Direct visualization of anionic electrons in an electride reveals inhomogeneities
Anionic electron within an electride was visualized with atomic resolution using differential phase-contrast imaging.
36 MATERIALS SCIENCE↗
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Results for “atomic resolution”
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Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii
Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold cell envelope integrity, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo–electron microscopy reconstructions ofAcinetobacter baumanniiTolQ in apo and TolR-bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a transmembrane funnel leading toward a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton nonpermeable stance, characterized by the TolQ pentamer’s flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers’ interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.
Science & Technology - Other Topics↗
Autonomous self-repair in piezoelectric molecular crystals
Living tissue uses stress-accumulated electrical charge to close wounds. Self-repairing synthetic materials, which are typically soft and amorphous, usually require external stimuli, prolonged physical contact, and long healing times. We overcome many of these limitations in piezoelectric bipyrazole organic crystals, which recombine following mechanical fracture without any external direction, autonomously self-healing in milliseconds with crystallographic precision. Kelvin probe force microscopy, birefringence experiments, and atomic-resolution structural studies reveal that these noncentrosymmetric crystals, with a combination of hydrogen bonds and dispersive interactions, develop large stress-induced opposite electrical charges on fracture surfaces, prompting an electrostatically driven precise recombination of the pieces via diffusionless self-healing.
Bhunia, Surojit↗
Topological grain boundary segregation transitions
Engineering the structure of grain boundaries (GBs) by solute segregation is a promising strategy to tailor the properties of polycrystalline materials. Solute segregation triggering phase transitions at GBs has been suggested theoretically to offer different pathways to design interfaces, but an understanding of their intrinsic atomistic nature is missing. Here, we combined atomic resolution electron microscopy and atomistic simulations to discover that iron segregation to GBs in titanium stabilizes icosahedral units (“cages”) that form robust building blocks of distinct GB phases. Owing to their five-fold symmetry, the iron cages cluster and assemble into hierarchical GB phases characterized by a different number and arrangement of the constituent icosahedral units. Our advanced GB structure prediction algorithms and atomistic simulations validate the stability of these observed phases and the high excess of iron at the GB that is accommodated by the phase transitions.
36 MATERIALS SCIENCE↗
Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate
Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.
Methanosarcina acetivorans↗
Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals
Abstract Direct Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.
36 MATERIALS SCIENCE↗
Structure of BTK kinase domain with the second-generation inhibitors acalabrutinib and tirabrutinib
Bruton’s tyrosine kinase (BTK) is the target of the therapeutic agent, Ibrutinib, that treats chronic lymphocyte leukemia (CLL), mantle cell lymphoma (MCL) and other B cell malignancies. Ibrutinib is a first in class, covalent BTK inhibitor that limits B-cell survival and proliferation. Designing new inhibitors of BTK has been an important objective for advancing development of improved therapeutic agents against cancer and autoimmune disorders. Based on the success of Ibrutinib, several second-generation irreversible BTK inhibitors have been developed that exhibit fewer off-target effects. However, the binding-mode and their interaction with Btk have not been experimentally determined and evaluated at atomic resolution. Here we determined the first crystal structure of the BTK kinase domain in complex with acalabrutinib. In addition, we report a structure of the BTK/tirabrutinib complex and compare these structures with previously solved structures. The structures provide insight in the superior selectivity reported for acalabrutinb and guide future BTK inhibitor development.
60 APPLIED LIFE SCIENCES↗
The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion
Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae , including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109 KSQD 112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109 AAAA 112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae .
59 BASIC BIOLOGICAL SCIENCES↗
Resonant X-ray scattering of biological assemblies
Understanding the relationship between structure and function for biological assemblies can guide identification of new therapeutics, design of biomaterials, and development of biotechnological processes. Resonant X-ray scattering provides a chemically-specific approach to characterize complex biological structures based on anomalous or resonant scattering from a specific element or chemical moiety. Anomalous or resonant diffraction can provide structural details with high atomic resolution, while resonant X-ray scattering can provide structural details with lower resolution through tender or soft X-rays. Furthermore, we review applications, challenges, and opportunities for resonant X-ray scattering in the field of structural biology.
