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"Electron diffraction"
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Quasicrystalline 30° twisted bilayer graphene as an incommensurate superlattice with strong interlayer coupling
by
Zhou, Shuyun
,
Chan, Chun Kai
,
Bao, Kejie
in
Applied Physical Sciences
,
Brillouin zones
,
Cones
2018
The interlayer coupling can be used to engineer the electronic structure of van der Waals heterostructures (superlattices) to obtain properties that are not possible in a single material. So far research in heterostructures has been focused on commensurate superlattices with a long-ranged Moiré period. Incommensurate heterostructures with rotational symmetry but not translational symmetry (in analogy to quasicrystals) are not only rare in nature, but also the interlayer interaction has often been assumed to be negligible due to the lack of phase coherence. Here we report the successful growth of quasicrystalline 30° twisted bilayer graphene (30°-tBLG), which is stabilized by the Pt(111) substrate, and reveal its electronic structure. The 30°-tBLG is confirmed by low energy electron diffraction and the intervalley double-resonance Raman mode at 1383 cm−1. Moreover, the emergence of mirrored Dirac cones inside the Brillouin zone of each graphene layer and a gap opening at the zone boundary suggest that these two graphene layers are coupled via a generalized Umklapp scattering mechanism—that is, scattering of a Dirac cone in one graphene layer by the reciprocal lattice vector of the other graphene layer. Our work highlights the important role of interlayer coupling in incommensurate quasicrystalline superlattices, thereby extending band structure engineering to incommensurate superstructures.
Journal Article
Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions
by
Brázda, Petr
,
Klementová, Mariana
,
Krysiak, Yaşar
in
3d electron diffraction
,
Accuracy
,
Crystal lattices
2022
Determination of lattice parameters from 3D electron diffraction (3D ED) data measured in a transmission electron microscope is hampered by a number of effects that seriously limit the achievable accuracy. The distortion of the diffraction patterns by the optical elements of the microscope is often the most severe problem. A thorough analysis of a number of experimental datasets shows that, in addition to the well known distortions, namely barrel-pincushion, spiral and elliptical, an additional distortion, dubbed parabolic, may be observed in the data. In precession electron diffraction data, the parabolic distortion leads to excitation-error-dependent shift and splitting of reflections. All distortions except for the elliptical distortion can be determined together with lattice parameters from a single 3D ED data set. However, the parameters of the elliptical distortion cannot be determined uniquely due to correlations with the lattice parameters. They can be determined and corrected either by making use of the known Laue class of the crystal or by combining data from two or more crystals. The 3D ED data can yield lattice parameter ratios with an accuracy of about 0.1% and angles with an accuracy better than 0.03°.
Journal Article
Ultrafast low-energy electron diffraction in transmission resolves polymer/graphene superstructure dynamics
2014
Two-dimensional systems such as surfaces and molecular monolayers exhibit a multitude of intriguing phases and complex transitions. Ultrafast structural probing of such systems offers direct time-domain information on internal interactions and couplings to a substrate or bulk support. We have developed ultrafast low-energy electron diffraction and investigate in transmission the structural relaxation in a polymer/graphene bilayer system excited out of equilibrium. The laser-pump/electron-probe scheme resolves the ultrafast melting of a polymer superstructure consisting of folded-chain crystals registered to a free-standing graphene substrate. We extract the time scales of energy transfer across the bilayer interface, the loss of superstructure order, and the appearance of an amorphous phase with short-range correlations. The high surface sensitivity makes this experimental approach suitable for numerous problems in ultrafast surface science.
