A Review of Transmission Electron Microscopy of Quasicrystals—How Are Atoms Arranged?
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WHAT IS...A Quasicrystal?, Volume 53, Number 8
?WHAT IS... a Quasicrystal? Marjorie Senechal The long answer is: no one is sure. But the short an- diagrams? The set of vertices of a Penrose tiling does— swer is straightforward: a quasicrystal is a crystal that was known before Shechtman’s discovery. But with forbidden symmetry. Forbidden, that is, by “The what other objects do, and how can we tell? The ques- Crystallographic Restriction”, a theorem that confines tion was wide open at that time, and I thought it un- the rotational symmetries of translation lattices in two- wise to replace one inadequate definition (the lattice) and three-dimensional Euclidean space to orders 2, 3, with another. That the commission still retains this 4, and 6. This bedrock of theoretical solid-state sci- definition today suggests the difficulty of the ques- ence—the impossibility of five-fold symmetry in crys- tion we deliberately but implicitly posed. By now a tals can be traced, in the mineralogical literature, back great many kinds of aperiodic crystals have been to 1801—crumbled in 1984 when Dany Shechtman, a grown in laboratories around the world; most of them materials scientist working at what is now the National are metals, alloys of two or three kinds of atoms—bi- Institute of Standards and Technology, synthesized nary or ternary metallic phases. None of their struc- aluminium-manganese crystals with icosahedral sym- tures has been “solved”. (For a survey of current re- metry. The term “quasicrystal”, hastily coined to label search on real aperiodic crystals see, for example, the such theretofore unthinkable objects, suggests the website of the international conference ICQ9, confusions that Shechtman’s discovery sowed. -
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 -
Quasicrystals a New Kind of Symmetry Sandra Nair First, Definitions
Quasicrystals A new kind of symmetry Sandra Nair First, definitions ● A lattice is a poset in which every element has a unique infimum and supremum. For example, the set of natural numbers with the notion of ordering by magnitude (1<2). For our purposes, we can think of an array of atoms/molecules with a clear sense of assignment. ● A Bravais lattice is a discrete infinite array of points generated by linear integer combinations of 3 independent primitive vectors: {n1a1 + n2a2 + n3a3 | n1, n2, n3 ∈ Z}. ● Crystal structures = info of lattice points + info of the basis (primitive) vectors. ● Upto isomorphism of point groups (group of isometries leaving at least 1 fixed point), 14 different Bravais lattice structures possible in 3D. Now, crystals... ● Loosely speaking, crystals are molecular arrangements built out of multiple unit cells of one (or more) Bravais lattice structures. ● Crystallographic restriction theorem: The rotational symmetries of a discrete lattice are limited to 2-, 3-, 4-, and 6-fold. ● This leads us to propose a “functional” definition: A crystal is a material that has a discrete diffraction pattern, displaying rotational symmetries of orders 2, 3, 4 and 6. ● Note: Order 5 is a strictly forbidden symmetry → important for us. Tessellations aka tilings Now that we have diffraction patterns to work with, we consider the question of whether a lattice structure tiles or tessellates the plane. This is where the order of the symmetry plays a role. The crystals are special, as they display translational symmetries. As such, the tiling of their lattice structures (which we could see thanks to diffraction patterns) are periodic- they repeat at regular intervals. -
Some Considerations Relating to the Dynamics of Quasicrystals
Some considerations relating to the dynamics of quasicrystals M. Pitk¨anen Email: [email protected]. http://tgdtheory.com/public_html/. November 12, 2012 Contents 1 The dynamics of quasicrystals, the dynamics of K¨ahleraction, symbolic dynamics, and the dynamics of self-organization 1 1.1 The non-determinism for the dynamics of quasicrystals contra non-determinism of K¨ahleraction . .1 1.2 The dynamics of quasicrystals as a model for fundamental dynamics or high level sym- bolic dynamics? . .2 1.3 Could ordered water layers around biomolecules be modelled as quasicrystal like structure?3 2 What could be the variational principle behind self-organization? 4 2.1 Why Negentropy Maximization Principle should favor quasicrystals? . .5 2.2 Maximal capacity to represent information with minimal metabolic energy costs as a basic variational principle? . .5 2.3 A possible realization for 4-D dynamics favoring quasicrystal like structures . .6 2.4 Summary . .7 1 The dynamics of quasicrystals, the dynamics of K¨ahlerac- tion, symbolic dynamics, and the dynamics of self-organization The dynamics of quasicrystals looks to me very interesting because it shares several features of the dynamics of K¨ahleraction defining the basic variational principle of classical TGD and defining the dynamics of space-time surfaces. In the following I will compare the basic features of the dynamics of quasicrystals to the dynamics of preferred extremals of K¨ahleraction [K1]. Magnetic body carrying dark matter is the fundamental intentional agent in TGD inspired quantum biology and the cautious proposal is that magnetic flux sheets could define the grid of 3-planes (or more general 3-surfaces) defining quasi-periodic background fields favoring 4-D quasicrystals or more general structures in TGD Universe. -