36 MATERIALS SCIENCE↗
Structure and Electronic Properties of Mesopores in Si PV Devices with PLEO Contacts
All current state-of-the-art silicon photovoltaic (PV) devices employ some flavor of passivating contact structure to minimize detrimental recombination while providing good conductivity. These properties are most often provided by a dielectric layer (SiNx, Al2O3, or SiOx) that is in contact with the crystalline silicon (c-Si) substrate. The effectiveness of these layers is heavily dependent on the nanoscale structure of both the dielectric layers and the crystalline silicon interface. As an example, the tunneling probability for charge carriers across thin SiOx layers, a process that is critical to maintain high conductivity, is extremely sensitive to the SiOx thickness. SiOx with a thickness below 2 nm readily allows charge carrier tunneling, whereas it is impeded for greater thicknesses. In the latter case it has been shown that modifications to the thermal processing schedule can induce disruptions, or pinholes, in thick SiOx layers that allow transport of charge carriers while maintaining excellent passivation. However, this requires higher temperatures processes that may inhibit widespread adoption by industry. Recently, another option has been presented that may circumvent the necessity for high temperature processing, namely metal assisted chemical etching (MACE). MACE relies on deposition of Ag nanoparticles onto the SiOx layers with subsequent electroless etching to form mesopores in the SiOx layers that are analogous to the pinholes created with high temperature processing. The size and density can be controlled based on the Ag nanoparticle deposition conditions. The resulting contact structure is known as polysilicon on locally etched oxide (PLEO) contacts. The nanoscale structure of the mesopores in PLEO contacts define the device level observables such as recombination current (Jo) and junction resistance. In this work we present atomic resolution transmission electron microscopy (TEM) analysis of mesopores in PLEO contacts formed with a different processing conditions to connect provide insight into how the nanoscale structure of the SiOx layer influences PV device properties. Additionally, we have previously used electron beam induced current (EBIC) to probe local transport properties in Si PV devices with a SiOx layer containing pinholes due to high temperature processing. Using EBIC we were able to directly show the enhance charge carrier transport through the pinholes. Here we also employ EBIC to study non-uniformities in charge carrier recombination and transport associated with mesopores in PLEO contacts and compare these results with our previous work on devices with pinholes in the SiOx formed through high temperature processes. The products of this work provide critical information that is required to both further optimize performance of Si PV devices with PLEO contact and to drive future adoption of this technology by industry.
ENGINEERING,SOLAR ENERGY↗
Gas delivery system for environmental transmission electron microscope
A portable, compact gas delivery system can support an environmental transmission electron microscope. Environment transmission electron microscopy provides researchers a unique capability of assessing a material's surface conditions at atomic resolution in a variety of reactive and oxidizing environments. The ability to precisely control the analysis chamber's environmental conditions over time is key to the success of a typical surface analysis. The gas delivery system provides the correct balance or pressure delivery precision, contamination control, and gas isolation.
Nogan, John Joseph↗
Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations
Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.
BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗
Static and dynamic properties of atomic nuclei with high-resolution potentials
Here, we compute ground-state and dynamical properties of 4 He and 16 O nuclei using as input high-resolution, phenomenological nucleon-nucleon and three-nucleon forces that are local in coordinate space. The nuclear Schrodinger equation for both nuclei is accurately solved employing the auxiliary-field diffusion Monte Carlo approach. For the 4 He nucleus, detailed benchmarks are carried out with the hyperspherical harmonics method. In addition to presenting results for the binding energies and radii, we also analyze the momentum distributions of these nuclei and their Euclidean response function corresponding to the isoscalar density transition. The latter quantity is particularly relevant for lepton-nucleus scattering experiments, as it paves the way to quantum Monte Carlo calculations of electroweak response functions of 16 O.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Investigation of spin and magnetism in two dimensional materials with atomic-scale spatial resolution (Final Technical Report)
Spintronics is an approach to energy-efficient electronics beyond silicon CMOS that utilizes the electron’s spin degree of freedom for memory and logic. The record spin diffusion length in graphene has generated considerable interest in two dimensional (2D) materials (i.e. graphene and beyond) as a platform for spintronics. Magnetism in 2D van der Waals materials may offer additional opportunities for tunability via strain, external fields, and layer-dependent quantum effects. The inherently atomic-scale nature of exchange interactions and the inherently all-surface nature of 2D sheets motivate an integrated approach combining atomic-scale magnetic characterization, epitaxial growth, and nanodevice fabrication. The mission of the research is to develop and utilize atomic-scale imaging of spin and magnetism via spin-polarized scanning tunneling microscopy (STM) in conjunction with atom-by-atom materials growth via molecular beam epitaxy (MBE) and nanoscale device fabrication to explore new frontiers of spintronics and quantum science in 2D materials. The PIs are particularly motivated by understanding how the magnetic and spin-dependent properties at the atomic scale lead to interesting and potentially useful phenomena in spintronic devices at the macroscopic scale.
