Deep generative priors for biomolecular 3D heterogeneous reconstruction from cryo-EM projections.

Cryo-electron microscopy has become a powerful tool to determine three-dimensional (3D) structures of rigid biological macromolecules from noisy micrographs with single-particle reconstruction. Recently, deep neural networks, e.g., CryoDRGN, have demonstrated conformational and compositional heterogeneity of complexes. However, the lack of ground-truth conformations poses a challenge to assess the performance of heterogeneity analysis methods. In this work, variational autoencoders (VAE) with three types of deep generative priors were learned for latent variable inference and heterogeneous 3D reconstruction via Bayesian inference. More specifically, VAEs with "Variational Mixture of Posteriors" priors (VampPrior-SPR), non-parametric exemplar-based priors (ExemplarPrior-SPR) and priors from latent score-based generative models (LSGM-SPR) were quantitatively compared with CryoDRGN. We built four simulated datasets composed of hypothetical continuous conformation or discrete states of the hERG K + channel. Empirical and quantitative comparisons of inferred latent representations were performed with affine-transformation-based metrics. These models with more informative priors gave better regularized, interpretable factorized latent representations with better conserved pairwise distances, less deformed latent distributions and lower within-cluster variances. They were also tested on experimental datasets to resolve compositional and conformational heterogeneity (50S ribosome assembly, cowpea chlorotic mottle virus, and pre-catalytic spliceosome) with comparable high resolution. Codes and data are available: https://github.com/benjamin3344/DGP-SPR.

Defect-Induced Secondary Crystals Drive Two-Dimensional to Three-Dimensional Morphological Evolution in the Co-Self-Assembly of Polyferrocenylsilane Block Copolymer and Homopolymer.

Bottom-up fabrication protocols for uniform 3D hierarchical structures in solution are rare. We report two different approaches to fabricate uniform 3D spherulites and their precursors using mixtures of poly(ferrocenyldimethylsilane) (PFS) block copolymer (BCP) and PFS homopolymer (HP). Both protocols are designed to promote defects in 2D assemblies that serve as intermediate structures. In a multistep seeded growth protocol, we add the BCP/HP mixture to (1D) rod-like PFS micelles in a selective solvent as first-generation seeds. This leads to 2D platelet structures. If this step is conducted at a high supersaturation, secondary crystals form on the basal surface of these platelets. Co-crystallization and rapid crystallization of BCP/HP promote the formation of defects that act as nucleation sites for secondary crystals, resulting in multilayer platelets. This is the key step. The multilayer platelets serve as second-generation seeds upon subsequent addition of BCP/HP blends and, with increasing supersaturation, lead to the sequential formation of uniform (3D) hedrites, sheaves, and spherulites. Similar structures can also be obtained by a simple one-pot direct self-assembly (heating-cooling-aging) protocol of PFS BCP/HP blends. In this case, for a carefully chosen but narrow temperature range, PFS HPs nucleate formation of uniform structures, and the annealing temperature regulates the supersaturation level. In both protocols, the competitive crystallization kinetics of HP/BCP affects the morphology. Both protocols exhibit broad generality. We believe the morphological transformation from 2D to 3D structures, regulated by defect formation, co-crystallization, and supersaturation levels, could apply to various semicrystalline polymers. Moreover, the 3D structures are sufficiently robust to serve as recoverable carriers for nanoparticle catalysts, exhibiting valuable catalytic activity and opening new possibilities for applications requiring exquisite 3D structures.

Polyferrocenylsilane Block Copolymer Spherulites in Dilute Solution.

