Research Papers Precession Electron Diffraction 1
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Introduction to Phasing Crystallography ISSN 0907-4449
research papers Acta Crystallographica Section D Biological Introduction to phasing Crystallography ISSN 0907-4449 Garry L. Taylor When collecting X-ray diffraction data from a crystal, we Received 30 August 2009 measure the intensities of the diffracted waves scattered from Accepted 22 February 2010 a series of planes that we can imagine slicing through the Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, crystal in all directions. From these intensities we derive the Scotland amplitudes of the scattered waves, but in the experiment we lose the phase information; that is, how we offset these waves when we add them together to reconstruct an image of our Correspondence e-mail: [email protected] molecule. This is generally known as the ‘phase problem’. We can only derive the phases from some knowledge of the molecular structure. In small-molecule crystallography, some basic assumptions about atomicity give rise to relationships between the amplitudes from which phase information can be extracted. In protein crystallography, these ab initio methods can only be used in the rare cases in which there are data to at least 1.2 A˚ resolution. For the majority of cases in protein crystallography phases are derived either by using the atomic coordinates of a structurally similar protein (molecular replacement) or by finding the positions of heavy atoms that are intrinsic to the protein or that have been added (methods such as MIR, MIRAS, SIR, SIRAS, MAD, SAD or com- binations of these). The pioneering work of Perutz, Kendrew, Blow, Crick and others developed the methods of isomor- phous replacement: adding electron-dense atoms to the protein without disturbing the protein structure. -
Appendix F. Glossary
Appendix F. Glossary 2DEG 2-dimensional electron gas A/D Analog to digital AAAR American Association for Aerosol Research ADC Analog-digital converter AEM Analytical electron microscopy AFM Atomic force microscope/microscopy AFOSR Air Force Office of Scientific Research AIST (Japan) Agency of Industrial Science and Technology AIST (Japan, MITI) Agency of Industrial Science and Technology AMLCD Active matrix liquid crystal display AMM Amorphous microporous mixed (oxides) AMO Atomic, molecular, and optical AMR Anisotropic magnetoresistance ARO (U.S.) Army Research Office ARPES Angle-resolved photoelectron spectroscopy ASET (Japan) Association of Super-Advanced Electronics Technologies ASTC Australia Science and Technology Council ATP (Japan) Angstrom Technology Partnership ATP Adenosine triphosphate B Magnetic flux density B/H loop Closed figure showing B (magnetic flux density) compared to H (magnetic field strength) in a magnetizable material—also called hysteresis loop bcc Body-centered cubic BMBF (Germany) Ministry of Education, Science, Research, and Technology (formerly called BMFT) BOD-FF Bond-order-dependent force field BRITE/EURAM Basic Research of Industrial Technologies for Europe, European Research on Advanced Materials program CAD Computer-assisted design CAIBE Chemically assisted ion beam etching CBE Chemical beam epitaxy 327 328 Appendix F. Glossary CBED Convergent beam electron diffraction cermet Ceramic/metal composite CIP Cold isostatic press CMOS Complementary metal-oxide semiconductor CMP Chemical mechanical polishing -
System Design and Verification of the Precession Electron Diffraction Technique
NORTHWESTERN UNIVERSITY System Design and Verification of the Precession Electron Diffraction Technique A DISSERTATION SUBMITTED TO THE GRADUATE SCHOOL IN PARTIAL FULFILLMENT OF THE REQUIREMENTS for the degree DOCTOR OF PHILOSOPHY Field of Materials Science and Engineering By Christopher Su-Yan Own EVANSTON, ILLINOIS First published on the WWW 01, August 2005 Build 05.12.07. PDF available for download at: http://www.numis.northwestern.edu/Research/Current/precession.shtml c Copyright by Christopher Su-Yan Own 2005 All Rights Reserved ii ABSTRACT System Design and Verification of the Precession Electron Diffraction Technique Christopher Su-Yan Own Bulk structural crystallography is generally a two-part process wherein a rough starting structure model is first derived, then later refined to give an accurate model of the structure. The critical step is the deter- mination of the initial model. As materials problems decrease in length scale, the electron microscope has proven to be a versatile and effective tool for studying many problems. However, study of complex bulk structures by electron diffraction has been hindered by the problem of dynamical diffraction. This phenomenon makes bulk electron diffraction very sensitive to specimen thickness, and expensive equip- ment such as aberration-corrected scanning transmission microscopes or elaborate methodology such as high resolution imaging combined with diffraction and simulation are often required to generate good starting structures. The precession electron diffraction technique (PED), which has the ability to significantly reduce dynamical effects in diffraction patterns, has shown promise as being a “philosopher’s stone” for bulk electron diffraction. However, a comprehensive understanding of its abilities and limitations is necessary before it can be put into widespread use as a standalone technique. -