Journal Article
Femtosecond time-resolved MeV electron diffraction
2015
We report the experimental demonstration of femtosecond electron diffraction using high-brightness MeV electron beams. High-quality, single-shot electron diffraction patterns for both polycrystalline aluminum and single-crystal 1T-TaS2 are obtained utilizing a 5 fC (∼3 × 104 electrons) pulse of electrons at 2.8 MeV. The high quality of the electron diffraction patterns confirms that electron beam has a normalized emittance of ∼50 nm rad. The transverse and longitudinal coherence length is ∼11 and ∼2.5 nm, respectively. The timing jitter between the pump laser and probe electron beam was found to be ∼100 fs (rms). The temporal resolution is demonstrated by observing the evolution of Bragg and superlattice peaks of 1T-TaS2 following an 800 nm optical pump and was found to be 130 fs. Our results demonstrate the advantages of MeV electrons, including large elastic differential scattering cross-section and access to high-order reflections, and the feasibility of ultimately realizing below 10 fs time-resolved electron diffraction.
Journal Article
Protein electrostatic potential Fourier maps calculated using the transferable aspherical atom model and the independent atom model across resolutions
by
Dominiak, Paulina Maria
,
Kulik, Marta
in
3d ed
,
3d electron diffraction
,
3d reconstruction and image processing
2025
Common sense tells us that experimental maps of lower (worse) resolution obtained from cryogenic electron microscopy or three-dimensional electron diffraction convey less information than maps of higher (better) resolution. However, information regarding the presence of charged moieties is more visible at lower resolutions. To investigate this phenomenon from a theoretical perspective, we analyzed the effects of truncation of data from the high-resolution end (from 1 Å to 8 Å) on theoretical Fourier images of the electrostatic potential of protein crystals, using both the popular independent atom model (IAM) of scattering factors and the more accurate transferable aspherical atom model (TAAM) combined with the UBDB/MATTS data bank. We compared our findings with those obtained for theoretical Fourier images of electron density maps associated with X-ray diffraction. Strikingly, when IAM is applied, there is almost no qualitative difference between the Fourier maps of electrostatic potential and electron density, regardless of their resolution. In contrast, the Fourier electrostatic potential maps calculated with TAAM, when of lower resolution, strongly differ from the electron density maps at the positions of charged moieties. Comparing TAAM and IAM, in the case of Fourier electrostatic potential maps, the relative difference between them is usually greatest at lower resolution maps, with a noticeable dependence on atom type and charge. In the case of Fourier electron density maps, this relative difference is much smaller and becomes more apparent in higher resolution maps. Thus, the use of accurate scattering factors is much more important for lower resolution data than for higher resolution data if one wants to investigate charged systems.
Journal Article
Crystal symmetry determination in electron diffraction using machine learning
by
Maryanovsky, Daniel
,
Vecchio, Kenneth S.
,
Kaufmann, Kevin
in
Algorithms
,
Artificial Intelligence
,
Crystal structure
2020
Electron backscatter diffraction (EBSD) is one of the primary tools for crystal structure determination. However, this method requires human input to select potential phases for Hough-based or dictionary pattern matching and is not well suited for phase identification. Automated phase identification is the first step in making EBSD into a high-throughput technique. We used a machine learning–based approach and developed a general methodology for rapid and autonomous identification of the crystal symmetry from EBSD patterns. We evaluated our algorithm with diffraction patterns from materials outside the training set. The neural network assigned importance to the same symmetry features that a crystallographer would use for structure identification.
Journal Article
Atomic Resolution Imaging of a Carbon Nanotube from Diffraction Intensities
by
Gao, M.
,
Vartanyants, I.
,
Zuo, J. M.
in
Carbon nanotubes
,
Clusters, nanoparticles, and nanocrystalline materials
,
Condensed matter: structure, mechanical and thermal properties
2003
Atomic imaging of three-dimensional structures has required a crystal in diffraction or a lens in electron imaging. Whereas diffraction achieves very high resolution by averaging over many cells, imaging gives localized structural information, such as the position of a single dopant atom. However, lens aberrations limit electron imaging resolution to about 1 angstrom. Resolution is reduced further by low contrast from weak scattering or from the limitations on electron dose for radiation-sensitive molecules. We show that both high resolution and high contrast can be achieved by imaging from diffraction with a nanometer-sized coherent electron beam. The phase problem is solved by oversampling and iterative phase retrieval. We apply this technique to image a double-wall carbon nanotube at 1-angstrom resolution, revealing the structure of two tubes of different helicities. Because the only requirement for imaging is a diffraction pattern sampled below the Nyquist frequency, our technique has the potential to image nonperiodic nanostructures, including biological macromolecules, at diffraction intensity-limited resolutions.
