Imposing Non-Crystallographic Symmetry Constraints on Multipole Populations and Defining Local Atomic Coordinate Systems

1980 ◽  
pp. 473-477
Author(s):  
Edwin D. Stevens
Keyword(s):  
Coordinate Systems ◽  
Crystallographic Symmetry ◽  
Symmetry Constraints

Mathematical aspects of molecular replacement. V. Isolating feasible regions in motion spaces

2020 ◽  
Vol 76 (2) ◽  
pp. 145-162
Author(s):  
Bernard Shiffman ◽  
Shengnan Lyu ◽  
Gregory S. Chirikjian
Keyword(s):  
Configuration Space ◽  
A Priori ◽  
Rigid Bodies ◽  
Molecular Replacement ◽  
Space Group ◽  
Fundamental Domains ◽  
Crystallographic Symmetry ◽  
Symmetry Constraints ◽  
Translation Space ◽  
The Right

This paper mathematically characterizes the tiny feasible regions within the vast 6D rotation–translation space in a full molecular replacement (MR) search. The capability to a priori isolate such regions is potentially important for enhancing robustness and efficiency in computational phasing in macromolecular crystallography (MX). The previous four papers in this series have concentrated on the properties of the full configuration space of rigid bodies that move relative to each other with crystallographic symmetry constraints. In particular, it was shown that the configuration space of interest in this problem is the right-coset space Γ\G, where Γ is the space group of the chiral macromolecular crystal and G is the group of rigid-body motions, and that fundamental domains F Γ\G can be realized in many ways that have interesting algebraic and geometric properties. The cost function in MR methods can be viewed as a function on these fundamental domains. This, the fifth and final paper in this series, articulates the constraints that bodies packed with crystallographic symmetry must obey. It is shown that these constraints define a thin feasible set inside a motion space and that they fall into two categories: (i) the bodies must not interpenetrate, thereby excluding so-called `collision zones' from consideration in MR searches; (ii) the bodies must be in contact with a sufficient number of neighbors so as to form a rigid network leading to a physically realizable crystal. In this paper, these constraints are applied using ellipsoidal proxies for proteins to bound the feasible regions. It is shown that the volume of these feasible regions is small relative to the total volume of the motion space, which justifies the use of ellipsoids as proxies for complex proteins in MR searches, and this is demonstrated with P1 (the simplest space group) and with P212121 (the most common space group in MX).

scholarly journals Finite auxetic deformations of plane tessellations

2013 ◽  
Vol 469 (2149) ◽  
pp. 20120465 ◽  
Author(s):  
Holger Mitschke ◽  
Vanessa Robins ◽  
Klaus Mecke ◽  
Gerd E. Schröder-Turk
Keyword(s):  
Deformation Behaviour ◽  
Deformation Mode ◽  
Energy Functional ◽  
Finite Deformations ◽  
Hexagonal Symmetry ◽  
Quadratic Equations ◽  
Crystallographic Symmetry ◽  
Auxetic Structures ◽  
Symmetry Constraints ◽  
Star Polygons

We systematically analyse the mechanical deformation behaviour, in particular Poisson's ratio, of floppy bar-and-joint frameworks based on periodic tessellations of the plane. For frameworks with more than one deformation mode, crystallographic symmetry constraints or minimization of an angular vertex energy functional are used to lift this ambiguity. Our analysis allows for systematic searches for auxetic mechanisms in archives of tessellations; applied to the class of one- or two-uniform tessellations by regular or star polygons, we find two auxetic structures of hexagonal symmetry and demonstrate that several other tessellations become auxetic when retaining symmetries during the deformation, in some cases with large negative Poisson ratios ν <−1 for a specific lattice direction. We often find a transition to negative Poisson ratios at finite deformations for several tessellations, even if the undeformed tessellation is infinitesimally non-auxetic. Our numerical scheme is based on a solution of the quadratic equations enforcing constant edge lengths by a Newton method, with periodicity enforced by boundary conditions.

Reference Coordinate System Requirements for Geophysics

1975 ◽  
Vol 26 ◽  
pp. 87-92
Author(s):  
P. L. Bender
Keyword(s):  
Coordinate System ◽  
Polar Motion ◽  
Main Part ◽  
Measurement Techniques ◽  
Reference Points ◽  
Angular Motion ◽  
Coordinate Systems ◽  
Axis Of Rotation ◽  
The Earth ◽  
Fixed System

