Machine Learning Refinement of In Situ Images Acquired by Low Electron Dose LC-TEM.

We have studied a machine learning (ML) technique for refining images acquired during in situ observation using liquid-cell transmission electron microscopy. Our model is constructed using a U-Net architecture and a ResNet encoder. For training our ML model, we prepared an original image dataset that contained pairs of images of samples acquired with and without a solution present. The former images were used as noisy images, and the latter images were used as corresponding ground truth images. The number of pairs of image sets was 1,204, and the image sets included images acquired at several different magnifications and electron doses. The trained model converted a noisy image into a clear image. The time necessary for the conversion was on the order of 10 ms, and we applied the model to in situ observations using the software Gatan DigitalMicrograph (DM). Even if a nanoparticle was not visible in a view window in the DM software because of the low electron dose, it was visible in a successive refined image generated by our ML model.

Chiral Spinodal-like Ordering of Homoimmiscible Water at Interface between Water and Chiral Ice III.

Diversity in structures of water endowed by a hydrogen-bonding network plays crucial roles in wide varieties of phenomena in nature. Chiral ordering of water molecules is an intriguing phenomenon from the viewpoint of bimolecular functions. However, experimental reports on chiral ordering have been limited to the water molecules interacting with biomolecules on the molecular scale. It remains unclear whether pure liquid water forms long-range chiral ordering without any interaction with biomolecules. Here, we show that chiral anisotropy can be observed in the macro/mesoscopic network pattern of an unknown water layer formed via spinodal phase separation-like dynamics at the interface between water and ice III with a chiral crystal structure. We named this unknown water homoimmiscible water. Our observations infer that the unknown water is a chiral liquid crystal. This possibility opens new avenues for a wide variety of research fields such as liquid polymorphism, biology, earth and planetary science, and so forth from the perspective of chirality.

Dissolution enables dolomite crystal growth near ambient conditions.

Crystals grow in supersaturated solutions. A mysterious counterexample is dolomite CaMg(CO3)2, a geologically abundant sedimentary mineral that does not readily grow at ambient conditions, not even under highly supersaturated solutions. Using atomistic simulations, we show that dolomite initially precipitates a cation-disordered surface, where high surface strains inhibit further crystal growth. However, mild undersaturation will preferentially dissolve these disordered regions, enabling increased order upon reprecipitation. Our simulations predict that frequent cycling of a solution between supersaturation and undersaturation can accelerate dolomite growth by up to seven orders of magnitude. We validated our theory with in situ liquid cell transmission electron microscopy, directly observing bulk dolomite growth after pulses of dissolution. This mechanism explains why modern dolomite is primarily found in natural environments with pH or salinity fluctuations. More generally, it reveals that the growth and ripening of defect-free crystals can be facilitated by deliberate periods of mild dissolution.

Anisotropy in spinodal-like dynamics of unknown water at ice V-water interface.

Experimentally demonstrating the existence of waters with local structures unlike that of common water is critical for understanding both the origin of the mysterious properties of water and liquid polymorphism in single component liquids. At the interfaces between water and ices Ih, III, and VI grown/melted under pressure, we previously discovered low- and high-density unknown waters, that are immiscible with the surrounding water. Here, we show, by in-situ optical microscopy, that an unknown water appears at the ice V-water interface via spinodal-like dynamics. The dewetting dynamics of the unknown water indicate that its characteristic velocity is ~ 90 m/s. The time evolution of the characteristic length of the spinodal-like undulation suggests that the dynamics may be described by a common model for spinodal decomposition of an immiscible liquid mixture. Spinodal-like dewetting dynamics of the unknown water transiently showed anisotropy, implying the property of a liquid crystal.

In Situ Transmission Electron Microscopy Study of Bubble Behavior Near the Surface of Ice Crystals by Using a Liquid Cell With a Peltier Cooling Holder.

