On the Progress of Scanning Transmission Electron Microscopy (STEM) Imaging in a Scanning Electron Microscope

Peptide nanozymes: An emerging direction for functional enzyme mimics

The abundance of molecules on early Earth likely enabled a wide range of prebiotic chemistry, with peptides playing a key role in the development of early life forms and the evolution of metabolic pathways. Among peptides, those with enzyme-like activities occupy a unique position between peptides and enzymes, combining both structural flexibility and catalytic functionality. However, their full potential remains largely untapped. Further exploration of these enzyme-like peptides at the nanoscale could provide valuable insights into modern nanotechnology, biomedicine, and even the origins of life. Hence, this review introduces the groundbreaking concept of "peptide nanozymes (PepNzymes)", which includes single peptides exhibiting enzyme-like activities, peptide-based nanostructures with enzyme-like activities, and peptide-based nanozymes, thus enabling the investigation of biological phenomena at nanoscale dimensions. Through the rational design of enzyme-like peptides or their assembly with nanostructures and nanozymes, researchers have found or created PepNzymes capable of catalyzing a wide range of reactions. By scrutinizing the interactions between the structures and enzyme-like activities of PepNzymes, we have gained valuable insights into the underlying mechanisms governing enzyme-like activities. Generally, PepNzymes play a crucial role in biological processes by facilitating small-scale enzyme-like reactions, speeding up molecular oxidation-reduction, cleavage, and synthesis reactions, leveraging the functional properties of peptides, and creating a stable microenvironment, among other functions. These discoveries make PepNzymes useful for diagnostics, cellular imaging, antimicrobial therapy, tissue engineering, anti-tumor treatments, and more while pointing out opportunities. Overall, this research provides a significant journey of PepNzymes' potential in various biomedical applications, pushing them towards new advancements.

Advances in bioinspired nanomaterials managing microbial biofilms and virulence: A critical analysis

Microbial virulence and biofilm formation stand as a big concern against the goal of achieving a green and sustainable future. Microbial pathogenesis is the process by which the microbes (bacterial, fungal, and viral) cause illness in their respective host organism. 'Nanotechnology' is a state-of-art discipline to address this problem. The use of conventional techniques against microbial proliferation has been challenging against the environment. To tackle this problem, there has been a revolution in this multi-disciplinary field, to address the aspect of bioinspired nanomaterials in the antibiofilm and antimicrobial sector. Bioinspired nanomaterials prove to be a potential antibiofilm and antimicrobial agent as they are non-hazardous to the environment and mostly synthesized using a single-step reduction protocol. They exhibit synergistic effects against bacterial, fungal, and viral pathogens and thereby, control the virulence. In this literature review, we have elucidated the potential of bioinspired nanoparticles as well as nanomaterials as a promising anti-microbial treatment pedagogy and throw light on the advancements in how smart photo-switchable platforms have been designed to exhibit both bacterial releasing as well as bacterial-killing properties. Certain limitations and possible outcomes of these bio-based nanomaterials have been discussed in the hope of achieving a green and sustainable ecosystem.

Wheat gluten amyloid fibrils: Conditions, mechanism, characterization, application, and future perspectives

Amyloid fibrils have excellent structural characteristics, such as a high aspect ratio, excellent stiffness, and a wide availability of functional groups on the surface. More studies are now focusing on the formation of amyloid fibrils using food proteins. Protein fibrillation is now becoming recognized as a promising strategy for enhancing the function of food proteins and expanding their range of applications. Wheat gluten is rich in glutamine (Q), hydrophobic amino acids, and the α-helix structure with high β-sheet tendency. These characteristics make it very easy for wheat gluten to form amyloid fibrils. The conditions, formation mechanism, characterization methods, and application of amyloid fibrils formed by wheat gluten are summarized in this review. Further exploration of amyloid fibrils formed by wheat gluten will reveal how they can play a significant role in food, biology, and other fields, especially in medicine.

