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At least 307 records · Page 17

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

59 BASIC BIOLOGICAL SCIENCES↗

Ultrafast-induced coherent acoustic phonons in the two-dimensional magnet CrSBr

Magnetism in two-dimensional (2D) van der Waals (vdW) crystals offers promising new directions for low-dimensional physics and devices. In this work, mega-electron volt (MeV) ultrafast electron diffraction was employed to investigate the ultrafast atomic dynamics of a novel, 2D vdW magnetic single-crystal CrSBr. Femtosecond (fs) optical pump pulses excited non-equilibrium atomic displacements shown to be coherent acoustic phonons (CAPs). Phonon frequencies were extracted by analyzing oscillations of different Bragg peak (BP) intensities and were determined to be GHz acoustic disturbances that propagated as strain waves. Phonon modes exhibit anisotropy with respect to the a and b crystal axes. Subharmonic phonon frequencies were also observed, and this provided a signature of nonlinear oscillatory coupling between the laser-induced pumping phonon frequency and secondary phonon frequencies. Thus, CrSBr was found to serve as a nonlinear phononic frequency converter. The ultrafast time dependence of the Bragg intensity was simulated by incorporating an oscillating deviation parameter ansatz into expressions for the dynamical scattering intensity yielded excellent modeling of the ultrafast structural dynamics of the photo-excited 2D crystal. Our work provides a foundation for exploring how fs light pulses can influence phonon dynamics in materials with strong spin-lattice coupling. These results suggest that CAPs can match the magnon frequencies and show the promise of CrSBr for use in optical-to-microwave transducers and phononic devices.

43 PARTICLE ACCELERATORS↗

Interface structures of inclined ZnO thin film on (0 1 1)-MgO substrate with bulk-like optical properties

Combining different phase structure materials with unique properties to design novel devices plays a significant role in the development of modern electronics. Here, we explore the characteristics of this type of complex interface and epitaxy structures based on the coupling between hexagonal ZnO film and cubic MgO substrate. The ZnO film was prepared by the molecular beam epitaxy technique on the MgO (0 1 1) substrate. The analysis results from the in situ reflection high energy electron diffraction patterns, X-ray diffraction (XRD)-pole figures and high resolution transmission electron microscopy images demonstrate that the film exhibits two-fold symmetry domains with a growth direction deviated from c-axis at about 31º along the [0 1 0] MgO or [0 $\bar{1}$ 0] MgO azimuth. Despite the intertwined diffusion from Zn and Mg atoms in the interface, which is the possible origin of a blue shift of about 0.083 eV in the Photoluminescence (PL) spectrum, the inclined film shows a full width at half maximum value that is close to the reported value from the high quality film. Finally, this work hopefully provides useful insights to the design and exploration of the novel optoelectronic devices that involve the integration of materials with different structure and different properties.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Liquid Interfacial Electron Microscopy Identifies Nanogalvanic Corrosion in Pearlitic Steel