Liquid cell transmission electron microscopy (LC-TEM) is a unique technique that permits in situ observations of various phenomena in liquids with high spatial and temporal resolutions. One difficulty with this technique is the control of the environmental conditions in the observation area. Control of the temperature ranging from room temperature to minus several tens of degrees Celsius, is desirable for controlling the supersaturation in various materials and for observing crystallization more easily. We have developed a cooling transmission electron microscopy specimen holder that uses Peltier devices, and we have combined it with a liquid cell to realize accurate temperature control in LC-TEM. We evaluated this system by using water as a specimen. Motionless bubbles, shown to be voids containing pressurized gas, formed in the specimen sometime after the temperature had reached -12°C. An electron diffraction pattern showed that the specimen turned into ice Ih after the formation of these bubbles, confirming that our system works properly and can induce crystallization. In addition, we analyzed the behavior of bubbles formed in the ice Ih, and we discussed the formation of these bubbles and their internal pressure.

Limited proteolysis of mycobacterial DNA-binding protein 1 with an extended, lysine-rich, intrinsically disordered region to unveil posttranslational modifications.

The basic, intrinsically disordered regions of eukaryotic histones and their bacterial counterparts are presumed to act as signaling hubs to regulate the compaction of chromosomes or nucleoids and various DNA processes such as gene expression, recombination, and DNA replication. Posttranslational modifications (PTMs) on these regions are pivotal in regulating chromosomal or nucleoid compaction and DNA processes. However, the low sequence complexity and the presence of short lysine-rich repeats in the regions have hindered the accurate determination of types and locations of PTMs using conventional proteomic procedures. We described a limited proteolysis protocol using trypsin to analyze PTMs on mycobacterial DNA-binding protein 1 (MDP1), a nucleoid-associated protein in mycobacterial species that possesses an extended, lysine-rich, intrinsically disordered region in its C-terminal domain. This limited proteolysis approach successfully revealed significant methylation on many lysine residues in the C-terminal domain of MDP1 purified from Mycobacterium tuberculosis, which was lacking in the corresponding region of recombinant MDP1 expressed in Escherichia coli.

Antibodies against native proteins of Mycobacterium tuberculosis can detect pulmonary tuberculosis patients.

Accurate point-of-care testing (POCT) is critical for managing tuberculosis (TB). However, current antibody-based diagnosis shows low specificity and sensitivity. To find proper antigen candidates for TB diagnosis by antibodies, we assessed IgGs responsiveness to Mycobacterium tuberculosis proteins in pulmonary TB (PTB) patients. We employed major secreted proteins, such as Rv1860, Ag85C, PstS1, Rv2878c, Ag85B, and Rv1926c that were directly purified from M. tuberculosis. In the first screening, we found that IgG levels were significantly elevated in PTB patients only against Rv1860, PstS1, and Ag85B among tested antigens. However, recombinant PstS1 and Ag85B from Escherichia coli (E. coli) couldn't distinguish PTB patients and healthy controls (HC). Recombinant Rv1860 was not checked due to its little expression. Then, the 59 confirmed PTB patients from Soetomo General Academic Hospital, Surabaya, Indonesia, and 102 HC were tested to Rv1860 and Ag85B only due to the low yield of the PstS1 from M. tuberculosis. The ROC analysis using native Ag85B and Rv1860 showed an acceptable area under curve for diagnosis, which is 0.812 (95% CI 0.734-0.890, p < 0.0001) and 0.821 (95% CI 0.752-0.890, p < 0.0001). This study indicates that taking consideration of native protein structure is key in developing TB's POCT by antibody-based diagnosis.

Low- and High-Density Unknown Waters at Ice-Water Interfaces.

Experimental confirmation of liquid polymorphs of water, high-density liquid (HDL) and low-density liquid (LDL), is desired for understanding not only the liquid state of matter but also the origin of the mysterious properties of water. However, this remains challenging because the liquid-liquid critical point of water lies in experimentally inaccessible supercooling conditions known as "no man's land". Here, we show by in situ optical microscopy that droplets and layers of low- and high-density unknown waters (LDUW and HDUW) appear macroscopically depending upon ice polymorphs at non-equilibrium interfaces between water and ices under experimentally accessible (de)pressurization conditions. These unknown waters were found to have characteristic velocities (about 20 and 100 m/s for LDUW and HDUW, respectively) different from water (about 40 m/s) and quasi-liquid layers (QLLs) (about 2 and 0.2 m/s for droplet and layer forms of QLLs, respectively). Our discoveries provide insight on liquid polymorphism of water.