High-Energy Electron Scattering in Thick Samples Evaluated by Bright-Field Transmission Electron Microscopy, Energy-Filtering Transmission Electron Microscopy, and Electron Tomography

Energy-filtering transmission electron microscopy (TEM) and bright-field TEM can be used to extract local sample thickness $t$ and to generate two-dimensional sample thickness maps. Electron tomography can be used to accurately verify the local $t$. The relations of log-ratio of zero-loss filtered energy-filtering TEM beam intensity ($I_{{\rm ZLP}}$) and unfiltered beam intensity ($I_{\rm u}$) versus sample thickness $t$ were measured for five values of collection angle in a microscope equipped with an energy filter. Furthermore, log-ratio of the incident (primary) beam intensity ($I_{\rm p}$) and the transmitted beam $I_{{\rm tr}}$ versus $t$ in bright-field TEM was measured utilizing a camera before the energy filter. The measurements were performed on a multilayer sample containing eight materials and thickness $t$ up to 800 nm. Local thickness $t$ was verified by electron tomography. The following results are reported:• The maximum thickness $t_{{\rm max}}$ yielding a linear relation of log-ratio, $\ln ( {I_{\rm u}}/{I_{{\rm ZLP}}})$ and $\ln ( {I_{\rm p}}/{I_{{\rm tr}}} )$, versus $t$.• Inelastic mean free path ($\lambda _{{\rm in}}$) for five values of collection angle.• Total mean free path ($\lambda _{{\rm total}}$) of electrons excluded by an angle-limiting aperture.• $\lambda _{{\rm in}}$ and $\lambda _{{\rm total}}$ are evaluated for the eight materials with atomic number from $\approx$10 to 79.The results can be utilized as a guide for upper limit of $t$ evaluation in energy-filtering TEM and bright-field TEM and for optimizing electron tomography experiments.

Quantification of STEM Images in High Resolution SEM for Segmented and Pixelated Detectors

The segmented semiconductor detectors for transmitted electrons in ultrahigh resolution scanning electron microscopes allow observing samples in various imaging modes. Typically, two standard modes of objective lens, with and without a magnetic field, differ by their resolution. If the beam deceleration mode is selected, then an electrostatic field around the sample is added. The trajectories of transmitted electrons are influenced by the fields below the sample. The goal of this paper is a quantification of measured images and theoretical study of the capability of the detector to collect signal electrons by its individual segments. Comparison of measured and ray-traced simulated data were difficult in the past. This motivated us to present a new method that enables better comparison of the two datasets at the cost of additional measurements, so-called calibration curves. Furthermore, we also analyze the measurements acquired using 2D pixel array detector (PAD) that provide a more detailed angular profile. We demonstrate that the radial profiles of STEM and/or 2D-PAD data are sensitive to material composition. Moreover, scattering processes are affected by thickness of the sample as well. Hence, comparing the two experimental and simulation data can help to estimate composition or the thickness of the sample.

High Resolution Powder Electron Diffraction in Scanning Electron Microscopy

A modern scanning electron microscope equipped with a pixelated detector of transmitted electrons can record a four-dimensional (4D) dataset containing a two-dimensional (2D) array of 2D nanobeam electron diffraction patterns; this is known as a four-dimensional scanning transmission electron microscopy (4D-STEM). In this work, we introduce a new version of our method called 4D-STEM/PNBD (powder nanobeam diffraction), which yields high-resolution powder diffractograms, whose quality is fully comparable to standard TEM/SAED (selected-area electron diffraction) patterns. Our method converts a complex 4D-STEM dataset measured on a nanocrystalline material to a single 2D powder electron diffractogram, which is easy to process with standard software. The original version of 4D-STEM/PNBD method, which suffered from low resolution, was improved in three important areas: (i) an optimized data collection protocol enables the experimental determination of the point spread function (PSF) of the primary electron beam, (ii) an improved data processing combines an entropy-based filtering of the whole dataset with a PSF-deconvolution of the individual 2D diffractograms and (iii) completely re-written software automates all calculations and requires just a minimal user input. The new method was applied to Au, TbF₃ and TiO₂ nanocrystals and the resolution of the 4D-STEM/PNBD diffractograms was even slightly better than that of TEM/SAED.