The nanoscale mechanisms of localized corrosion in low carbon steels have remained elusive due to the complexity of studying the degradative material behavior at nanoscale solid-liquid interfaces. We identified various steps in the nanogalvanic corrosion processes using in-situ liquid-cell scanning transmission electron microscopy (STEM) using a microfluidic holder by Hummingbird Scientific. Initial work, performed at low magnification, identified the initiation point on a 1018 low-carbon steel surface. This initiation point was determined to be a triple junction of two ferrite grains bridging a cementite grain in contact with a baseline electrolyte of 6 uM CO2 dissolved in a buffered (2.78 uM Na2SO4) aqueous solution, pH 6.1. The pre-etched low-carbon steel surface was prepared using focused ion beam lift-out procedures to extract a cross-section of the low-carbon steel surface, which then was thinned to about 150 nm and transferred to a SiN membrane microfluidic window. The transfer was made using a lift-out needle to attach the low-carbon steel lamella to the corner of the SiN window, and then Pt/C deposition held the lamella in contact with the window while it was released from the lift out needle. To identify the triple point on the low carbon steel lamella, prior to attachment on the SiN window, the sample was characterized for compositional variations with energy dispersive x-ray spectroscopy mapping, grain orientation and phase mapping with precession electron diffraction, and thickness mapping with energy filtered transmission electron microscopy. This pre-characterization prior to the in-situ experiment provided a map of the multiphase and multigrain structure, where the in-situ liquid cell imaging provided a clear understanding of the initiation point on the sample. These data were cross-correlated to paint a holistic picture of the triple junction site, enabling low electron-fluence in-situ snapshot imaging to avoid dominating the native corrosion reactions with effects from the incident electron beam. This initial result identified that localized, nanogalvanic corrosion at the phase interface was the dominant corrosion process in the low-carbon steel, so we next targeted the observation of an array of these nanogalvanic features phase boundaries in a pearlite grain. Near-surface ferrite/cementite phase interfaces that typify pearlitic low-carbon steel were extracted, pre-characterized, and imaged for the in-situ corrosion processes. The sample was a cross-section from a pearlite grain, with alternating ferrite and cementite grains that extended microns down from the pre-etched low-carbon steel pipe surface. After contact with a buffered aqueous solution, the phase boundaries between the ferrite and cementite began to dissolve, with observable material loss and thickness changes in the dark-field and bright-field STEM images. Within minutes, the corrosion front proceeded deeper into the material, claiming a thin layer of ferrite around all exposed phase boundaries before progressing laterally into the ferrite matrix, converting the ferrite to corrosion product normal to each buried cementite grain. Formation of the corrosion product causes a volumetric expansion, creating a lateral wedging force that mechanically ejects the cementite grains from their grooves and leaves behind percolation channels into the steel substructure. Rapid and deleterious, this nanogalvanic corrosion pathway represents an important target for understanding and preventing run-away degradation in this common building material. Observation of this corrosion mechanism was enabled by the combination of pre-characterization using standard structural, grain, and compositional analysis in the TEM, which provides maps for understanding the reaction propagation captured in low-dose, in-situ, liquid-cell STEM.

corrosion↗

Toward accurate measurement of electromagnetic field by retrieving and refining the center position of non-uniform diffraction disks in Lorentz 4D-STEM

Recent advancement in scanning transmission electron microscopy (STEM) allows the use of 4D-STEM, a technique that captures an electron diffraction pattern at each scan point in STEM, to measure electrostatic and magnetic potential and field in materials. However, accurate measurement, separation of the magnetic and electric signals, and removal of artifacts remain challenging, especially in the presence of complex non-uniform diffraction contrast within the disks. In this work, based on dynamic simulations of 4D-STEM patterns built upon superstructures consisting of millions of atoms to account for different sample thickness and edge geometries, we show how the shape and intensity distribution of the central disk are affected by multiple scattering. We propose a robust refinement procedure through iteration of the spin-sensitive peak position of the disk-center in the circular Hough transform filtered images from experimental Lorentz 4D-STEM dataset after minimizing the possible artifacts, such as those due to the change of thickness, dynamic scattering, and scanning process. We verify that caution must be taken as in practice the rigid-disk-shift model used to reconstruct induction maps can easily break down due to disk-protrusion when there exists a nonconstant phase gradient or thickness within the width of the probe. Through quantitative analysis and comparing experiment with calculation the effect of the non-spin-related intensity distribution inside the disk as well as that causes the disk shift due to the intensity-protrusion can be removed, and high-quality magnetic field mapping is possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Multifunctional Cu 2 TSiS 4 (T = Mn and Fe): Polar Semiconducting Antiferromagnets with Nonlinear Optical Properties

In this work, Cu 2 TSiS 4 (T = Mn and Fe) polycrystalline and single-crystal materials were prepared with high-temperature solid-state and chemical vapor transport methods, respectively. The polar crystal structure (space group Pmn2 1 ) consists of chains of corner-sharing and distorted CuS 4 , Mn/FeS 4 , and SiS 4 tetrahedra, which is confirmed by Rietveld refinement using neutron powder diffraction data, X-ray single-crystal refinement, electron diffraction, energy-dispersive X-ray spectroscopy, and second harmonic generation (SHG) techniques. Magnetic measurements indicate that both compounds order antiferromagnetically at 8 and 14 K, respectively, which is supported by the temperature-dependent (100–2 K) neutron powder diffraction data. Additional magnetic reflections observed at 2 K can be modeled by magnetic propagation vectors k = (1/2,0,1/2) and k = (1/2,1/2,1/2) for Cu 2 MnSiS 4 and Cu 2 FeSiS 4 , respectively. The refined antiferromagnetic structure reveals that the Mn/Fe spins are canted away from the ac plane by about 14°, with the total magnetic moments of Mn and Fe being 4.1(1) and 2.9(1) μ B , respectively. Both compounds exhibit an SHG response with relatively modest second-order nonlinear susceptibilities. Density functional theory calculations are used to describe the electronic band structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mapping structural heterogeneity at the nanoscale with scanning nano-structure electron microscopy (SNEM)