Journal Article
Imaging ultrafast molecular dynamics with laser-induced electron diffraction
by
Sistrunk, Emily
,
Xu, Junliang
,
Blaga, Cosmin I.
in
639/638/563/981
,
639/766/25
,
639/766/930/2735
2012
Molecular structures are imaged with sub-ångström precision and exposure times of a few femtoseconds.
Catching up with molecular dynamics
Molecular imaging, or the determination of the positions of atoms in molecules, is an important technique in the physical, chemical and biological sciences. But going beyond mere structure determination, recent technical developments offer the tantalizing prospect of access to ultrafast snapshots of biological molecules and condensed-phase systems undergoing structural changes. One approach uses laser-ionized bursts of coherent electron wave packets to self-interrogate the parent molecular structure. Here, Blaga
et al
. use this laser-induced electron diffraction (LIED) method to map the structural responses of oxygen and nitrogen molecules to ionization. By measuring a 0.1-ångström displacement in the oxygen bond length occurring in a time interval of about 5 femtoseconds, the authors establish LIED as a promising approach for imaging of gas-phase molecules with unprecedented spatio-temporal resolution.
Establishing the structure of molecules and solids has always had an essential role in physics, chemistry and biology. The methods of choice are X-ray and electron diffraction, which are routinely used to determine atomic positions with sub-ångström spatial resolution. Although both methods are currently limited to probing dynamics on timescales longer than a picosecond, the recent development of femtosecond sources of X-ray pulses and electron beams suggests that they might soon be capable of taking ultrafast snapshots of biological molecules
1
,
2
and condensed-phase systems
3
,
4
,
5
,
6
undergoing structural changes. The past decade has also witnessed the emergence of an alternative imaging approach based on laser-ionized bursts of coherent electron wave packets that self-interrogate the parent molecular structure
7
,
8
,
9
,
10
,
11
. Here we show that this phenomenon can indeed be exploited for laser-induced electron diffraction
10
(LIED), to image molecular structures with sub-ångström precision and exposure times of a few femtoseconds. We apply the method to oxygen and nitrogen molecules, which on strong-field ionization at three mid-infrared wavelengths (1.7, 2.0 and 2.3 μm) emit photoelectrons with a momentum distribution from which we extract diffraction patterns. The long wavelength is essential for achieving atomic-scale spatial resolution, and the wavelength variation is equivalent to taking snapshots at different times. We show that the method has the sensitivity to measure a 0.1 Å displacement in the oxygen bond length occurring in a time interval of ∼5 fs, which establishes LIED as a promising approach for the imaging of gas-phase molecules with unprecedented spatio-temporal resolution.
Journal Article
Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
by
Duarte, Jose M.
,
Sekharan, Monica
,
Feng, Zukang
in
Archives & records
,
BASIC BIOLOGICAL SCIENCES
,
Biochemistry & Molecular Biology
2022
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.
Journal Article
An Atomic-Level View of Melting Using Femtosecond Electron Diffraction
by
Dwyer, Jason R.
,
Jordan, Robert E.
,
Siwick, Bradley J.
in
Aluminum
,
Aluminum (Metal)
,
Atomic structure
2003
We used 600-femtosecond electron pulses to study the structural evolution of aluminum as it underwent an ultrafast laser-induced solid-liquid phase transition. Real-time observations showed the loss of long-range order that was present in the crystalline phase and the emergence of the liquid structure where only short-range atomic correlations were present; this transition occurred in 3.5 picoseconds for thin-film aluminum with an excitation fluence of 70 millijoules per square centimeter. The sensitivity and time resolution were sufficient to capture the time-dependent pair correlation function as the system evolved from the solid to the liquid state. These observations provide an atomic-level description of the melting process, in which the dynamics are best understood as a thermal phase transition under strongly driven conditions.
Journal Article