Crystal Lattice-Induced Stress modulates Photoinduced Jahn-Teller Distortion Dynamics.

Efficient photoredox chemical transformations are essential to the development of novel, cost-effective, and environmentally friendly synthetic methodologies. The concept of the entatic state in bioinorganic catalysis proposes that a preorganized structural configuration can reduce the energy barriers associated with chemical reactions. This concept provides one of the guiding principles to enhance catalytic efficiency by maintaining high-energy conformations close to the reaction's transition state.

Liquid Phase Electron Microscopy of Bacterial Ultrastructure.

Recent advances in liquid phase scanning transmission electron microscopy (LP-STEM) have enabled the study of dynamic biological processes at nanometer resolutions, paving the way for live-cell imaging using electron microscopy. However, this technique is often hampered by the inherent thickness of whole cell samples and damage from electron beam irradiation. These restrictions degrade image quality and resolution, impeding biological interpretation.

Diffusion distribution model for damage mitigation in scanning transmission electron microscopy.

Despite the widespread use of Scanning Transmission Electron Microscopy (STEM) for observing the structure of materials at the atomic scale, a detailed understanding of some relevant electron beam damage mechanisms is limited. Recent reports suggest that certain types of damage can be modelled as a diffusion process and that the accumulation effects of this process must be kept low in order to reduce damage. We therefore develop an explicit mathematical formulation of spatiotemporal diffusion processes in STEM that take into account both instrument and sample parameters.

High-speed 4-dimensional scanning transmission electron microscopy using compressive sensing techniques.

Here we show that compressive sensing allows 4-dimensional (4-D) STEM data to be obtained and accurately reconstructed with both high-speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4-D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition.

The Potential of Subsampling and Inpainting for Fast Low-Dose Cryo FIB-SEM Imaging.

Traditional image acquisition for cryo focused ion-beam scanning electron microscopy (FIB-SEM) tomography often sees thousands of images being captured over a period of many hours, with immense data sets being produced. When imaging beam sensitive materials, these images are often compromised by additional constraints related to beam damage and the devitrification of the material during imaging, which renders data acquisition both costly and unreliable. Subsampling and inpainting are proposed as solutions for both of these aspects, allowing fast and low-dose imaging to take place in the Focused ion-beam scanning electron microscopy FIB-SEM without an appreciable loss in image quality.

Cryo-electron ptychography: Applications and potential in biological characterisation.

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions.

Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples.

Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations.

Phosphinecarboxamide based InZnP QDs - an air tolerant route to luminescent III-V semiconductors.

We describe a new synthetic methodology for the preparation of high quality, emission tuneable InP-based quantum dots (QDs) using a solid, air- and moisture-tolerant primary phosphine as a group-V precursor. This presents a significantly simpler synthetic pathway compared to the state-of-the-art precursors currently employed in phosphide quantum dot synthesis which are volatile, dangerous and air-sensitive, P(Si(CH)).

Mapping Nanoscale Electrostatic Field Fluctuations around Graphene Dislocation Cores Using Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM).

Defects in crystalline lattices cause modulation of the atomic density, and this leads to variations in the associated electrostatics at the nanoscale. Mapping these spatially varying charge fluctuations using transmission electron microscopy has typically been challenging due to complicated contrast transfer inherent to conventional phase contrast imaging. To overcome this, we used four-dimensional scanning transmission electron microscopy (4D-STEM) to measure electrostatic fields near point dislocations in a monolayer.

Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast.

Multi-synaptic boutons are a feature of CA1 hippocampal connections in the stratum oriens.

Excitatory synapses are typically described as single synaptic boutons (SSBs), where one presynaptic bouton contacts a single postsynaptic spine. Using serial section block-face scanning electron microscopy, we found that this textbook definition of the synapse does not fully apply to the CA1 region of the hippocampus. Roughly half of all excitatory synapses in the stratum oriens involved multi-synaptic boutons (MSBs), where a single presynaptic bouton containing multiple active zones contacted many postsynaptic spines (from 2 to 7) on the basal dendrites of different cells.

Towards real-time STEM simulations through targeted subsampling strategies.

Scanning transmission electron microscopy images can be complex to interpret on the atomic scale as the contrast is sensitive to multiple factors such as sample thickness, composition, defects and aberrations. Simulations are commonly used to validate or interpret real experimental images, but they come at a cost of either long computation times or specialist hardware such as graphics processing units. Recent works in compressive sensing for experimental STEM images have shown that it is possible to significantly reduce the amount of acquired signal and still recover the full image without significant loss of image quality, and therefore it is proposed here that similar methods can be applied to STEM simulations.