Self-assembly of block copolymers (BCP) into uniform 3D structures in solution is an extremely rare phenomenon. Furthermore, the investigation of general prerequisites for fabricating a specific uniform 3D structure remains unknown and challenging. Here, through a simple one-pot direct self-assembly (heating and cooling) protocol, we show that uniform spherulite-like structures and their precursors can be prepared with various poly(ferrocenyldimethylsilane) (PFS) BCPs in a variety of polar and non-polar solvents. These structures all evolve from elongated lamellae into hedrites, sheaf-like micelles, and finally spherulites as the annealing temperature and supersaturation degree are increased. The key feature leading to this growth trajectory is the formation of secondary crystals by self-nucleation on the surface of early-elongated lamellae. We identified general prerequisites for fabricating PFS BCP spherulites in solution. These include corona/PFS core block ratios in the range of 1-5.5 that favor the formation of 2D structures as well as the development of secondary crystals on the basal faces of platelets at early stages of the self-assembly. The one-pot direct self-assembly provides a general protocol to form uniform spherulites and their precursors consisting of PFS BCPs that match these prerequisites. In addition, we show that manipulation of various steps in the direct self-assembly protocol can regulate the size and shape of the structures formed. These general concepts show promise for the fabrication and optimization of spherulites and their precursors from semicrystalline BCPs with interesting optical, electronic, or biomedical properties using the one-pot direct self-assembly protocol.

"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture.

The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.

Uniform 1D Micelles and Patchy & Block Comicelles via Scalable, One-Step Crystallization-Driven Block Copolymer Self-Assembly.

Fiber-like (1D) core-crystalline micelles of uniform length can be obtained in protocols involving multiple steps from block copolymers (BCPs) in which crystallization of the core-forming polymer drives the self-assembly. Here we report a systematic study that shows that adding small amounts (<5 w/w%) of a homopolymer corresponding to the core-forming block of the BCP enables uniform 1D micelles (mean lengths Ln = 0.6 to 9.7 µm) to be obtained in a single step, simply by heating the mixture in a selective solvent followed by slow cooling. A series of poly(ferrocenyldimethylsilane) (PFS) BCPs with different corona-forming blocks and different compositions as well as PFS homopolymers of different lengths were examined. Dye labeling and confocal fluorescence microscopy showed that the homopolymer ends up in the center of the micelle, signaling that it served as the initial seed for epitaxial micelle growth. The rate of unimer addition was strongly enhanced by the length of the PFS block, and this enabled more complex structures to be formed in one-pot self-assembly experiments from mixtures of two or three BCPs with different PFS block lengths. Furthermore, BCP mixtures that included PFS-b-PI (PI = polyisoprene) and PFS-b-PDMS with similar PFS block lengths resulted in simultaneous addition to growing micelles, resulting in a patchy block that could be visualized by staining the vinyl groups of the PI with Pt nanoparticles. This approach also enabled scale up, so that uniform 1D micelles of controlled architecture can be obtained at concentrations of 10 w/w % solids or more.

Influence of the Sodium Precursor on the Cubic-to-Hexagonal Phase Transformation and Controlled Preparation of Uniform NaNdF4 Nanoparticles.