Quasicrystals
Volume 106, Number 6, November–December 2001 Journal of Research of the National Institute of Standards and Technology [J. Res. Natl. Inst. Stand. Technol. 106, 975–982 (2001)] Quasicrystals Volume 106 Number 6 November–December 2001 John W. Cahn The discretely diffracting aperiodic crystals Key words: aperiodic crystals; new termed quasicrystals, discovered at NBS branch of crystallography; quasicrystals. National Institute of Standards and in the early 1980s, have led to much inter- Technology, disciplinary activity involving mainly Gaithersburg, MD 20899-8555 materials science, physics, mathematics, and crystallography. It led to a new un- Accepted: August 22, 2001 derstanding of how atoms can arrange [email protected] themselves, the role of periodicity in na- ture, and has created a new branch of crys- tallography. Available online: http://www.nist.gov/jres 1. Introduction The discovery of quasicrystals at NBS in the early Crystal periodicity has been an enormously important 1980s was a surprise [1]. By rapid solidification we had concept in the development of crystallography. Hau¨y’s made a solid that was discretely diffracting like a peri- hypothesis that crystals were periodic structures led to odic crystal, but with icosahedral symmetry. It had long great advances in mathematical and experimental crys- been known that icosahedral symmetry is not allowed tallography in the 19th century. The foundation of crys- for a periodic object [2]. tallography in the early nineteenth century was based on Periodic solids give discrete diffraction, but we did the restrictions that periodicity imposes. Periodic struc- not know then that certain kinds of aperiodic objects can tures in two or three dimensions can only have 1,2,3,4, also give discrete diffraction; these objects conform to a and 6 fold symmetry axes. -
Conformal Quasicrystals and Holography
Conformal Quasicrystals and Holography Latham Boyle1, Madeline Dickens2 and Felix Flicker2;3 1Perimeter Institute for Theoretical Physics, Waterloo, Ontario N2L 2Y5, Canada, N2L 2Y5 2Department of Physics, University of California, Berkeley, California 94720, USA 3Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, United Kingdom Recent studies of holographic tensor network models defined on regular tessellations of hyperbolic space have not yet addressed the underlying discrete geometry of the boundary. We show that the boundary degrees of freedom naturally live on a novel structure, a conformal quasicrystal, that pro- vides a discrete model of conformal geometry. We introduce and construct a class of one-dimensional conformal quasicrystals, and discuss a higher-dimensional example (related to the Penrose tiling). Our construction permits discretizations of conformal field theories that preserve an infinite discrete subgroup of the global conformal group at the cost of lattice periodicity. I. INTRODUCTION dom [12{24]. Meanwhile, quantum information theory provides a unifying language for these studies in terms of entanglement, quantum circuits, and quantum error A central topic in theoretical physics over the past two correction [25]. decades has been holography: the idea that a quantum These investigations have gradually clarified our un- theory in a bulk space may be precisely dual to another derstanding of the discrete geometry in the bulk. There living on the boundary of that space. The most concrete has been a common expectation, based on an analogy and widely-studied realization of this idea has been the with AdS/CFT [1{3], that TNs living on discretizations AdS/CFT correspondence [1{3], in which a gravitational of a hyperbolic space define a lattice state of a critical theory living in a (d + 1)-dimensional negatively-curved system on the boundary and vice-versa. -
2007 136Th Annual Meeting & Exhibition Linking Science and Technology for Global Solutions
