Universal dynamics in an isolated one-dimensional Bose gas far from equilibrium.

Understanding the behaviour of isolated quantum systems far from equilibrium and their equilibration is one of the most pressing problems in quantum many-body physics1,2. There is strong theoretical evidence that sufficiently far from equilibrium a wide variety of systems-including the early Universe after inflation3-6, quark-gluon matter generated in heavy-ion collisions7-9, and cold quantum gases4,10-14-exhibit universal scaling in time and space during their evolution, independent of their initial state or microscale properties. However, direct experimental evidence is lacking. Here we demonstrate universal scaling in the time-evolving momentum distribution of an isolated, far-from-equilibrium, one-dimensional Bose gas, which emerges from a three-dimensional ultracold Bose gas by means of a strong cooling quench. Within the scaling regime, the time evolution of the system at low momenta is described by a time-independent, universal function and a single scaling exponent. The non-equilibrium scaling describes the transport of an emergent conserved quantity towards low momenta, which eventually leads to the build-up of a quasi-condensate. Our results establish universal scaling dynamics in an isolated quantum many-body system, which is a crucial step towards characterizing time evolution far from equilibrium in terms of universality classes. Universality would open the possibility of using, for example, cold-atom set-ups at the lowest energies to simulate important aspects of the dynamics of currently inaccessible systems at the highest energies, such as those encountered in the inflationary early Universe.

Structural Analysis and Intrinsic Enzyme Mimicking Activities of Ligand-Free PtAg Nanoalloys.

Nanozymes are nanomaterials with biocatalytic properties under physiological conditions and are one class of artificial enzymes to overcome the high cost and low stability of natural enzymes. However, surface ligands on nanomaterials will decrease the catalytic activity of the nanozymes by blocking the active sites. To address this limitation, ligand-free PtAg nanoclusters (NCs) are synthesized and applied as nanozymes for various enzyme-mimicking reactions. By taking advantage of the mutual interaction of zeolitic imidazolate frameworks (ZIF-8) and Pt precursors, a good dispersion of PtAg bimetal NCs with a diameter of 1.78 ± 0.1 nm is achieved with ZIF-8 as a template. The incorporation of PtAgNCs in the voids of ZIF-8 is confirmed with structural analysis using the atomic pair-distribution function and powder X-ray diffraction. Importantly, the PtAgNCs present good catalytic activity for various enzyme-mimicking reactions, including peroxidase-/catalase- and oxidase-like reactions. Further, this work compares the catalytic activity between PtAg NCs and PtAg nanoparticles with different compositions and finds that these two nanozymes present a converse dependency of Ag-loading on their activity. This study contributes to the field of nanozymes and presents a potential option to prepare ligand-free bimetal biocatalysts with sizes in the nanocluster regime.

The Elusive Structure of Levocetirizine Dihydrochloride Determined by Electron Diffraction.

Levocetirizine is an orally administrated, second-generation antihistaminic active pharmaceutical ingredient that has been used to treat symptoms of allergy and long-term hives for over 25 years. Despite the wide use of this compound, its crystal structure has remained unknown. Here we report the application of 3D electron diffraction (3D ED)/Micro-crystal electron diffraction (MicroED) to determine the crystal structure of Levocetirizine dihydrochloride directly from crystalline powders that were extracted from commercially available tablets containing the compound. We also showcase the utility of dynamical refinement to unambiguously assign absolute configuration. The results highlight the immense potential of 3D ED/MicroED for structure elucidation of components of microcrystalline mixtures that obviates the need to grow large-size single crystals and the use of complementary analytical techniques, which could be important for identification as well as for primary structural characterization.

Environmental Liquid Cell Technique for Improved Electron Microscopic Imaging of Soft Matter in Solution.

Liquid-phase transmission electron microscopy is a technique for simultaneous imaging of the structure and dynamics of specimens in a liquid environment. The conventional sample geometry consists of a liquid layer tightly sandwiched between two Si3N4 windows with a nominal spacing on the order of 0.5 µm. We describe a variation of the conventional approach, wherein the Si3N4 windows are separated by a 10-µm-thick spacer, thus providing room for gas flow inside the liquid specimen enclosure. Adjusting the pressure and flow speed of humid air inside this environmental liquid cell (ELC) creates a stable liquid layer of controllable thickness on the bottom window, thus facilitating high-resolution observations of low mass-thickness contrast objects at low electron doses. We demonstrate controllable liquid thicknesses in the range 160 ± 34 to 340 ± 71 nm resulting in corresponding edge resolutions of 0.8 ± 0.06 to 1.7 ± 0.8 nm as measured for immersed gold nanoparticles. Liquid layer thickness 40 ± 8 nm allowed imaging of low-contrast polystyrene particles. Hydration effects in the ELC have been studied using poly-N-isopropylacrylamide nanogels with a silica core. Therefore, ELC can be a suitable tool for in situ investigations of liquid specimens.

Photochromism of Amphiphilic Dithienylethenes as Langmuir-Schaefer Films.

Surface pressure-area isotherms were recorded under different irradiation conditions for single-component Langmuir films of three photochromic amphiphilic dithienylethenes. Nonirradiated films of these photochromic amphiphiles were mechanically stable. In addition, a shift of the isotherms to larger mean molecular areas was observed for films prepared from UV-light-irradiated dithienylethenes. Unexpectedly, a significant expansion was observed for a film prepared from visible-light-irradiated dithienylethene incorporating large branched alkyl chains. Upon further study, atomic force microscopy and transmission electron microscopy images of Langmuir-Schaefer films revealed that this pronged dialkyl derivative undergoes a photoinduced change in morphology, as circular aggregates coalesce into larger continuous aggregated structures. Nevertheless, its photoisomerization was completely reversible as single-component multilayer thin films upon direct UV or visible light irradiation.