Here, in this work, we explore the use of scanning electron diffraction (also known as 4D-STEM) coupled with electron atomic pair distribution function analysis (ePDF) to understand the local order (structure and chemistry) as a function of position in a complex multicomponent system, a hot rolled, Ni-encapsulated, Zr 65 Cu 17.5 Ni 10 Al 7.5 bulk metallic glass (BMG), with a spatial resolution of 3 nm. We show that it is possible to gain insight into the chemistry and chemical clustering/ordering tendency in different regions of the sample, including in the vicinity of nano-scale crystallites that are identified from virtual dark field images and in heavily deformed regions at the edge of the BMG. In addition to simpler analysis, unsupervised machine learning was used to extract partial PDFs from the material, modeled as a quasi-binary alloy, and map them in space. These maps allowed key insights not only into the local average composition, as validated by EELS, but also a unique insight into chemical short-range ordering tendencies in different regions of the sample during formation. The experiments are straightforward and rapid and, unlike spectroscopic measurements, don’t require energy filters on the instrument. We spatially map different quantities of interest (QoI’s), defined as scalars that can be computed directly from positions and widths of ePDF peaks or parameters refined from fits to the patterns. We developed a flexible and rapid data reduction and analysis software framework that allows experimenters to rapidly explore images of the sample on the basis of different QoI’s. The power and flexibility of this approach are explored and described in detail. Because of the fact that we are getting spatially resolved images of the nanoscale structure obtained from ePDFs we call this approach scanning nano-structure electron microscopy (SNEM), and we believe that it will be powerful and useful extension of current 4D-STEM methods.

36 MATERIALS SCIENCE↗

Degeneracy in Intercalated Pb Phases under Buffer-Layer Graphene on SiC(0001) and Diffuse Moiré Spots in Surface Diffraction

First-principles density functional theory (DFT) is used to analyze the stability of Pb intercalated phases under buffer layer graphene on SiC(0001) as a function of the supercell size, Pb coverage, and degree of Pb ordering. By comparing the chemical potentials of such two-dimensional Pb structures, here we find that there is a family of structurally distinct thermodynamically preferred Pb subsurface configurations with minute stability differences. These differences are comparable to the thermal energies at about 450 °C, where the Pb intercalated phases are grown. High-resolution surface-diffraction experiments using Spot Profile Analysis Low-Energy Electron Diffraction (SPA-LEED) confirm this high degree of degeneracy of the Pb intercalated phases from broad, low-intensity moiré spots observed exclusively from intercalated Pb. The low intensity of the moiré spots implies the coexistence of structurally different subsurface Pb phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IMS Rapid Response FY21 Summary Report for: Integrating Patterned Probes with Four-Dimensional Scanning Transmission Electron Microscopy for Unrivaled Crystallographic Structure Determination in Nanomaterials

The initial goal of our 4-dimensional scanning transmission electron microscopy (4D-STEM)-based project was to develop strain resolution two orders of magnitude better than what is now currently possible with electron-based scattering techniques, all while collecting scattering information from 7 different tilt axes at one time [multi-beam electron diffraction (MBED)1 ] through the development of a new electron probe-forming aperture with non-circular features (patterned probes 2 ). We set out to accomplish this through a collaboration with Drs. Colin Ophus and Ben Savitsky at Lawrence Berkeley Laboratory (they are the world-leading experts in developing the complex computational codes required to perform orientation analysis and quantitative strain mapping on our 4D-STEM data sets. We are motivated to invest in this area as it will be the only technique sensitive enough to perform three- dimensional automated crystallographic orientation mapping (ACOM) and strain mapping for materials exposed to external stimulus (a focus of our larger efforts).