Optical Ptychographic Phase Tomography
University College London Final year project Optical Ptychographic Phase Tomography Supervisors: Author: Prof. Ian Robinson Qiaoen Luo Dr. Fucai Zhang March 20, 2013 Abstract The possibility of combining ptychographic iterative phase retrieval and computerised tomography using optical waves was investigated in this report. The theoretical background and historic developments of ptychographic phase retrieval was reviewed in the first part of the report. A simple review of the principles behind computerised tomography was given with 2D and 3D simulations in the following chapters. The sample used in the experiment is a glass tube with its outer wall glued with glass microspheres. The tube has a diameter of approx- imately 1 mm and the microspheres have a diameter of 30 µm. The experiment demonstrated the successful recovery of features of the sam- ple with limited resolution. The results could be improved in future attempts. In addition, phase unwrapping techniques were compared and evaluated in the report. This technique could retrieve the three dimensional refractive index distribution of an optical component (ideally a cylindrical object) such as an opitcal fibre. As it is relatively an inexpensive and readily available set-up compared to X-ray phase tomography, the technique can have a promising future for application at large scale. Contents List of Figures i 1 Introduction 1 2 Theory 3 2.1 Phase Retrieval . .3 2.1.1 Phase Problem . .3 2.1.2 The Importance of Phase . .5 2.1.3 Phase Retrieval Iterative Algorithms . .7 2.2 Ptychography . .9 2.2.1 Ptychography Principle . .9 2.2.2 Ptychographic Iterative Engine . -
A Review of Transmission Electron Microscopy of Quasicrystals—How Are Atoms Arranged?
crystals Review A Review of Transmission Electron Microscopy of Quasicrystals—How Are Atoms Arranged? Ruitao Li 1, Zhong Li 1, Zhili Dong 2,* and Khiam Aik Khor 1,* 1 School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; [email protected] (R.L.); [email protected] (Z.L.) 2 School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore * Correspondence: [email protected] (Z.D.); [email protected] (K.A.K.); Tel.: +65-6790-6727 (Z.D.); +65-6592-1816 (K.A.K.) Academic Editor: Enrique Maciá Barber Received: 30 June 2016; Accepted: 15 August 2016; Published: 26 August 2016 Abstract: Quasicrystals (QCs) possess rotational symmetries forbidden in the conventional crystallography and lack translational symmetries. Their atoms are arranged in an ordered but non-periodic way. Transmission electron microscopy (TEM) was the right tool to discover such exotic materials and has always been a main technique in their studies since then. It provides the morphological and crystallographic information and images of real atomic arrangements of QCs. In this review, we summarized the achievements of the study of QCs using TEM, providing intriguing structural details of QCs unveiled by TEM analyses. The main findings on the symmetry, local atomic arrangement and chemical order of QCs are illustrated. Keywords: quasicrystal; transmission electron microscopy; symmetry; atomic arrangement 1. Introduction The revolutionary discovery of an Al–Mn compound with 5-fold symmetry by Shechtman et al. [1] in 1982 unveiled a new family of materials—quasicrystals (QCs), which exhibit the forbidden rotational symmetries in the conventional crystallography. -
X-Ray Crystallography
X-ray Crystallography Prof. Leonardo Scapozza Pharmceutical Biochemistry School of Pharmaceutical Sciences University of Geneva, University of Lausanne E-mail: [email protected] Aim • Introduce the students to X-ray crystallography • Give the students the tools to “evaluate” a X-ray structure based scientific paper 1 Outline • The History of X-ray • The Principle of X-ray • The Steps towards the 3D structure – Crystallization – X-ray diffraction and data collection – From Pattern of Diffraction to Electron Density – X-ray structure quality assessment An extract of a structure paper 2.1. Crystallization • The hTK1 was cloned as N-terminal thrombin-cleavable His6–tagged fusion protein missing 14 amino acids of the N-terminus and 40 amino acids of the C–terminus of the wild type hTK1 sequence of 234 amino acids (this construct is further on called hTK1). The purified hTK1, consisting of residues 15-194 of the wild type sequence plus an N–terminal extension of 15 residues containing a His6–tag, was eluted from gel filtration column at a concentration of approximate 7 mg/ml with a buffer containing 5 mM Tris at pH 7.2, 10 mM NaCl and 10 mM DTT. For protein crystallization we used the hanging drop method at 23°C. Initial conditions for crystallization were found using Crystal screen Cryo no. 40 (Hampton Research). The protein solution was mixed in a 1:1 ratio with crystallization buffer (0.095 mM tri–sodium citrate pH 5.5, 12% PEG 4000, 10% isopropanol) to set up drops of 6 μl. The reservoir contained 500 μl of crystallization buffer. -