Nanoscaled Morphology and Mechanical Properties of a Biomimetic Polymer Surface on a Silicone Hydrogel Contact Lens

Materials taking advantage of the characteristics of biological tissues are strongly sought after in medical science and bioscience. On the natural corneal tissue surface, the highly soft and lubricated surface is maintained by composite structures composed of hydrophilic biomolecules and substrates. To mimic this structure, the surface of a silicone hydrogel contact lens was modified with a biomimetic phospholipid polymer, poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), and the nanoscaled morphology and mechanical properties of the surface were confirmed with advanced surface characterization and imaging techniques under an aqueous medium. Concavities and convexities on the nanometer order were recognized on the surface. The surface was completely covered with a PMPC layer and remained intact even after 30 days of clinical use in a human ocular environment. The mechanical properties of the natural corneal tissue and the PMPC-modified surface were similar in the living environment, that is, low modulus and frictional properties comparable to natural tissues. These results show the validity of material preparation by biomimetic methods. The methodologies developed in this study may contribute to future development of human-friendly medical devices.

Probing Antimicrobial Halloysite/Biopolymer Composites with Electron Microscopy: Advantages and Limitations

Halloysite is a tubular clay nanomaterial of the kaolin group with a characteristic feature of oppositely charged outer and inner surfaces, allowing its selective spatial modification. The natural origin and specific properties of halloysite make it a potent material for inclusion in biopolymer composites with polysaccharides, nucleic acids and proteins. The applications of halloysite/biopolymer composites range from drug delivery and tissue engineering to food packaging and the creation of stable enzyme-based catalysts. Another important application field for the halloysite complexes with biopolymers is surface coatings resistant to formation of microbial biofilms (elaborated communities of various microorganisms attached to biotic or abiotic surfaces and embedded in an extracellular polymeric matrix). Within biofilms, the microorganisms are protected from the action of antibiotics, engendering the problem of hard-to-treat recurrent infectious diseases. The clay/biopolymer composites can be characterized by a number of methods, including dynamic light scattering, thermo gravimetric analysis, Fourier-transform infrared spectroscopy as well as a range of microscopic techniques. However, most of the above methods provide general information about a bulk sample. In contrast, the combination of electron microscopy with energy-dispersive X-ray spectroscopy allows assessment of the appearance and composition of biopolymeric coatings on individual nanotubes or the distribution of the nanotubes in biopolymeric matrices. In this review, recent contributions of electron microscopy to the studies of halloysite/biopolymer composites are reviewed along with the challenges and perspectives in the field.

Powder Nano-Beam Diffraction in Scanning Electron Microscope: Fast and Simple Method for Analysis of Nanoparticle Crystal Structure

We introduce a novel scanning electron microscopy (SEM) method which yields powder electron diffraction patterns. The only requirement is that the SEM microscope must be equipped with a pixelated detector of transmitted electrons. The pixelated detectors for SEM have been commercialized recently. They can be used routinely to collect a high number of electron diffraction patterns from individual nanocrystals and/or locations (this is called four-dimensional scanning transmission electron microscopy (4D-STEM), as we obtain two-dimensional (2D) information for each pixel of the 2D scanning array). Nevertheless, the individual 4D-STEM diffractograms are difficult to analyze due to the random orientation of nanocrystalline material. In our method, all individual diffractograms (showing randomly oriented diffraction spots from a few nanocrystals) are combined into one composite diffraction pattern (showing diffraction rings typical of polycrystalline/powder materials). The final powder diffraction pattern can be analyzed by means of standard programs for TEM/SAED (Selected-Area Electron Diffraction). We called our new method 4D-STEM/PNBD (Powder NanoBeam Diffraction) and applied it to three different systems: Au nano-islands (well diffracting nanocrystals with size ~20 nm), small TbF3 nanocrystals (size < 5 nm), and large NaYF4 nanocrystals (size > 100 nm). In all three cases, the STEM/PNBD results were comparable to those obtained from TEM/SAED. Therefore, the 4D-STEM/PNBD method enables fast and simple analysis of nanocrystalline materials, which opens quite new possibilities in the field of SEM.