36 MATERIALS SCIENCE↗

Electronic and magnetic properties of hole-doped topological kagome Fe 1−𝑥 ⁢Mn 𝑥 ⁢Sn thin films

We have investigated the electronic and magnetic structures of topological kagome Fe 1−𝑥 ⁢Mn 𝑥 ⁢Sn (0 ≤ 𝑥 ≤ 0.3) thin films via neutron diffraction, electronic transport measurements, and ab initio density functional theory (DFT) to understand the interplay between hole doping, magnetism, and the electronic structures. Temperature-dependent neutron diffraction measurements on parent FeSn reveal the Néel temperature to be 𝑇 N ∼ 355 K and the underlying A-type antiferromagnetic ordering is associated with a wave vector 𝒒 = (001/2). Upon Mn doping to 𝑥 = 0.15, 𝑇 N decreases slightly while the magnetic ordering vector remains the same. Resistivity measurements show metallic characteristics and in-plane anisotropy down to 10 K for all the investigated samples. The effects of hole doping are mapped in terms of electronic ground state calculations via DFT which show that the Dirac point is moved closer to the Fermi level (𝐸 F ) and the flat bands get pushed away from 𝐸 F upon hole doping. However, a comparison between hole-doped Fe 1−𝑥⁢ Mn 𝑥⁢ Sn and electron-doped Fe 1−𝑥 ⁢Co 𝑥 ⁢Sn indicates that the Néel temperature does not scale with the position of 𝐸 F relative to the flat band. Furthermore, our results establish the antiferromagnetic state of FeSn and Fe 1−𝑥 ⁢Mn 𝑥⁢ Sn films at room temperature, laying the groundwork for future studies of magnetism in kagome heterostructures.

36 MATERIALS SCIENCE↗

Exploring Functional Materials by Understanding Beam‐Sample Interactions

Abstract Ultra‐low‐dose electron diffraction is performed with a double metal cyanide catalyst (DMC) to understand how electron irradiation stimulates structural alterations in functional materials. The commonly fading diffraction patterns with dose accumulation depend on the irradiated area and the beam current even when below 50 femto Amperes. Heat generation is observed and modeled by statistical, inelastic scattering events to describe how phonon excitations modulate radiation hardness. Specifically, the characteristic 1/e‐decay of Bragg intensities from DMC is delayed from 6 to 30 eÅ −2 at room temperature, which is comparable to the effect of embedding radiation soft matter in ice. DMC's radiation hardness is enhanced by a latency dose that forms during a phase transformation. This unifying model predicts that a critical dose rate exists for any material that varies between 0.1 and 10 4 eÅ −2 s −1 because of a material dependent competition of heat generation and spread. It shows that Brillouin scattering causes time dependent perturbations in electron irradiated solids that trigger time‐temperature‐transformations on a time scale of nanoseconds to microseconds at room temperature, which is not included in traditional models describing the decay of Bragg intensities by radiolysis.

Kisielowski, Christian↗

Accurate prediction of mega-electron-volt electron beam properties from UED using machine learning

To harness the full potential of the ultrafast electron diffraction (UED) and microscopy (UEM), we must know accurately the electron beam properties, such as emittance, energy spread, spatial-pointing jitter, and shot-to-shot energy fluctuation. Owing to the inherent fluctuations in UED/UEM instruments, obtaining such detailed knowledge requires real-time characterization of the beam properties for each electron bunch. While diagnostics of these properties exist, they are often invasive, and many of them cannot operate at a high repetition rate. Here, we present a technique to overcome such limitations. Employing a machine learning (ML) strategy, we can accurately predict electron beam properties for every shot using only parameters that are easily recorded at high repetition rate by the detector while the experiments are ongoing, by training a model on a small set of fully diagnosed bunches. Applying ML as real-time noninvasive diagnostics could enable some new capabilities, e.g., online optimization of the long-term stability and fine single-shot quality of the electron beam, filtering the events and making online corrections of the data for time-resolved UED, otherwise impossible. This opens the possibility of fully realizing the potential of high repetition rate UED and UEM for life science and condensed matter physics applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Near-Threshold Photoemission from Graphene-Coated Cu(110)