SIM-STEM Lab: Incorporating Compressed Sensing Theory for Fast STEM Simulation.

Recently it has been shown that precise dose control and an increase in the overall acquisition speed of atomic resolution scanning transmission electron microscope (STEM) images can be achieved by acquiring only a small fraction of the pixels in the image experimentally and then reconstructing the full image using an inpainting algorithm. In this paper, we apply the same inpainting approach (a form of compressed sensing) to simulated, sub-sampled atomic resolution STEM images. We find that it is possible to significantly sub-sample the area that is simulated, the number of g-vectors contributing the image, and the number of frozen phonon configurations contributing to the final image while still producing an acceptable fit to a fully sampled simulation.

Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures.

Three dimensional scaffolded DNA origami with inorganic nanoparticles has been used to create tailored multidimensional nanostructures. However, the image contrast of DNA is poorer than those of the heavy nanoparticles in conventional transmission electron microscopy at high defocus so that the biological and non-biological components in 3D scaffolds cannot be simultaneously resolved using tomography of samples in a native state. We demonstrate the use of electron ptychography to recover high contrast phase information from all components in a DNA origami scaffold without staining.

Trainable segmentation for transmission electron microscope images of inorganic nanoparticles.

We present a trainable segmentation method implemented within the python package ParticleSpy. The method takes user labelled pixels, which are used to train a classifier and segment images of inorganic nanoparticles from transmission electron microscope images. This implementation is based on the trainable Waikato Environment for Knowledge Analysis (WEKA) segmentation, but is written in python, allowing a large degree of flexibility and meaning it can be easily expanded using other python packages.

Direct Visualisation of the Surface Atomic Active Sites of Carbon-Supported Co O Nanocrystals via High-Resolution Phase Restoration.

The atomic arrangement of the terminating facets on spinel Co O nanocrystals is strongly linked to their catalytic performance. However, the spinel crystal structure offers multiple possible surface terminations depending on the synthesis. Thus, understanding the terminating surface atomic structure is essential in developing high-performance Co O nanocrystals.

Applications of deep learning in electron microscopy.

We review the growing use of machine learning in electron microscopy (EM) driven in part by the availability of fast detectors operating at kiloHertz frame rates leading to large data sets that cannot be processed using manually implemented algorithms. We summarize the various network architectures and error metrics that have been applied to a range of EM-related problems including denoising and inpainting. We then provide a review of the application of these in both physical and life sciences, highlighting how conventional networks and training data have been specifically modified for EM.

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable optimization of sample geometries, data acquisition schemes and instrument parameters.

Structural insight into [Fe-S-Mo] motif in electrochemical reduction of N over Fe-supported molecular MoS.

The catalytic synthesis of NH from the thermodynamically challenging N reduction reaction under mild conditions is currently a significant problem for scientists. Accordingly, herein, we report the development of a nitrogenase-inspired inorganic-based chalcogenide system for the efficient electrochemical conversion of N to NH, which is comprised of the basic structure of [Fe-S-Mo]. This material showed high activity of 8.

Quantifying the performance of a hybrid pixel detector with GaAs:Cr sensor for transmission electron microscopy.

Hybrid pixel detectors (HPDs) have been shown to be highly effective for diffraction-based and time-resolved studies in transmission electron microscopy, but their performance is limited by the fact that high-energy electrons scatter over long distances in their thick Si sensors. An advantage of HPDs compared to monolithic active pixel sensors is that their sensors do not need to be fabricated from Si. We have compared the performance of the Medipix3 HPD with a Si sensor and a GaAs:Cr sensor using primary electrons in the energy range of 60-300 keV.

High Loading of Transition Metal Single Atoms on Chalcogenide Catalysts.

Transition metal doped chalcogenides are one of the most important classes of catalysts that have been attracting increasing attention for petrochemical and energy related chemical transformations due to their unique physiochemical properties. For practical applications, achieving maximum atom utilization by homogeneous dispersion of metals on the surface of chalcogenides is essential. Herein, we report a detailed study of a deposition method using thiourea coordinated transition metal complexes.

Atomic resolution HOLZ-STEM imaging of atom position modulation in oxide heterostructures.

It is shown that higher order Laue zone (HOLZ) rings in high energy electron diffraction are specific to individual columns of atoms, and show different strengths, structure and radii for different atom columns along the same projection in a structure. An atomic resolution 4-dimensional STEM dataset is recorded from a <110> direction in a perovskite trilayer, where only the central LaFeO layer should show a period doubling that gives rise to an extra HOLZ ring. Careful comparison between experiment and multislice simulations is used to understand the origins of all features in the patterns.