Guidelines for Regulated Cell Death Assays: A Systematic Summary, A Categorical Comparison, A Prospective

Over the past few years, the field of regulated cell death continues to expand and novel mechanisms that orchestrate multiple regulated cell death pathways are being unveiled. Meanwhile, researchers are focused on targeting these regulated pathways which are closely associated with various diseases for diagnosis, treatment, and prognosis. However, the complexity of the mechanisms and the difficulties of distinguishing among various regulated types of cell death make it harder to carry out the work and delay its progression. Here, we provide a systematic guideline for the fundamental detection and distinction of the major regulated cell death pathways following morphological, biochemical, and functional perspectives. Moreover, a comprehensive evaluation of different assay methods is critically reviewed, helping researchers to make a reliable selection from among the cell death assays. Also, we highlight the recent events that have demonstrated some novel regulated cell death processes, including newly reported biomarkers (e.g., non-coding RNA, exosomes, and proteins) and detection techniques.

Orientation mapping of graphene using 4D STEM-in-SEM

A scanning diffraction technique is implemented in the scanning electron microscope. The technique, referred to as 4D STEM-in-SEM (four-dimensional scanning transmission electron microscopy in the scanning electron microscope), collects a diffraction pattern from each point on a sample which is saved to disk for further analysis. The diffraction patterns are collected using an on-axis lens-coupled phosphor/CCD arrangement. Synchronization between the electron beam and the camera exposure is accomplished with off-the-shelf data acquisition hardware. Graphene is used as a model system to test the sensitivity of the instrumentation and develop some basic analysis techniques. The data show interpretable diffraction patterns from monolayer graphene with integration times as short as 0.5 ms with a beam current of 245 pA (7.65×105 incident electrons per pixel). Diffraction patterns are collected at a rate of ca. 100/s from the mm to nm length scales. Using a grain boundary as a 'knife-edge', the spatial resolution of the technique is demonstrated to be ≤5.6nm (edge-width 25 % to 75 %). Analysis of the orientation of the diffraction patterns yields an angular (orientation) precision of ≤0.19∘ (full width at half maximum) for unsupported monolayer graphene. In addition, it is demonstrated that the 4D datasets have the information content necessary to analyze complex and heterogeneous multilayer graphene films.

Low energy nano diffraction (LEND) - A versatile diffraction technique in SEM

Electron diffraction is a powerful characterization method that is used across different fields and in different instruments. In particular, the power of transmission electron microscopy (TEM) largely relies on the capability to switch between imaging and diffraction mode enabling identification of crystalline phases and in-depth studies of crystal defects, to name only examples. In contrast, while diffraction techniques have found their way into the realm of scanning electron microscopy (SEM) in the form of electron backscatter diffraction and related techniques, on-axis transmission diffraction is still in its infancy. Here we present a simple but versatile setup that enables a 'diffraction mode' in SEM using a fluorescent screen and a dedicated in vacuo camera. With this setup spot-like nano-beam diffraction patterns of thin samples can be acquired with electron energies as low as 500 eV. We therefore coin the name Low Energy Nano Diffraction (LEND). Diffraction patterns can be recorded from single positions on the sample or integrated over selected areas by adjustable scan patterns. Besides showing the principal application of the technique to standard materials such as gold and silicon we also explore the application to graphene and other 2D materials. Besides single pattern measurements, also full 4D-STEM diffraction mappings are demonstrated. Finally, we show how the integration of a versatile diffraction mode in SEM enables a thorough analysis performed with a single instrument.

Differential electron scattering cross-sections at low electron energies: The influence of screening parameter

For quantitative electron microscopy the comparison of measured and simulated data is essential. Monte Carlo (MC) simulations are well established to calculate the high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) intensities on a non-atomic scale. In this work we focus on the importance of the screening parameter in differential screened Rutherford cross-sections for MC simulations and on the contribution of the screening parameter to the atomic-number dependence of the HAADF-STEM intensity at electron energies ≤ 30 keV. Materials investigated were chosen to cover a wide range of atomic numbers Z to study the Z dependence of the screening parameter. Comparison of measured and simulated HAADF-STEM intensities with different screening parameters known from the literature were tested and failed to generally describe the experimental data. Hence, the screening parameter was adapted to obtain the best match between experimental and MC-simulated HAADF-STEM intensities. The Z dependence of the HAADF-STEM intensity was derived.