Feasibility of control of particle assembly by dielectrophoresis in liquid-cell transmission electron microscopy.

Liquid-cell transmission electron microscopy (LC-TEM) is a useful technique for observing phenomena in liquid samples with spatial and temporal resolutions similar to those of conventional transmission electron microscopy (TEM). This method is therefore expected to permit the visualization of phenomena previously inaccessible to conventional optical microscopy. However, dynamic processes such as nucleation are difficult to observe by this method because of difficulties in controlling the condition of the sample liquid in the observation area. To approach this problem, we focused on dielectrophoresis, in which electrodes are used to assemble particles, and we investigated the phenomena that occurred when an alternating-current signal was applied to an electrode in an existing liquid cell by using a phase-contrast optical microscope (PCM) and TEM. In PCM, we observed that colloidal particles in a solution were attracted to the electrodes to form assemblies, that the particles aligned along the electric field to form pearl chains and that the pearl chains accumulated to form colloidal crystals. However, these phenomena were not observed in the TEM study because of differences in the design of the relevant holders. The results of our study imply that the particle assembly by using dielectrophoretic forces in LC-TEM should be possible, but further studies, including electric device development, will be required to realize this in practice.

Possible embryos and precursors of crystalline nuclei of calcium carbonate observed by liquid-cell transmission electron microscopy.

Several different building blocks or precursors play an important role in the early stages of the crystallization of calcium carbonate (CaCO3). Many studies have been conducted over a long period to elucidate the fundamental processes involved in this crystallization. Here, we report the role of an amorphous phase and embryo at the beginning of the nucleation of CaCO3 from solutions of relatively low supersaturation. Prenucleation crystals formed in amorphous calcium carbonate (ACC) at a significantly large formation rate of 2 × 1022 m-3 s-1, suggesting that a low interfacial energy exists between the ACC and crystals. Only one calcite crystal exceeded the size for a critical nucleus (∼104 molecules) in 150 pre-nucleation crystals. Each pre-nucleation crystal might consist of a different polymorph, and ACCs have a similar composition and structure. A particle-detection algorithm, used in conjunction with machine learning, suggested that an embryo with a characteristic structure exists in solution and might play a crucial role in nucleation. No similar embryonic structure could be observed immediately after the dissolution of pre-nucleation particles, implying that their dissolution process is not simply the reverse process of their growth. This method should provide a new approach to understanding nucleation processes.

Early Detection of Nucleation Events From Solution in LC-TEM by Machine Learning.

To support the detection, recording, and analysis of nucleation events during in situ observations, we developed an early detection system for nucleation events observed using a liquid-cell transmission electron microscope. Detectability was achieved using the machine learning equivalent of detection by humans watching a video numerous times. The detection system was applied to the nucleation of sodium chloride crystals from a saturated acetone solution of sodium chlorate. Nanoparticles with a radius of more greater than 150 nm were detected in a viewing area of 12 µm × 12 µm by the detection system. The analysis of the change in the size of the growing particles as a function of time suggested that the crystal phase of the particles with a radius smaller than 400 nm differed from that of the crystals larger than 400 nm. Moreover, the use of machine learning enabled the detection of numerous nanometer sized nuclei. The nucleation rate estimated from the machine-learning-based detection was of the same order as that estimated from the detection using manual procedures.

Fast Improvement of TEM Images with Low-Dose Electrons by Deep Learning.

Low electron dose observation is indispensable for observing various samples using a transmission electron microscope; consequently, image processing has been used to improve transmission electron microscopy (TEM) images. To apply such image processing to in situ observations, we here apply a convolutional neural network to TEM imaging. Using a dataset that includes short-exposure images and long-exposure images, we develop a pipeline for processed short-exposure images, based on end-to-end training. The quality of images acquired with a total dose of approximately $5$$e^{-}$ per pixel becomes comparable to that of images acquired with a total dose of approximately $1{,}000$$e^{-}$ per pixel. Because the conversion time is approximately 8 ms, in situ observation at 125 fps is possible. This imaging technique enables in situ observation of electron-beam-sensitive specimens.