In this article, the brightness of electron beams emitted from photocathode sources plays a critical role in determining the performance of x-ray free-electron lasers and ultrafast electron-diffraction applications. In order to achieve the maximum brightness, the electrons need to be emitted from a photocathode with the lowest-possible mean transverse energy (MTE). Recent investigations have shown that capping a Cu(110) photocathode with a monolayer of graphene can protect the quantum efficiency (QE) from long-term exposure to varying vacuum conditions. However, there have been no studies that investigate the effects that a monolayer of graphene has on the MTE. Here, we report on measurements of a graphene-coated Cu(110) single crystal near the photoemission threshold for room and liquid-nitrogen temperatures. At room temperature, a minimum MTE of 25 meV is measured at 295 nm. At liquid-nitrogen temperatures, a minimum MTE of 9 meV is measured at the photoemission threshold of 290 nm.

36 MATERIALS SCIENCE↗

Linker Vacancy Engineering of a Robust ftw–type Zr–MOF for Hexane Isomers Separation

Discrimination of physically similar molecules by porous solids represents an important yet challenging task in industrially relevant chemical separations. Precisely controlled pore dimension and/or tailored pore surface functionality are crucial to achieve high-efficiency separation. Metal-organic frameworks (MOFs) are promising candidates for these challenging separations in light of their structural diversity as well as highly adjustable pore dimension/functionality. We report here a microporous, ftw-type Zr-based MOF structure, HIAM-410 (HIAM=Hoffmann Institute of Advanced Materials), built on hexanuclear Zr 6 cluster and pyrene-1,3,6,8-tetracarboxylate (ptc 4– ). Its crystallographic structure has been determined using continuous rotation electron diffraction (cRED) technique combined with Rietveld refinement against powder X-ray diffraction data, aided by low-dose high-resolution transmission electron microscopy (HRTEM) imaging. The compound features exceptional framework stability that is comparable to the prototype MOF UiO-66. Interestingly, the linker vacancies in the pristine MOF structure could be partially restored by post-synthetic linker insertion. Its separation capability of hexane isomers is enhanced substantially upon the linker vacancy engineering. As a result, the restored structure exhibits efficient splitting of monobranched and dibranched hexane isomers at both room temperature and industrially relevant temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the interfacial structure and crystallinity for direct growth of Mn 3 Sn(0001) on sapphire (0001) by molecular beam epitaxy

The Kagome antiferromagnet Mn 3 Sn has garnered a lot of attention due to the presence of interesting properties such as anomalous Hall effects and Nernst effects. Until now, few papers have been reported to grow using molecular beam epitaxy with a buffer layer or on other substrates. In this paper, we discuss the synthesis of crystalline Mn 3 Sn layers, prepared on Al 2 O 3 (0001) without a buffer layer using molecular beam epitaxy. The growth is monitored in-situ using reflection high energy electron diffraction and measured ex-situ using X-ray diffraction, Rutherford back-scattering, and cross-sectional scanning transmission electron microscopy. The samples were deposited at 524 ± 5 °C, with an Mn: Sn atomic flux ratio of 3.2:1 for 90 minutes. Orientation relationships between the Mn 3 Sn films and the sapphire substrates are determined from in-plane and out-of-plane measurements. Our analysis indicates that the resulting film is predominantly c−plane oriented. Lastly, the samples prepared in this way were found to be discontiguous, showing a 3-dimensional morphology. According to first-principles calculations, the Mn 3 Sn exhibits a displaced Kagome structure in the very first stages of growth, for 2ML and 4ML growth on Al 2 O 3 (0001). This result is corroborated by calculating the surface formation energies and explains the observed RHEED patterns.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Accelerator physics at NSLS-II: research accomplishments in 2020

NSLS-II accelerator physicists provide scientific support for user operations, as well as for improvements and developments of the accelerator systems. This work includes optimization of the NSLS-II performance with high beam current and low vertical emittance, improvement of the beam stability, development of new software tools for operations and beam studies. The accelerator physicists productively worked on a number of research activities such as the conceptual design of NSLS-II accelerator upgrade; design and optimization of advanced low-emittance lattices; development of novel methods to study nonlinear beam dynamics; ultrafast electron diffraction and microscopy. The physicists also contributed to the BNL electron-ion collider project, to the APS and ALS upgrade projects. Research accomplishments achieved in 2020, are summarized in this report.

43 PARTICLE ACCELERATORS↗