The Effects of Vinegar Processing on the Changes in the Physical Properties of Frankincense Related to the Absorption of the Main Boswellic Acids

Boswellic acids (BAs), as the main components of frankincense, exhibit notable anti-inflammatory properties. However, their pharmaceutical development has been severely limited by their poor oral bioavailability. Traditional Chinese medicinal processing, called Pao Zhi, is believed to improve bioavailability, yet the mechanism is still completely unclear. Previous research suggested that the bioavailability of a drug can be influenced by physical properties. This paper was designed to investigate the physical properties of frankincense and processed frankincense, including the surface morphology, particle size, polydispersity index (PDI), zeta potential (ZP), specific surface area, porosity, and viscosity. The differences in the intestinal absorption characteristics and equilibrium solubilities between frankincense and processed frankincense were determined by an ultra-high-performance liquid chromatography coupled with a triple quadrupole electrospray tandem mass spectrometry (UHPLC-TQ-MS) analysis method. The results showed that vinegar processing can alter the surface morphology, decrease the particle size and PDI, raise the absolute values of the ZP, specific surface area and porosity, and drop the viscosity of frankincense. Meanwhile, the rates of absorption and dissolution of the main BAs were increased after the processing of frankincense. The present study proves that the physical properties were changed after processing, in which case the bioavailability of frankincense was enhanced.

Improving the imaging capability of an on-axis transmission Kikuchi detector

Transmission Kikuchi Diffraction (TKD) in the scanning electron microscope has been developing at a fast pace since its introduction less than a decade ago. The recently presented on-axis detector configuration, with its optimized geometry, has significantly increased the signal yield and facilitated the acquisition of STEM images in bright field (BF) and dark field (DF) mode, in addition to the automated orientation mapping of nanocrystalline electron transparent samples. However, the physical position of the integrated imaging system, located outside the detector screen, requires its movement in order to combine high resolution STEM images with high resolution orientation measurements. The difference between the two positions makes it impossible to acquire optimal signals simultaneously, leading to challenges when investigating site-specific nanocrystalline microstructures. To eliminate this drawback, a new imaging capability was added at the centre of the on-axis TKD detector, thus enabling acquisition of optimal quality BF images and orientation maps without detector movement. The advantages brought about by this new configuration are presented and the associated limitations are discussed.

Electron beam broadening in electron-transparent samples at low electron energies