2007 136th Annual Meeting & Exhibition Linking Science and Technology for Global Solutions Technical Program Program-at-a-Glance ..............................................................2 Session Listing .......................................................................8 Monday AM ...........................................................................16 Monday PM ............................................................................63 Tuesday AM .........................................................................117 Tuesday PM .........................................................................164 Wednesday AM ...................................................................223 Wednesday PM ...................................................................274 Thursday AM .......................................................................327 General Posters ..................................................................359 Index ....................................................................................363 2007 136th Annual Meeting & Exhibition Monday Tuesday Wednesday Thursday ROOM AM PM AM PM AM PM AM Materials Materials Intellectual Intellectual Materials Materials Materials Processing under Processing under Property in Property in Processing under Processing under Processing under the Influence of the Influence of Materials Materials the Influence of the Influence of the Influence of External Fields: External Fields: Science: Patents, Science: Patents, External Fields: External Fields: -
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. -
Nanotechnology and Quasicrystals: from Self Assembly to Photonic Applications
Nanotechnology and Quasicrystals: From self assembly to photonic applications. Ron Lifshitz Raymond and Beverly Sackler School of Physics & Astronomy Tel Aviv University, 69978 Tel Aviv, Israel. After providing a concise overview on quasicrystals and their discovery more than a quarter of a century ago, I consider the unexpected interplay between nanotechnology and quasiperiodic crystals. Of particular relevance are efforts to fabricate artificial functional micro- or nanostructures, as well as efforts to control the self-assembly of nanostructures, where current knowledge about the possibility of having long-range order without periodicity can provide significant advantages. I discuss examples of systems ranging from artificial metamaterials for photonic applications, through self-assembled soft matter, to surface waves and optically-induced nonlinear photonic quasicrystals. 1 Nanotechnology and quasicrystals? When organizers of the NATO Advanced Research Workshop on nanotechnology, held in St. Petersburg in June 2008, asked me to deliver a keynote lecture on quasicrystals I was certain that they had made a mistake. I have been studying quasicrystals for over 15 years and investigating nanomechanical systems for just about a decade, and although one always finds connections between different scientific fields, I had never expected such an invitation. Nevertheless, the organizers insisted and explained that they wanted to learn about the possibility of exploiting nontrivial symmetries—perhaps imitating what viruses do—and in general, learn the lesson of a scientific community that was forced by nature to keep an open mind and “think outside of the box”. This chapter is motivated by my presentation on quasicrystals at the NATO ARW on nanotechnology in St. -
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). -
Table of Contents (PDF)
January 31, 2012 u vol. 109 u no. 5 u 1355–1808 Cover image: A bright pink seed pod and older senescent seed pods harboring black seeds are shown on the terminal structure, called a cephalium, of a Melocactus plant. Fang Chen et al. found that the dark coats enveloping the seeds of Melocactus, other cactus species, and the vanilla orchid contain a lignin polymer formed by the oxidative polymerization of an unusual monolignol known as caffeyl alcohol. The findings could help researchers develop lignin bioengineering methods while also providing insights into the diversity of land plants. See the article by Chen et al. on pages 1772–1777. Image courtesy of Broderick Stearns (Samuel Roberts Noble Foundation, Ardmore, OK). From the Cover 1772 Lignin polymers in nature 1396 Extraterrestrial quasicrystals 1437 Magnetic fields and enzyme reactions 1607 Timing cytokine secretion from T cells 1691 Antibiotics in agriculture Contents COMMENTARIES 1357 Are biochemical reactions affected by weak magnetic fields? THIS WEEK IN PNAS P. J. Hore See companion article on page 1437 1355 In This Issue 1359 Travels in time: Assessing the functional complexity of T cells W. Nicholas Haining See companion article on page 1607 LETTERS (ONLINE ONLY) E206 Femtosecond laser vaporization that preserves PNAS PLUS (AUTHOR SUMMARIES) protein-folded structure: An unproven idea Kathrin Breuker, Owen S. Skinner, and Fred W. McLafferty BIOLOGICAL SCIENCES E207 Reply to Breuker et al.: How laser electrospray mass spectrometry (LEMS) measures condensed phase BIOCHEMISTRY protein -
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.