P<0.001) and mean HER2 copies per nucleus (R=0.897, P<0.001). Overall agreement was 96.0% (95 out of 99 cases, ĸ0.882). Three of the four discordant cases were equivocal for either fluorescence in-situ hybridisation or dual in-situ hybridisation. The results of immunohistochemistry 0/1+ and 3+ cases showed 100% concordance between the two assays. The failure rate was 0.96% for fluorescence in-situ hybridisation and 3.85% for dual in-situ hybridisation. Cases that failed for fluorescence in-situ hybridisation were successful for dual in-situ hybridisation and vice versa. CONCLUSIONS: Our study showed that dual in-situ hybridisation is a reliable and useful option for HER2 testing in breast cancer.

Molecular profiling reveals prognostically significant subtypes of canine lymphoma.

We performed genomewide gene expression analysis of 35 samples representing 6 common histologic subtypes of canine lymphoma and bioinformatics analyses to define their molecular characteristics. Three major groups were defined on the basis of gene expression profiles: (1) low-grade T-cell lymphoma, composed entirely by T-zone lymphoma; (2) high-grade T-cell lymphoma, consisting of lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma not otherwise specified; and (3) B-cell lymphoma, consisting of marginal B-cell lymphoma, diffuse large B-cell lymphoma, and Burkitt lymphoma. Interspecies comparative analyses of gene expression profiles also showed that marginal B-cell lymphoma and diffuse large B-cell lymphoma in dogs and humans might represent a continuum of disease with similar drivers. The classification of these diverse tumors into 3 subgroups was prognostically significant, as the groups were directly correlated with event-free survival. Finally, we developed a benchtop diagnostic test based on expression of 4 genes that can robustly classify canine lymphomas into one of these 3 subgroups, enabling a direct clinical application for our results.

One dimensional wormhole corrosion in metals.

Corrosion is a ubiquitous failure mode of materials. Often, the progression of localized corrosion is accompanied by the evolution of porosity in materials previously reported to be either three-dimensional or two-dimensional. However, using new tools and analysis techniques, we have realized that a more localized form of corrosion, which we call 1D wormhole corrosion, has previously been miscategorized in some situations. Using electron tomography, we show multiple examples of this 1D and percolating morphology. To understand the origin of this mechanism in a Ni-Cr alloy corroded by molten salt, we combined energy-filtered four-dimensional scanning transmission electron microscopy and ab initio density functional theory calculations to develop a vacancy mapping method with nanometer-resolution, identifying a remarkably high vacancy concentration in the diffusion-induced grain boundary migration zone, up to 100 times the equilibrium value at the melting point. Deciphering the origins of 1D corrosion is an important step towards designing structural materials with enhanced corrosion resistance.

Reverse line blot probe design and polymerase chain reaction optimization for bloodmeal analysis of ticks from the eastern United States.

Determining the host preference of vector ticks is vital to elucidating the eco-epidemiology of the diseases they spread. Detachment of ticks from captured hosts can provide evidence of feeding on those host species, but only for those species that are feasible to capture. Recently developed, highly sensitive molecular assays show great promise in allowing host selection to be determined from minute traces of host DNA that persist in recently molted ticks. Using methods developed in Europe as a starting-point, we designed 12S rDNA mitochondrial gene probes suitable for use in a reverse line blot (RLB) assay of ticks feeding on common host species in the eastern United States. This is the first study to use the 12S mitochondrial gene in a RLB bloodmeal assay in North America. The assay combines conventional PCR with a biotin-labeled primer and reverse line blots that can be stripped and rehybridized up to 20 times, making the method less expensive and more straightforward to interpret than previous methods of tick bloodmeal identification. Probes were designed that target the species, genus, genus group, family, order, or class of eight reptile, 13 birds, and 32 mammal hosts. After optimization, the RLB assay correctly identified the current hostspecies for 99% of ticks [Amblyomma americanum (L.) and eight other ixodid tick species] collected directly from known hosts. The method identified previous-host DNA for approximately half of all questing ticks assayed. Multiple bloodmeal determinations were obtained in some instances from feeding and questing ticks; this pattern is consistent with previous RLB studies but requires further investigation. Development of this probe library, suitable for eastern U.S. ecosystems, opens new avenues for eco-epidemiological investigations of this region's tick-host systems.

Borrelia burgdorferi not detected in widespread Ixodes scapularis (Acari: Ixodidae) collected from white-tailed deer in Tennessee.

Lyme disease (LD), caused by the bacterium Borrelia burgdorferi and transmitted in the eastern United States by blacklegged ticks, Ixodes scapularis Say, is classified as nonendemic in Tennessee and surrounding states in the Southeast. Low incidence of LD in these states has been attributed, in part, to vector ticks being scarce or absent; however, tick survey data for many counties are incomplete or out of date. To improve our knowledge of the distribution, abundance, and Borrelia spp. prevalence of I. scapularis, we collected ticks from 1,018 hunter-harvested white-tailed deer (Odocoileus virginianus (Zimmerman)) from 71 of 95 Tennessee counties in fall 2007 and 2008. In total, 160 deer (15.7%) from 35 counties were infested with adult I. scapularis; 30 of these counties were new distributional records for this tick. The mean number of I. scapularis collected per infested deer was 5.4 +/- 0.6 SE. Of the 883 I. scapularis we removed from deer, none were positive for B. burgdorferi and one tested positive for B. miyamotoi. Deer are not reservoir hosts for B. burgdorferi; nevertheless, past surveys in northern LD-endemic states have readily detected B. burgdoreferi in ticks collected from deer. We conclude that I. scapularis is far more widespread in Tennessee than previously reported. The absence of detectable B. burgdorferi infection among these ticks suggests that the LD risk posed by I. scapularis in the surveyed areas of Tennessee is much lower than in LD-endemic areas of the Northeast and upper Midwest.