Scanning transmission electron microscopy (STEM) at low primary electron energies has received increasing attention in recent years because knock-on damage can be avoided and high contrast for weakly scattering materials is obtained. However, the broadening of the electron beam in the sample is pronounced at low electron energies, which degrades resolution and limits the maximum specimen thickness. In this work, we have studied electron beam broadening in materials with atomic numbers Z between 10 and 32 (MgO, Si, SrTiO₃ , Ge) and thicknesses up to 900 nm. Beam broadening is directly measured using a multisegmented STEM detector installed in a scanning electron microscope at electron energies between 15 and 30 keV. For experimental reasons, the electron beam diameter is defined to contain only 68% of the total intensity instead of the commonly used 90% of the total beam intensity. The measured beam diameters can be well described with calculated ones based on a recently published model by Gauvin and Rudinsky. Using the concept of anomalous diffusion the Hurst exponent H is introduced that varies between 0.5 and 1 for different scattering regimes depending on t/Λ_el with the specimen thickness t and the elastic mean free path length Λ_el . The calculations also depend on the fraction of the beam intensity that defines the electron beam diameter. A Hurst exponent H of 1 is characteristic for the ballistic scattering regime with t/Λ_el → 0 and can be excluded for the experimental conditions of our study with 6 ≦ t/Λ_el ≦ 30. We deduced H = 0.75 from measured beam diameters which is larger than H = 0.5 that is expected under diffusion conditions. The deviation towards larger H values can be rationalised by our definition of electron diameter that contains only 68% of the total beam intensity and requires therefore larger sample thicknesses before the diffusion regime is reached. Our results clearly deviate from previous analytical approaches to describe beam broadening (Goldstein et al., Reed, Williams et al., Kohl and Reimer). Measured beam diameters are compared with simulated ones, which are obtained by solving the electron transport equation. This approach is advantageous compared to the commonly used Monte Carlo simulations because it is an exact solution of the electron transport equation and requires less computer time. Simulated beam diameter agree well with the experimental data and yield H = 0.80. LAY DESCRIPTION: In scanning transmission electron microscopy (STEM), a focused electron beam is scanned over an electron-transparent sample and an image is formed by detecting the intensity of the transmitted electrons by a STEM detector. STEM resolution is ultimately limited by the electron beam diameter and can be better than 0.1 nm for the best microscopes. However, the electron-beam diameter increases with increasing specimen thickness because electrons are scattered by the interaction of the specimen material and electrons. Electron scattering leads to a change of the electron propagation direction and reduces focusing of the electron beam. The associated electron-beam broadening degrades the lateral resolution of STEM and generally limits the maximum specimen thickness that can be imaged with good resolution. STEM is up to now mainly performed at high electron energies of 80 keV and above. Lower electron energies are beneficial for the study of weakly scattering and radiation-sensitive materials but electron beam broadening becomes more pronounced with decreasing electron energies. Knowledge of beam broadening is therefore particularly important for the interpretation of STEM images that are taken with low-energy electrons. In this work we have studied electron-beam broadening in different materials with thicknesses up to 900 nm at low electron energies between 15  and 30 keV. Beam broadening is directly measured with a newly developed technique. We compare measured beam diameters with different models on beam broadening from literature and find that only a recently published model is well suited to describe the experimental results under our experimental conditions. In addition, beam broadening is simulated by modelling electron propagation in the specimen. The simulation results agree well with the measured beam diameters.

Analysis of crystal defects by scanning transmission electron microscopy (STEM) in a modern scanning electron microscope

Dislocations and stacking faults are important crystal defects, because they strongly influence material properties. As of now, transmission electron microscopy (TEM) is the most frequently used technique to study the properties of single dislocations and stacking faults. Specifically, the Burgers vector b of dislocations or displacement vector R of stacking faults can be determined on the basis of the g·b = n (g·R = n) criterion by setting up different two-beam diffraction conditions with an imaging vector g. Based on the reciprocity theorem, scanning transmission electron microscopy (STEM) can also be applied for defect characterization, but has been less frequently used up to now. In this work, we demonstrate g·b = n (g·R = n) analyses of dislocations and stacking faults in GaN by STEM imaging in a scanning electron microscope. The instrument is equipped with a STEM detector, double-tilt TEM specimen holder, and a charge-coupled-device camera for the acquisition of on-axis diffraction patterns. The latter two accessories are mandatory to control the specimen orientation, which has not been possible before in a scanning electron microscope.

Three-Dimensional Reconstruction of Erythrocytes Using the Novel Method For Corrective Realignment of the Transmission Electron Microscopy Cross-Section Images

The detailed kinetics study of erythrocyte deformability is useful for the early diagnosis of blood diseases and for monitoring the blood rheology. Present solutions for a three-dimensional (3D) reconstruction of erythrocytes has a limited potential. This study aimed to use erythrocyte transmission electron images (ETIs) to evaluate the morphological relationship between adjacent ETIs and generate erythrocytes 3D model. First, ultrathin serial sections of skeletal muscle tissue were obtained using an ultramicrotome. Further, the set of ETIs in a capillary were captured by transmission electron microscopy. The images were aligned by translations and rotations using custom software to optimize the morphological relationship between adjacent ETIs. These coordinate transformations exploit the unique principal axis of inertia of each image to define the body coordinate system and hence provide the means to accurately reconnect the adjacent ETIs. The sum of the distances between the corresponding points on the boundary of adjacent ETIs was minimized and, further, was optimized by using physiological relationship between the adjacent ETIs. The analysis allowed to define precise virtual relationship between the adjacent erythrocytes. Finally, extracted erythrocytes' cross-section images allowed to generate 3D model of the erythrocytes.