NaLnF4 nanoparticles (NPs) with lighter lanthanides (where Ln = La, Ce, Nd, or Pr) are more difficult to prepare than those with heavier lanthanides [Naduviledathu et al. Chem Mater., 2014, 26, 5689]. Our knowledge is weakest for NaLnF4 NPs with the lowest atomic mass lanthanides (Yan's group 1: La to Nd) and more advanced for group 2 (Sm to Tb) NaLnF4 NPs [Mai et al., J. Am. Chem. Soc., 2006, 128, 6426]. Here we focus on the synthesis of NaNdF4 NPs. We employed the high-temperature chemical coprecipitation method and explored the influence of a wide range of synthesis parameters (e.g., reaction time and temperature, precursor ratios (Na+/Nd3+ and F-/Nd3+), choice of a sodium precursor (Na-oleate or NaOH), and the amount of oleic acid) on the size and uniformity of the NPs obtained. We tried to identify "sweet spots" in the reaction space that led to uniform NaNdF4 NPs with sizes appropriate for mass tag applications in mass cytometry. We were able to obtain NPs with a variety of sizes in the range of 5-38 nm with several different shapes (e.g., polyhedra, spheres, and rods). XRD patterns recorded for aliquots collected at different reaction time intervals revealed that NaNdF4 nucleated in the cubic phase (α) and then transformed to the hexagonal phase (ß) as the reaction progressed up to 2 h. A very striking observation was that the NPs synthesized using NaOH as a reactant preferred to remain in the α-phase, and for a lower reaction temperature (285 °C), did not undergo a phase transformation to the ß-phase over 2 h of reaction time. Under similar experimental conditions, NPs prepared using Na-oleate exhibited an α → ß phase transformation. Nevertheless, NaNdF4 NPs prepared at a higher temperature (315 °C) using either of the Na+ precursors exhibited the α → ß phase transformation over time. This transition, however, appeared to be faster in the case of the NPs synthesized using Na-oleate. We found that, in many instances, syntheses carried out using Na-oleate produced more uniform NPs compared to those synthesized using NaOH. Under the conditions we employed for the Na-oleate precursor, the NPs initially formed were polydisperse spheres that evolved into irregular polyhedra and eventually formed more uniform rod-shaped NPs. The aspect ratio of the final NPs depended on the Na+/Nd3+ precursor ratio. High-resolution transmission electron micrographs and corresponding fast Fourier transform of the data provided information about the preferred growth direction of the NaNdF4 nanorods.

Spherulite-Like Micelles.

One-dimensional (1D) and 2D structures by crystallization-driven self-assembly of block copolymers (BCPs) can form fascinating hierarchical structures through secondary self-assembly. But examples of 3D structures formed via hierarchical self-assembly are rare. Here we report seeded growth experiments in decane of a poly(ferrocenyldimethylsilane) BCP with an amphiphilic corona forming block in which lenticular platelets grow into classic spherulite-like uniform colloidally stable structures. These 3D objects are spherically symmetric on the exterior, but asymmetric near the core, where there is a more open structure consisting of sheaf-like leaves. The most remarkable aspect of these experiments is that growth stops at different stages of growth process, depending upon how much unimer is added in the seeded growth step. The system provides a model for studying spherulitic growth where real-time observations on their growth at different stages remains challenging.

Conversion of Metal-Organic Cage to Ligand-Free Ultrasmall Noble Metal Nanocluster Catalysts Confined within Mesoporous Silica Nanoparticle Supports.

Supported ultrasmall noble metal nanocluster-based (UNMN-based) catalysts are one of the most important classes of solid materials for heterogeneous catalysis. In this work, we present a novel strategy for the controlled synthesis of ligand-free UNMN nanocatalysts based on in situ reduction of a palladium-based (Pd-based) metal-organic cage (MOC) confined within monosized, thiol-modified mesoporous silica nanoparticle (MSN) supports. By taking advantage of the high mutual solubility of MOCs and MSNs in DMSO and the strong interactions between the thiol-modified MSN pore wall and MOC surface, a good dispersion of MOC molecules was achieved throughout the MSN support. The close correspondence of the MSN pore diameter (ca. 5.0 nm) with the diameter of the MOC (ca. 4.0 nm) confines MOC packing to approximately a monolayer. Based on this spatial constraint and electrostatic binding of the MOC to the thiol-modified MSN pore surface, in situ MOC reduction followed by metal atom diffusion, coalescence, and anchoring on the active sites resulted in ligand-free Pd-based UNMNs of approximately 0.9 ± 0.2 nm in diameter decorating the MSN pore surfaces. Control experiments of the reduction of a conventional palladium source or the reduction of free, unconstrained cages in solution under the same conditions only produced large metal nanocrystals (NP, >2 nm), confirming the importance of confined reduction to achieve a highly catalytically active surface. In light of this strategy, two catalytic experiments including the reaction of 4-nitrophenol to 4-aminophenol and the Suzuki C-C coupling reaction show superior catalytic activity of the engineered MSN-supported UNMN nanocatalysts compared to their free form and state of the art commercial catalysts. We believe that our new strategy will open new avenues for artificially designed UNMN-inspired nanoarchitectures for wide applications.