Decoupling electron and phonon transport in single-nanowire hybrid materials for high-performance thermoelectrics.

Organic-inorganic hybrids have recently emerged as a class of high-performing thermoelectric materials that are lightweight and mechanically flexible. However, the fundamental electrical and thermal transport in these materials has remained elusive due to the heterogeneity of bulk, polycrystalline, thin films reported thus far. Here, we systematically investigate a model hybrid comprising a single core/shell nanowire of Te-PEDOT:PSS. We show that as the nanowire diameter is reduced, the electrical conductivity increases and the thermal conductivity decreases, while the Seebeck coefficient remains nearly constant-this collectively results in a figure of merit, ZT, of 0.54 at 400 K. The origin of the decoupling of charge and heat transport lies in the fact that electrical transport occurs through the organic shell, while thermal transport is driven by the inorganic core. This study establishes design principles for high-performing thermoelectrics that leverage the unique interactions occurring at the interfaces of hybrid nanowires.

Prismatic 2.0 - Simulation software for scanning and high resolution transmission electron microscopy (STEM and HRTEM).

Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned over a sample's surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging methods have made STEM one of the most important tools for atomic-resolution materials science. Many of these imaging methods rely on accurate imaging and diffraction simulations in order to interpret experimental results. However, STEM simulations have traditionally required large calculation times, as modeling the electron scattering requires a separate simulation for each of the typically millions of probe positions. We have created the Prismatic simulation code for fast simulation of STEM experiments with support for multi-CPU and multi-GPU (graphics processing unit) systems, using both the conventional multislice and our recently-introduced PRISM method. In this paper, we introduce Prismatic version 2.0, which adds many new algorithmic improvements, an updated graphical user interface (GUI), post-processing of simulation data, and additional operating modes such as plane-wave TEM. We review various aspects of the simulation methods and codes in detail and provide various simulation examples. Prismatic 2.0 is freely available both as an open-source package that can be run using a C++ or Python command line interface, or GUI, as well within a Docker container environment.

High-prevalence Borrelia miyamotoi infection among [corrected] wild turkeys (Meleagris gallopavo) in Tennessee.

During spring and fall 2009, 60 wild turkeys (Meleagris gallopavo) harvested by Tennessee hunters were surveyed for Borrelia spp. by sampling their blood, tissue, and attached ticks. In both seasons, 70% of turkeys were infested with juvenile Amblyomma americanum; one spring turkey hosted an adult female Ixodes brunneus. Polymerase chain reaction assays followed by DNA sequencing indicated that 58% of the turkeys were positive for the spirochete Borrelia miyamotoi, with tissue testing positive more frequently than blood (P = 0.015). Sequencing of the 16S-23S rRNA intergenic spacer indicated > or = 99% similarity to previously published sequences of the North American strain of this spirochete. Positive turkeys were present in both seasons and from all seven middle Tennessee counties sampled. No ticks from the turkeys tested positive for any Borrelia spp. This is the first report of B. miyamotoi in birds; the transmission pathways and epidemiological significance of this high-prevalence spirochetal infection remain uncertain.

Supported black phosphorus nanosheets as hydrogen-evolving photocatalyst achieving 5.4% energy conversion efficiency at 353 K.

Solar-driven water splitting using powdered catalysts is considered as the most economical means for hydrogen generation. However, four-electron-driven oxidation half-reaction showing slow kinetics, accompanying with insufficient light absorption and rapid carrier combination in photocatalysts leads to low solar-to-hydrogen energy conversion efficiency. Here, we report amorphous cobalt phosphide (Co-P)-supported black phosphorus nanosheets employed as photocatalysts can simultaneously address these issues. The nanosheets exhibit robust hydrogen evolution from pure water (pH = 6.8) without bias and hole scavengers, achieving an apparent quantum efficiency of 42.55% at 430 nm and energy conversion efficiency of over 5.4% at 353 K. This photocatalytic activity is attributed to extremely efficient utilization of solar energy (~75% of solar energy) by black phosphorus nanosheets and high-carrier separation efficiency by amorphous Co-P. The hybrid material design realizes efficient solar-to-chemical energy conversion in suspension, demonstrating the potential of black phosphorus-based materials as catalysts for solar hydrogen production.

Atomically Altered Hematite for Highly Efficient Perovskite Tandem Water-Splitting Devices.

Photoelectrochemical (PEC) cells are attractive for storing solar energy in chemical bonds through cleaving of water into oxygen and hydrogen. Although hematite (α-Fe2 O3 ) is a promising photoanode material owing to its chemical stability, suitable band gap, low cost, and environmental friendliness, its performance is limited by short carrier lifetimes, poor conductivity, and sluggish kinetics leading to low (solar-to-hydrogen) STH efficiency. Herein, we combine solution-based hydrothermal growth and a post-growth surface exposure through atomic layer deposition (ALD) to show a dramatic enhancement of the efficiency for water photolysis. These modified photoanodes show a high photocurrent of 3.12 mA cm-2 at 1.23 V versus RHE, (>5 times higher than Fe2 O3 ) and a plateau photocurrent of 4.5 mA cm-2 at 1.5 V versus RHE. We demonstrate that these photoanodes in tandem with a CH3 NH3 PbI3 perovskite solar cell achieves overall unassisted water splitting with an STH conversion efficiency of 3.4 %, constituting a new benchmark for hematite-based tandem systems.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.