UV-Induced Formation of Ice XI Observed Using an Ultra-High Vacuum Cryogenic Transmission Electron Microscope and its Implications for Planetary Science.

The occurrence of hydrogen atom-ordered form of ice Ih, ice XI, in the outer Solar System has been discussed based on laboratory experiments because its ferroelectricity influences the physical processes in the outer Solar System. However, the formation of ice XI in that region is still unknown due to a lack of formation conditions at temperatures higher than 72 K and the effect of UV-rays on the phase transition from ice I to ice XI. As a result, we observed the UV-irradiation process on ice Ih and ice Ic using a newly developed ultra-high vacuum cryogenic transmission electron microscope. We found that ice Ih transformed to ice XI at temperatures between 75 and 140 K with a relatively small UV dose. Although ice Ic partially transformed to ice XI at 83 K, the rate of transformation was slower than for ice Ih. These findings point to the formation of ice XI at temperatures greater than 72 K via UV irradiation of ice I crystals in the Solar System; icy grains and the surfaces of icy satellites in the Jovian and Saturnian regions.

Radiolysis-Induced Crystallization of Sodium Chloride in Acetone by Electron Beam Irradiation.

In situ liquid cell transmission electron microscopy (LC-TEM) is an innovative method for studying the processes involved in the formation of crystals in liquids. However, it is difficult to capture early stages of crystallization because of the small field of view and the unfavorable changes in sample composition resulting from electron-beam radiolysis. Nevertheless, if the radiolysis required to induce the crystallization of a sample could be controlled in LC-TEM, this would be advantageous for observing the crystallization process. Here, we examined this possibility by using a mixture of sodium chlorate (NaClO3) and acetone in the LC-TEM. The electron beam induced the formation of dendritic crystals in a saturated acetone solution of NaClO3; moreover, these crystals consisted of sodium chloride (NaCl), rather than NaClO3, suggesting that chloride ions (Cl−), which were not present in the initial solution, were generated by radiolysis of chlorate ions ${\rm \lpar ClO}_3^- \rpar$. As a result, the solution then supersaturated with NaCl because its solubility in acetone is much lower than that of NaClO3. The combination of radiolysis and a solvent in which a solute is much less soluble is potentially useful for establishing crystallization conditions for materials that are difficult to crystallize directly in LC-TEM experiments.

Time-Resolved Observation of Evolution of Amyloid-ß Oligomer with Temporary Salt Crystals.

The aggregation behavior of amyloid-ß (Aß) peptides remains unclarified despite the fact that it is closely related to the pathogenic mechanism of Alzheimer's disease. Aß peptides form diverse oligomers with various diameters before nucleation, making clarification of the mechanism involved a complex problem with conventional macroscopic analysis methods. Time-resolved single-molecule level analysis in bulk solution is thus required to fully understand their early stage aggregation behavior. Here, we perform time-resolved observation of the aggregation dynamics of Aß oligomers in bulk solution using liquid-state transmission electron microscopy. Our observations reveal previously unknown behaviors. The most important discovery is that a salt crystal can precipitate even with a concentration much lower than its solubility, and it then dissolves in a short time, during which the aggregation reaction of Aß peptides is significantly accelerated. These findings will provide new insights in the evolution of the Aß oligomer.

High-Density Liquid Water at a Water-Ice Interface.

Because ice surfaces catalyze various key chemical reactions impacting nature and human life, the structure and dynamics of interfacial layers between water vapor and ice have been extensively debated with attention to the quasi-liquid layer. Other interfaces between liquid water and ice remain relatively underexplored, despite their importance and abundance on the Earth and icy extraterrestrial bodies. By in situ optical microscopy, we found that a high-density liquid layer, distinguishable from bulk water, formed at the interface between water and high-pressure ice III or VI, when they were grown or melted in a sapphire anvil cell. The liquid layer showed a bicontinuous pattern, indicating that immiscible waters with distinct structures were separated on the interfaces in a similar manner to liquid-liquid phase separation through spinodal decomposition. Our observations not only provide a novel opportunity to explore ice surfaces but also give insight into the two kinds of structured water.