Thermal Stability of Metal Nanocrystals: An Investigation of the Surface and Bulk Reconstructions of Pd Concave Icosahedra.

Despite the remarkable success in controlling the synthesis of metal nanocrystals, it still remains a grand challenge to stabilize and preserve the shapes or internal structures of metastable kinetic products. In this work, we address this issue by systematically investigating the surface and bulk reconstructions experienced by a Pd concave icosahedron when subjected to heating up to 600 °C in vacuum. We used in situ high-resolution transmission electron microscopy to identify the equilibration pathways of this far-from-equilibrium structure. We were able to capture key structural transformations occurring during the thermal annealing process, which were mechanistically rationalized by implementing self-consistent plane-wave density functional theory (DFT) calculations. Specifically, the concave icosahedron was found to evolve into a regular icosahedron via surface reconstruction in the range of 200-400 °C, and then transform into a pseudospherical crystalline structure through bulk reconstruction when further heated to 600 °C. The mechanistic understanding may lead to the development of strategies for enhancing the thermal stability of metal nanocrystals.

Patchy Nanofibers from the Thin Film Self-Assembly of a Conjugated Diblock Copolymer.

An unexpected morphology comprising patchy nanofibers can be accessed from the self-assembly of an all-conjugated, polyselenophene-block-polythiophene copolymer. This morphology consists of very small (<10 nm), polythiophene- and polyselenophene-rich domains and is unprecedented for both conjugated polymers and diblock copolymers in general. We propose that the patchy morphology occurs from the enhanced miscibility of the blocks arising from the longer alkyl chains in comparison to similar block copolymers with shorter alkyl chains, which fully phase separate, as well as the difference in rigidity between the polythiophene and polyselenophene blocks. This work demonstrates a facile way to tune the self-assembly behavior of conjugated block copolymers by modification of the side chain substituents.

In situ TEM tensile testing of carbon-linked graphene oxide nanosheets using a MEMS device.

This paper reports in situ transmission electron microscopy (TEM) tensile testing of carbon-linked graphene oxide nanosheets using a monolithic TEM compatible microelectromechanical system device. The set-up allows direct on-chip nanosheet thickness mapping, high resolution electron beam linking of a pre-fractured nanosheet, and mechanical tensile testing of the nanosheet. This technique enables simultaneous mechanical and high energy electron beam characterization of 2D nanomaterials.

Strengthening in Graphene Oxide Nanosheets: Bridging the Gap between Interplanar and Intraplanar Fracture.

Graphene oxide (GO) is a layered material comprised of hierarchical features which possess vastly differing characteristic dimensions. GO nanosheets represent the critical hierarchical structure which bridges the length-scale of monolayer and bulk material architectures. In this study, the strength and fracture behavior of GO nanosheets were examined. Under uniaxial loading, the tensile strength of the nanosheets was measured to be as high as 12 ± 4 GPa, which approaches the intrinsic strength of monolayer GO and is orders of magnitude higher than that of bulk GO materials. During mechanical failure, brittle fracture was observed in a highly localized region through the cross-section of the nanosheets without interlayer pull-out. This transition in the failure behavior from interplanar fracture, common for bulk GO, to intraplanar fracture, which dominates failure in monolayer GO, is responsible for the high strength measured in the nanosheets. Molecular dynamics simulations indicate that the elastic release from the propagation of intraplanar cracks initiates global fracture due to interlayer load transmission through hydrogen bond networks within the gallery space of the GO nanosheets. Furthermore, the GO nanosheet strength and stiffness were found to be strongly correlated to the effective volume and thickness of the samples, respectively. These findings help to bridge the understanding of the mechanical behavior of hierarchical GO materials and will ultimately guide the application of this intermediate scale material.

