66 research outputs found

    py4DSTEM: a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

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    Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project

    Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure

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    The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.This work was funding by the National Natural Science Foundation of China (41977279), the Fundamental Research Funds for the Central Universities (2662020SKPY002 and 2662022SKYJ006), the Key Technology R & D Program of Hubei Province (2021BBA258) and the Major Project of Hubei Hongshan Laboratory (2022hszd013).Peer ReviewedPostprint (published version

    Shock-Induced Amorphization in Covalently Bonded Solids

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    Pulsed lasers with a power of the order of terawatts, once deposited on a target surface, will launch a stress pulse that propagates into material. Owing to the ultrashort duration of the laser pulses, unprecedented experimental conditions which combine high pressures (and/or shear stresses), strain rates and temperatures can be generated in materials, yielding a yet unexplored regime of study: materials science at extremes. High-power, short-duration, laser-driven, shock compression and recovery experiments were carried out on four covalently bonded materials, namely, silicon (Si), germanium (Ge), boron carbide (B4C) and silicon carbide (SiC). These materials were chosen because of their high Peierls-Nabarro stress and negative Clapeyron slope. The profile of the shock waves was measured by a velocity interferometer system for any reflectors (VISAR). The shock deformation microstructure has been revealed by high resolution transmission electron microscopy and all the materials exhibit shock-induced amorphization. For Si and Ge with [001] orientation, two distinct amorphous regions were identified: (i) a bulk amorphous layer close to the surface and (ii) amorphous bands initially aligned with {111} slip planes. The VISAR measurements show that the estimated thresholds for such a crystalline-to-amorphous transition is estimated to be ~10 GPa (for silicon) and ~4 GPa (for germanium). Further increase of the shock stress leads to the crystallization of amorphous domain into nanocrystals with high density of nano-twins. For polycrystalline boron carbide, only amorphous bands inclined to the direction of shock wave propagation have been observed at a shock stress above ~45 GPa. At lower shock stress, planar faults have been seen below the shocked surface. For [0001] oriented monocrystalline silicon carbide, in addition to the amorphous bands inclined to the shock direction, some amorphous bands perpendicular to the direction of shock wave propagation were observed. We propose that the amorphization is produced by the combined effect of high magnitude hydrostatic and shear stresses under dynamic shock compression. This study reveals that amorphization is a general inelastic deformation mechanisms in covalently bonded elements and compounds subjected to shock compression. Their formation yields a decrease in the overall hydrostatic and deviatoric elastic energy. Shock-induced defects play a very important role in the onset of amorphization. Calculations of the free energy changes with pressure and shear, using the Patel-Cohen methodology, agree with the experimental results. Molecular dynamics simulation corroborates the amorphization, showing that it is initiated by the nucleation and propagation of partial dislocations. The nucleation of amorphization is analyzed by classical nucleation theory

    Amorphization-mediated plasticity

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    Grain boundary phase transformation in a CrCoNi complex concentrated alloy

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    The phase-transformation-like behavior of grain boundaries, where their chemistry, structure and properties change discontinuously, is emerging as a fundamental interest in the context of grain boundary engineering. The cases studied so far pertain primarily to elemental metals and dilute alloy systems. The next step of complexity would be a system still of a single phase structure but involving multiple and concentrated elements. The recently emerging high/medium entropy alloys (H/MEAs), alternatively known as complex concentration alloys (CCAs), fit the bill in this regard. Here we use CoCrNi as a model CCA to highlight that intricate interatomic interactions influence the grain boundary element distribution and consequently phase transitions. By combining classical molecular dynamics simulations and first-principles density functional theory calculations, we reveal that grain boundary phase transition temperature is sensitive to the grain boundary atomic configuration. The CCA grain boundary with random atomic distribution is more apt to transform due to a larger thermodynamic driving force and faster diffusion kinetics, compared to a hypothetical reference that bears the same bulk properties but no distinguishable constituent components. In contrast, when the three elements redistribute with local Ni-clustering and Co & ndash;Cr ordering in the grain boundary structure, diffusion is rendered more sluggish, delaying grain boundary phase transformation. Our work is a step forward in understanding critical phenomena in grain boundaries and CCAs, and enriches the knowledge base for materials design via grain boundary engineering. (c) 2021 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved
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