Development of Rotation Electron Diffraction As a Fully Automated And
Bin Wang Development of rotation electron Development of rotation electron diffraction as a fully automated and accurate method for structure determination and accurate automated as a fully diffraction electron of rotation Development diffraction as a fully automated and accurate method for structure determination Bin Wang Bin Wang was born in Shanghai, China. He received his B.Sc in chemistry from Fudan University in China in 2013, and M.Sc in material chemistry from Cornell University in the US in 2015. His research mainly focused on method development for TEM. ISBN 978-91-7797-646-2 Department of Materials and Environmental Chemistry Doctoral Thesis in Inorganic Chemistry at Stockholm University, Sweden 2019 Development of rotation electron diffraction as a fully automated and accurate method for structure determination Bin Wang Academic dissertation for the Degree of Doctor of Philosophy in Inorganic Chemistry at Stockholm University to be publicly defended on Monday 10 June 2019 at 13.00 in Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B. Abstract Over the past decade, electron diffraction methods have aroused more and more interest for micro-crystal structure determination. Compared to traditional X-ray diffraction, electron diffraction breaks the size limitation of the crystals studied, but at the same time it also suffers from much stronger dynamical effects. While X-ray crystallography has been almost thoroughly developed, electron crystallography is still under active development. To be able to perform electron diffraction experiments, adequate skills for using a TEM are usually required, which makes ED experiments less accessible to average users than X-ray diffraction. Moreover, the relatively poor data statistics from ED data prevented electron crystallography from being widely accepted in the crystallography community. -
Principles of the Phase Contrast (Electron) Microscopy
Principles of Phase Contrast (Electron) Microscopy Marin van Heel (Version 16 Sept. 2018) CNPEM / LNNnano, Campinas, Brazil ([email protected]) (© 1980 – 2018) 1. Introduction: In phase-contrast light and electron microscopy, one exploits the wave properties of photons and electrons respectively. The principles of imaging with waves are the realm of “Fourier Optics”. As a very first “Gedankenexperiment”, let us think back to days when we – as children – would focus the (parallel) light waves from the (far away) sun on a piece of paper in order to set it alight. What lesson did we learn from these early scientific experiments (Fig. 1)? Fig. 1: Plane parallel waves are focussed into a single point in the back focal plane of a positive lens (with focal distance “F”). The plane waves are one wavelength (“λ”) apart. The object here is just a plain piece of glass place in the object plane. In Fig. 1, the plane waves illuminate an object that is merely a flat sheet of glass and thus the waves exiting the object on right are plane waves indistinguishable from the incident waves. These plane waves are converted into convergent waves by a simple positive lens, which waves then reach a focus in the back focal plane. This optical system is capable of converting a “constant” plane wave in the front focal plane into a single point in the back focal plane. 1 Fig. 2: A single point scatterer in the object plane leads to secondary (“scattered”) concentric waves emerging from that point in the object. Since the object is placed in the front focal plane, these scattered or “diffracted” secondary waves become plane waves hitting the back focal plane of the system. -
Phase Problem in X-Ray Crystallography, and Its Solution Reciprocal Directions and Spacings from the Real Lattice
Phase Problem in X-ray Secondary article Crystallography, and Its Article Contents . The Phase Problem in X-ray Crystallography Solution . Patterson Methods . Direct Methods Kevin Cowtan, University of York, UK . Multiple Isomorphous Replacement . Multiwavelength Anomalous Dispersion (MAD) X-ray crystallography can provide detailed information about the structure of biological . Molecular Replacement molecules if the ‘phase problem’ can be solved for the molecule under study. The . Phase Improvement phase problem arises because it is only possible to measure the amplitude of diffraction . Summary spots: information on the phase of the diffracted radiation is missing. Techniques are available to reconstruct this information. The Phase Problem in X-ray called the unit cell. It is convenient to define crystal axes a, b Crystallography and c defining the unit cell in three dimensions. Scattering along directions reflecting the lattice repeat will be X-ray diffraction provides one of the most important tools reinforced by every repeat of the unit cell, and will be for examining the three-dimensional (3D) structure of strong; scattering along all other directions will be weak. biological macromolecules. The physics of diffraction As a result, the full diffraction pattern of the crystal is a requires that in order to resolve features of atomic pattern of spots, forming a three-dimensional lattice with structure it is necessary to employ radiation with a wavelength of the order of atomic spacing or smaller. X- rays have suitable wavelength, and interact with the Scattered waves are electrons of the atoms. However, the interaction between out of phase X-rays and electrons is weak, and such energetic radiation causes ionization of the constituent atoms of the molecule, damaging the molecule under study. -