High mobility of lattice molecules and defects during the early stage of protein crystallization.

Protein crystals are expected to be useful not only for their molecular structure analysis but also as functional materials due to their unique properties. Although the generation and the propagation of defects during crystallization play critical roles in the final properties of protein crystals, the dynamics of these processes are poorly understood. By time-resolved liquid-cell transmission electron microscopy, we observed that nanosized crystal defects are surprisingly mobile during the early stages of the crystallization of a lysozyme as a model protein. This highly dynamic behavior of defects reveals that the lattice molecules are mobile throughout the crystal structure. Moreover, the disappearance of the defects indicated that intermolecular bonds can break and reform rapidly with little energetic cost, as reported in theoretical studies. All these findings are in marked contrast to the generally accepted notion that crystal lattices are rigid with very limited mobility of individual lattice molecules.

Sounding-rocket microgravity experiments on alumina dust.

Alumina (Al2O3) is believed to be the first major condensate to form in the gas outflow from oxygen-rich evolved stars because of the refractoriness and that α-Al2O3 (corundum, most stable polymorph) is a potential origin of a 13 µm feature that appears close to stars. However, no one has directly reproduced the 13 µm feature experimentally, and it has remained as a noteworthy unidentified infrared band. Here, we report nucleation experiments on Al2O3 nanoparticles monitored by a specially designed infrared spectrometer in the microgravity environment of a sounding rocket. The conditions approximate to those around asymptotic giant branch (AGB) stars. The measured spectra of the nucleated Al2O3 show a sharp feature at a wavelength of 13.55 µm and comparable in width to that observed near oxygen-rich AGB stars. Our finding that α-Al2O3 nucleates under certain condition provides a solid basis to elaborate condensation models of dust around oxygen-rich evolved stars.

Self-assembly of MoO3 needles in gas current for cubic formation pathway.

Nucleation and subsequent rapid growth are enigmatic due to the unrevealed pathways. Despite the relatively simpler mechanism compared to nucleation and growth in solution, that in vapor has received little attention. The largest hindrance to unveiling this process may be observing the rapid and mesoscopic-scale phenomena. To overcome this hindrance, we combine an experimental approach with in situ spatial scanning Fourier-transform infrared spectroscopy, which reveals the nucleating and growing nanoparticles in vapor. The nanoparticles are then collected at different evolutionary stages and analyzed by ex situ transmission electron microscopy (TEM). Needle-shaped molybdenum oxide (MoO3) nanoparticles were formed within ∼0.1 s after homogeneous nucleation from a highly supersaturated vapor. Over one second, the needle particles gradually evolved into a cubic shape by fusion in a crystallographically favored orientation in a free-flying state in vapor. The similar sizes of the elongated axes of the needle and cubic structures suggest an additional growth stage, in which the needle particles become the growth units of the cubic particles. The morphology of a final crystal should reflect the formation environment of the particle because growing crystals are sensitive to the formation conditions such as temperature, concentration, and impurities. Although nucleation under very high supersaturation induces the anisotropic growth of the needle particles, this information of the initial nucleation environment is lost in the final cubic crystal. These findings enrich our understanding of pathways in the nucleation and growth of nanoparticles and provide new insights into the growth stages driven by oriented attachment.

Fast crystalline ice formation at extremely low temperature through water/neon matrix sublimation.

Crystalline ice formation requires water molecules to be sufficiently mobile to find and settle on the thermodynamically most stable site. Upon cooling, however, diffusion and rearrangement become increasingly kinetically difficult. Water ice grown by the condensation of water vapor in laboratory is thus generally assumed to be in a metastable amorphous form below 100 K. Here, we demonstrate the possibility of crystalline ice formation at extremely low temperature using a water/neon matrix (1/1000, 30 000 monolayers) prepared at 6 K, which is subsequently warmed to 11-12 K. In situ infrared spectroscopy revealed the assembly of the dispersed water molecules, forming crystalline ice I during the sublimation of the neon matrix for 40-250 seconds. This finding indicates that the high mobility of the water molecules during matrix sublimation can overcome the kinetic barrier to form crystals even at extremely low temperature.