Pd@Pt Core-Shell Concave Decahedra: A Class of Catalysts for the Oxygen Reduction Reaction with Enhanced Activity and Durability.

We report a facile synthesis of multiply twinned Pd@Pt core-shell concave decahedra by controlling the deposition of Pt on preformed Pd decahedral seeds. The Pt atoms are initially deposited on the vertices of a decahedral seed, followed by surface diffusion to other regions along the edges/ridges and then across the faces. Different from the coating of a Pd icosahedral seed, the Pt atoms prefer to stay at the vertices and edges/ridges of a decahedral seed even when the deposition is conducted at 200 °C, naturally generating a core-shell structure covered by concave facets. The nonuniformity in the Pt coating can be attributed to the presence of twin boundaries at the vertices, as well as the {100} facets and twin defects along the edges/ridges of a decahedron, effectively trapping the Pt adatoms at these high-energy sites. As compared to a commercial Pt/C catalyst, the Pd@Pt concave decahedra show substantial enhancement in both catalytic activity and durability toward the oxygen reduction reaction (ORR). For the concave decahedra with 29.6% Pt by weight, their specific (1.66 mA/cm(2)Pt) and mass (1.60 A/mgPt) ORR activities are enhanced by 4.4 and 6.6 times relative to those of the Pt/C catalyst (0.36 mA/cm(2)Pt and 0.32 A/mgPt, respectively). After 10,000 cycles of accelerated durability test, the concave decahedra still exhibit a mass activity of 0.69 A/mgPt, more than twice that of the pristine Pt/C catalyst.

Formation of Soluble Mercury Oxide Coatings: Transformation of Elemental Mercury in Soils.

The impact of mercury (Hg) on human and ecological health has been known for decades. Although a treaty signed in 2013 by 147 nations regulates future large-scale mercury emissions, legacy Hg contamination exists worldwide and small-scale releases will continue. The fate of elemental mercury, Hg(0), lost to the subsurface and its potential chemical transformation that can lead to changes in speciation and mobility are poorly understood. Here, we show that Hg(0) beads interact with soil or manganese oxide solids and X-ray spectroscopic analysis indicates that the soluble mercury coatings are HgO. Dissolution studies show that, after reacting with a composite soil, >20 times more Hg is released into water from the coated beads than from a pure liquid mercury bead. An even larger, >700 times, release occurs from coated Hg(0) beads that have been reacted with manganese oxide, suggesting that manganese oxides are involved in the transformation of the Hg(0) beads and creation of the soluble mercury coatings. Although the coatings may inhibit Hg(0) evaporation, the high solubility of the coatings can enhance Hg(II) migration away from the Hg(0)-spill site and result in potential changes in mercury speciation in the soil and increased mercury mobility.

Rational defect introduction in silicon nanowires.

The controlled introduction of planar defects, particularly twin boundaries and stacking faults, in group IV nanowires remains challenging despite the prevalence of these structural features in other nanowire systems (e.g., II-VI and III-V). Here we demonstrate how user-programmable changes to precursor pressure and growth temperature can rationally generate both transverse twin boundaries and angled stacking faults during the growth of <111> oriented Si nanowires. We leverage this new capability to demonstrate prototype defect superstructures. These findings yield important insight into the mechanism of defect generation in semiconductor nanowires and suggest new routes to engineer the properties of this ubiquitous semiconductor.

In-situ TEM study from the perspective of holders.

During the in situ transmission electron microscopy (TEM) observations, the diverse functionalities of different specimen holders play a crucial role. We hereby provide a comprehensive overview of the main types of holders, associated technologies and case studies pertaining to the widely employed heating and gas heating methods, from their initial developments to the latest advancement. In addition to the conventional approaches, we also discuss the emergence of holders that incorporate a micro-electro-mechanical system (MEMS) chip for in situ observations. The MEMS technology offers a multitude of functions within a single chip, thereby enhancing the capabilities and versatility of the holders. MEMS chips have been utilized in environmental-cell designs, enabling customized fabrication of diverse shapes. This innovation has facilitated their application in conducting in situ observations within gas and liquid environments, particularly in the investigation of catalytic and battery reactions. We summarize recent noteworthy studies conducted using in situ liquid TEM. These studies highlight significant advancements and provide valuable insights into the utilization of MEMS chips in environmental-cells, as well as the expanding capabilities of in situ liquid TEM in various research domains.