Visualization of Cellular Components in a Mammalian Cell with Liquid-Cell Transmission Electron Microscopy.

We present liquid-cell transmission electron microscopy (liquid-cell TEM) imaging of fixed and non-fixed prostate cancer cells (PC3 and LNCaP) with high resolution in a custom developed silicon nitride liquid cell. Fixed PC3 cells were imaged for 90-120 min without any discernable damage. High contrast on the cellular structures was obtained even at low electron doses (~2.5 e-/nm2 per image). The images show distinct structures of cell compartments (nuclei and nucleoli) and cell boundaries without any further sample embedding, dehydration, or staining. Furthermore, we observed dynamics of vesicles trafficking from the cell membrane in consecutive still frames in a non-fixed cell. Our findings show that liquid-cell TEM, operated at low electron dose, is an excellent tool to investigate dynamic events in non-fixed cells with enough spatial resolution (few nm) and natural amplitude contrast to follow key intracellular processes.

STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials.

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.

The Cryo-EM structures of two amphibian antimicrobial cross-ß amyloid fibrils.

The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-ß fibrils of mated ß-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight ß-sheet interfaces. This cross-ß cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked ß-sheets allowing a rounded compactness of the fibril. The kinked ß-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids.

The effect of secondary electrons on radiolysis as observed by in liquid TEM: The role of window material and electrical bias.

The effect of window material on electron beam induced phenomena in liquid phase electron microscopy (LPEM) is an interesting yet under-explored subject. We have studied the differences of electron beam induced gold nanoparticle (AuNP) growth subject to three encapsulation materials: Silicon Nitride (Si3N4), carbon and formvar. We find Si3N4 liquid cells (LCs) to result in significantly higher AuNP growth yield as compared to LCs employing the other two materials. In all cases, an electrical bias of the entire LC structures significantly affected particle growth. We demonstrate an inverse correlation of the AuNP growth rate with secondary electron (SE) emission from the windows. We attribute these differences at least in part to variations in SE emission dynamics, which is seen as a combination of material and bias dependent SE escape flux (SEEF) and SE return flux (SERF). Furthermore, our model predictions qualitatively match electrochemistry expectations.

Serial Electron Diffraction Data Processing With diffractem and CrystFEL.

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.

Serial protein crystallography in an electron microscope.

Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.

Low-dose cryo electron ptychography via non-convex Bayesian optimization.

Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic or near-atomic resolution. However, applications are so far mainly limited to radiation-hard samples, because the required doses are too high for imaging biological samples at high resolution. We propose the use of non-convex Bayesian optimization to overcome this problem, and show via numerical simulations that the dose required for successful reconstruction can be reduced by two orders of magnitude compared to previous experiments. As an important application we suggest to use this method for imaging single biological macromolecules at cryogenic temperatures and demonstrate 2D single-particle reconstructions from simulated data with a resolution up to 5.4 Å at a dose of 20e - /Å2. When averaging over only 30 low-dose datasets, a 2D resolution around 3.5 Å is possible for macromolecular complexes even below 100 kDa. With its independence from the microscope transfer function, direct recovery of phase contrast, and better scaling of signal-to-noise ratio, low-dose cryo electron ptychography may become a promising alternative to Zernike phase-contrast microscopy.

Visualization of multimerization and self-assembly of DNA-functionalized gold nanoparticles using in-liquid transmission electron microscopy.

Base-pairing stability in DNA-gold nanoparticle (DNA-AuNP) multimers along with their dynamics under different electron beam intensities was investigated with in-liquid transmission electron microscopy (in-liquid TEM). Multimer formation was triggered by hybridization of DNA oligonucleotides to another DNA strand (Hyb-DNA) related to the concept of DNA origami. We analyzed the degree of multimer formation for a number of samples and a series of control samples to determine the specificity of the multimerization during the TEM imaging. DNA-AuNPs with Hyb-DNA showed an interactive motion and assembly into 1D structures once the electron beam intensity exceeds a threshold value. This behavior was in contrast with control studies with noncomplementary DNA linkers where statistically significantly reduced multimerization was observed and for suspensions of citrate-stabilized AuNPs without DNA, where we did not observe any significant motion or aggregation. These findings indicate that DNA base-pairing interactions are the driving force for multimerization and suggest a high stability of the DNA base pairing even under electron exposure.

All-optical switch and transistor gated by one stored photon.

The realization of an all-optical transistor, in which one "gate" photon controls a "source" light beam, is a long-standing goal in optics. By stopping a light pulse in an atomic ensemble contained inside an optical resonator, we realized a device in which one stored gate photon controls the resonator transmission of subsequently applied source photons. A weak gate pulse induces bimodal transmission distribution, corresponding to zero and one gate photons. One stored gate photon produces fivefold source attenuation and can be retrieved from the atomic ensemble after switching more than one source photon. Without retrieval, one stored gate photon can switch several hundred source photons. With improved storage and retrieval efficiency, our work may enable various new applications, including photonic quantum gates and deterministic multiphoton entanglement.