36 MATERIALS SCIENCE↗
High-resolution spectroscopy of neutral Yb atoms in a solid Ne matrix
Here, we present an experimental and theoretical study of the absorption and emission spectra of Yb atoms in a solid Ne matrix at a resolution of 0.025 nm. Five absorption bands were identified as due to transitions from the 4 f 14 5 d 0 6 s 2 1 S 0 ground-state configuration to 4 f 14 5 d 0 6 s 6 p and 4 f 13 5 d 1 6 s 2 configurations. The two lowest-energy bands were assigned to outer-shell transitions to 6 s 6 p 3 P 1 and 1 P 1 atomic states and displayed the structure of a broad doublet and an asymmetric triplet, respectively. The remaining three higher-frequency bands were assigned to inner-shell transitions to distinct J = 1 states arising from the 4 f 13 5 d 1 6 s 2 configuration and were highly structured with narrow linewidths. A classical simulation was performed to identify the stability and symmetry of possible trapping sites in the Ne crystal. It showed that the overarching 1 + 2 structure of the high-frequency bands could be predominantly ascribed to crystal-field splitting in the axial field of a 10-atom vacancy of C 4 v symmetry. Their prominent substructures were shown to be manifestations of phonon sidebands associated with the zero-phonon lines on each crystal-field state. Unprecedented for a metal–rare-gas system, resolution of individual phonon states on an allowed electronic transition was possible under excitation spectroscopy which reflects the semiquantum nature of solid Ne. In contrast to the absorption spectra, emission spectra produced by steady-state excitation into the 1 P 1 absorption band consisted of simple, unstructured fluorescence bands.
74 ATOMIC AND MOLECULAR PHYSICS↗
Probing layered structure of Inconel 625 coatings prepared by magnetron sputtering
Coating/substrate interface and oxide layers present in Inconel 625 film may cause significant impacts on its corrosion behavior. However, layered structure of Inconel 625 coatings remains poorly understood due to its requirement of high spatial resolution. Here we have applied X-ray reflectometry (XRR) to probe the layered structure of magnetron-sputtered Inconel 625 film with atomic spatial resolution. Our results indicate that there exists a 2 nm thick Cr-rich Inconel sublayer underneath the principal film. On top of the principal film, it is found a 2 nm thick oxide layer mainly consisting of NiO. In addition, we detected ~2 Å contamination layer on the sapphire substrate, although argon ion sputter cleaning had been applied to the substrate prior to deposition. By comparing the coatings with different deposition time, we observed that the thickness of principal Inconel 625 layer grows linearly with deposition time, with all other layers remaining constant. Our findings provide insight into the layered structures of Inconel 625 coatings with atomic-scale spatial resolution, and provide directions for future efforts that aim to improve the corrosion resistance of Inconel 625 coatings.
14 SOLAR ENERGY↗
Revealing the complex chemistry of grain boundaries in K-doped BaFe 2 As 2 with atom probe tomography
Iron-based superconductors have attractive properties for high-field applications, but there is a lack of understanding of the effect of grain boundary chemistry on the in-field performance. The near atomic-scale resolution, ppm sensitivity and 3D analysis offered by atom probe tomography make it a powerful tool to investigate the nanoscale structure and chemistry of these defects in fine-grained K-doped BaFe 2 As 2 samples. A computational method to systematically extract and compare the Gibbsian interfacial excess of chemical species across grain boundaries has been explored in this work. The robustness of the method has been tested by evaluating the effects of selected variables on simulated APT datasets. The accuracy and precision of the calculated Gibbsian interfacial excess were found to be stable over a range of analysis conditions: varying grain boundary widths and detection efficiencies, spatial precisions below 1.5 nm, and bin widths between 1.2 and 1.6 nm. For the K-doped BaFe 2 As 2 samples studied, segregation of As, Ba, K and impurities of O, Na, and Sb were found at grain boundaries. The Gibbsian excess values were found to vary widely between different boundaries, showing the complexity of the grain boundary chemistry in this material. Possible links between the observed critical current density (Jc) of these samples and their nano- and micro-structure have also been investigated and discussed.
36 MATERIALS SCIENCE↗
Visualizing Millisecond Atomic Dynamics of Nanocrystals in Liquid
Atomic structures of nanomaterials are inherently dynamic and continuously reshaped through interactions with chemical species and external stimuli. Such dynamics are further amplified as the size and dimensionality of nanomaterials decrease. Despite advances in analytical methods, it remains challenging to capture the structural dynamics of nanomaterials in reactive environments with both atomic spatial resolution and commensurate temporal resolution. Here, in this study, we directly visualize atomic-scale dynamics of gold (Au) nanocrystals in reactive liquid environments with millisecond-speed liquid-cell electron microscopy (EM) and deep-learning denoising. We uncover reversible fluctuations in the local crystallinity of Au nanocrystals dependent on the surrounding chemical environment. These transient fluctuations, driven by interactions at nanocrystal–liquid interfaces, critically influence the dissolution kinetics and grain boundary relaxation. By overcoming the spatiotemporal limitations in conventional liquid-cell EM, our findings provide insights into how transient nanoscale structures dictate the stability and reactivity of nanomaterials.
Kang, Sungsu [University of Chicago, IL (United St↗