Simultaneous secondary electron microscopy in the scanning transmission electron microscope with applications for in situ studies.

Scanning/transmission electron microscopy (STEM) is a powerful characterization tool for a wide range of materials. Over the years, STEMs have been extensively used for in situ studies of structural evolution and dynamic processes. A limited number of STEM instruments are equipped with a secondary electron (SE) detector in addition to the conventional transmitted electron detectors, i.e. the bright-field (BF) and annular dark-field (ADF) detectors. Such instruments are capable of simultaneous BF-STEM, ADF-STEM and SE-STEM imaging. These methods can reveal the 'bulk' information from BF and ADF signals and the surface information from SE signals for materials <200 nm thick. This review first summarizes the field of in situ STEM research, followed by the generation of SE signals, SE-STEM instrumentation and applications of SE-STEM analysis. Combining with various in situ heating, gas reaction and mechanical testing stages based on microelectromechanical systems (MEMS), we show that simultaneous SE-STEM imaging has found applications in studying the dynamics and transient phenomena of surface reconstructions, exsolution of catalysts, lunar and planetary materials and mechanical properties of 2D thin films. Finally, we provide an outlook on the potential advancements in SE-STEM from the perspective of sample-related factors, instrument-related factors and data acquisition and processing.

In situ TEM investigation of congruent phase transition and structural evolution of nanostructured silicon/carbon anode for lithium ion batteries.

It is well-known that upon lithiation, both crystalline and amorphous Si transform to an armorphous Li(x)Si phase, which subsequently crystallizes to a (Li, Si) crystalline compound, either Li(15)Si(4) or Li(22)Si(5). Presently, the detailed atomistic mechanism of this phase transformation and the degradation process in nanostructured Si are not fully understood. Here, we report the phase transformation characteristic and microstructural evolution of a specially designed amorphous silicon (a-Si) coated carbon nanofiber (CNF) composite during the charge/discharge process using in situ transmission electron microscopy and density function theory molecular dynamic calculation. We found the crystallization of Li(15)Si(4) from amorphous Li(x)Si is a spontaneous, congruent phase transition process without phase separation or large-scale atomic motion, which is drastically different from what is expected from a classic nucleation and growth process. The a-Si layer is strongly bonded to the CNF and no spallation or cracking is observed during the early stages of cyclic charge/discharge. Reversible volume expansion/contraction upon charge/discharge is fully accommodated along the radial direction. However, with progressive cycling, damage in the form of surface roughness was gradually accumulated on the coating layer, which is believed to be the mechanism for the eventual capacity fade of the composite anode during long-term charge/discharge cycling.

Peltier cooling for the reduction of carbon contamination in scanning electron microscopy.

We used a novel Peltier anticontamination device (PAC) to reduce carbon contamination upon electron beam irradiation in scanning electron microscopy through a reduction of hydrocarbon molecules in the specimen chamber. Unlike liquid-nitrogen based cold traps, the PAC operates free of user maintenance and is suitable for lengthy imaging sessions without degradation of the anticontamination performance. Its performance as an alternative cold trap method provides considerable reduction of electron beam-assisted carbon build-up. We compared the thickness of carbon contamination deposited upon prolonged electron beam scans with the PAC system on and off. Topographical structures of the carbon build-up were characterized using atomic force microscopy. We report that under identical beam parameters, thickness of the carbon contamination was reduced by over 79 % for area scans (1.2 × 1.2 µm2), and by two orders of magnitude for stationary point scans when the PAC cooling mode is engaged.