Three-Dimensional Electron Crystallography of Protein Microcrystals Dan Shi†, Brent L Nannenga†, Matthew G Iadanza†, Tamir Gonen*
RESEARCH ARTICLE elife.elifesciences.org Three-dimensional electron crystallography of protein microcrystals Dan Shi†, Brent L Nannenga†, Matthew G Iadanza†, Tamir Gonen* Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Abstract We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology. DOI: 10.7554/eLife.01345.001 Introduction X-ray crystallography depends on large and well-ordered crystals for diffraction studies. Crystals are *For correspondence: gonent@ solids composed of repeated structural motifs in a three-dimensional lattice (hereafter called ‘3D janelia.hhmi.org crystals’). The periodic structure of the crystalline solid acts as a diffraction grating to scatter the †These authors contributed X-rays. For every elastic scattering event that contributes to a diffraction pattern there are ∼10 inelastic equally to this work events that cause beam damage (Henderson, 1995). -
Three-Dimensional Electron Diffraction for Structural Analysis of Beam-Sensitive Metal-Organic Frameworks
crystals Review Three-Dimensional Electron Diffraction for Structural Analysis of Beam-Sensitive Metal-Organic Frameworks Meng Ge, Xiaodong Zou and Zhehao Huang * Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden; [email protected] (M.G.); [email protected] (X.Z.) * Correspondence: [email protected] Abstract: Electrons interact strongly with matter, which makes it possible to obtain high-resolution electron diffraction data from nano- and submicron-sized crystals. Using electron beam as a radia- tion source in a transmission electron microscope (TEM), ab initio structure determination can be conducted from crystals that are 6–7 orders of magnitude smaller than using X-rays. The rapid development of three-dimensional electron diffraction (3DED) techniques has attracted increasing interests in the field of metal-organic frameworks (MOFs), where it is often difficult to obtain large and high-quality crystals for single-crystal X-ray diffraction. Nowadays, a 3DED dataset can be acquired in 15–250 s by applying continuous crystal rotation, and the required electron dose rate can be very low (<0.1 e s−1 Å−2). In this review, we describe the evolution of 3DED data collection techniques and how the recent development of continuous rotation electron diffraction techniques improves data quality. We further describe the structure elucidation of MOFs using 3DED techniques, showing examples of using both low- and high-resolution 3DED data. With an improved data quality, 3DED can achieve a high accuracy, and reveal more structural details of MOFs. Because the physical Citation: Ge, M.; Zou, X.; Huang, Z. -
Diffraction from One- and Two-Dimensional Quasicrystalline Gratings N
Diffraction from one- and two-dimensional quasicrystalline gratings N. Ferralis, A. W. Szmodis, and R. D. Diehla) Department of Physics and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802 ͑Received 9 December 2003; accepted 2 April 2004͒ The diffraction from one- and two-dimensional aperiodic structures is studied by using Fibonacci and other aperiodic gratings produced by several methods. By examining the laser diffraction patterns obtained from these gratings, the effects of aperiodic order on the diffraction pattern was observed and compared to the diffraction from real quasicrystalline surfaces. The correspondence between diffraction patterns from two-dimensional gratings and from real surfaces is demonstrated. © 2004 American Association of Physics Teachers. ͓DOI: 10.1119/1.1758221͔ I. INTRODUCTION tural unit. The definition of a crystal included the require- ment of periodicity until 1992.14 Aperiodicity and tradition- In the past 5–10 years, there has been considerable inter- ally forbidden rotational symmetries introduce features in est in the structure of the surfaces of quasicrystal alloys, diffraction patterns that make interpretation by the traditional which provide realizations of quasicrystalline order in two means more complex. Simulations can provide a means for dimensions.1 The best-known examples of two-dimensional building intuition of the effects of quasicrystalline order on ͑2D͒ quasicrystal structures might be the tilings generated by diffraction patterns without resorting to