AbstractFive important geodynamical quantities which are closely linked are: 1) motions of points on the Earth’s surface; 2)polar motion; 3) changes in UT1-UTC; 4) nutation; and 5) motion of the geocenter. For each of these we expect to achieve measurements in the near future which have an accuracy of 1 to 3 cm or 0.3 to 1 milliarcsec.From a metrological point of view, one can say simply: “Measure each quantity against whichever coordinate system you can make the most accurate measurements with respect to”. I believe that this statement should serve as a guiding principle for the recommendations of the colloquium. However, it also is important that the coordinate systems help to provide a clear separation between the different phenomena of interest, and correspond closely to the conceptual definitions in terms of which geophysicists think about the phenomena.In any discussion of angular motion in space, both a “body-fixed” system and a “space-fixed” system are used. Some relevant types of coordinate systems, reference directions, or reference points which have been considered are: 1) celestial systems based on optical star catalogs, distant galaxies, radio source catalogs, or the Moon and inner planets; 2) the Earth’s axis of rotation, which defines a line through the Earth as well as a celestial reference direction; 3) the geocenter; and 4) “quasi-Earth-fixed” coordinate systems.When a geophysicists discusses UT1 and polar motion, he usually is thinking of the angular motion of the main part of the mantle with respect to an inertial frame and to the direction of the spin axis. Since the velocities of relative motion in most of the mantle are expectd to be extremely small, even if “substantial” deep convection is occurring, the conceptual “quasi-Earth-fixed” reference frame seems well defined. Methods for realizing a close approximation to this frame fortunately exist. Hopefully, this colloquium will recommend procedures for establishing and maintaining such a system for use in geodynamics. Motion of points on the Earth’s surface and of the geocenter can be measured against such a system with the full accuracy of the new techniques.The situation with respect to celestial reference frames is different. The various measurement techniques give changes in the orientation of the Earth, relative to different systems, so that we would like to know the relative motions of the systems in order to compare the results. However, there does not appear to be a need for defining any new system. Subjective figures of merit for the various system dependon both the accuracy with which measurements can be made against them and the degree to which they can be related to inertial systems.The main coordinate system requirement related to the 5 geodynamic quantities discussed in this talk is thus for the establishment and maintenance of a “quasi-Earth-fixed” coordinate system which closely approximates the motion of the main part of the mantle. Changes in the orientation of this system with respect to the various celestial systems can be determined by both the new and the conventional techniques, provided that some knowledge of changes in the local vertical is available. Changes in the axis of rotation and in the geocenter with respect to this system also can be obtained, as well as measurements of nutation.

2.2. Working Group 2: Conceptual Definitions of Reference Coordinate Systems for Earth Dynamics

1975 ◽  
Vol 26 ◽  
pp. 21-26
Keyword(s):  
Coordinate System ◽  
Working Group ◽  
General Character ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
Group 2 ◽  
Definition Of ◽  
Earth Dynamics

An ideal definition of a reference coordinate system should meet the following general requirements:1. It should be as conceptually simple as possible, so its philosophy is well understood by the users.2. It should imply as few physical assumptions as possible. Wherever they are necessary, such assumptions should be of a very general character and, in particular, they should not be dependent upon astronomical and geophysical detailed theories.3. It should suggest a materialization that is dynamically stable and is accessible to observations with the required accuracy.

Note on Selection of Coordinate Systems for Geodynamics

1975 ◽  
Vol 26 ◽  
pp. 395-407
Author(s):  
S. Henriksen
Keyword(s):  
Sea Level ◽  
The Other ◽  
Coordinate Systems ◽  
Mean Sea Level ◽  
The Earth ◽  
The One ◽  
Static Systems ◽  
Selection Of

The first question to be answered, in seeking coordinate systems for geodynamics, is: what is geodynamics? The answer is, of course, that geodynamics is that part of geophysics which is concerned with movements of the Earth, as opposed to geostatics which is the physics of the stationary Earth. But as far as we know, there is no stationary Earth – epur sic monere. So geodynamics is actually coextensive with geophysics, and coordinate systems suitable for the one should be suitable for the other. At the present time, there are not many coordinate systems, if any, that can be identified with a static Earth. Certainly the only coordinate of aeronomic (atmospheric) interest is the height, and this is usually either as geodynamic height or as pressure. In oceanology, the most important coordinate is depth, and this, like heights in the atmosphere, is expressed as metric depth from mean sea level, as geodynamic depth, or as pressure. Only for the earth do we find “static” systems in use, ana even here there is real question as to whether the systems are dynamic or static. So it would seem that our answer to the question, of what kind, of coordinate systems are we seeking, must be that we are looking for the same systems as are used in geophysics, and these systems are dynamic in nature already – that is, their definition involvestime.

The Role of VLBI in the Establishment of Coordinate Systems

1975 ◽  
Vol 26 ◽  
pp. 293-295 ◽  
Author(s):  
I. Zhongolovitch
Keyword(s):  
General Solution ◽  
Future Development ◽  
Rational Approach ◽  
Radio Telescopes ◽  
Coordinate Systems ◽  
Tectonic Plates ◽  
Astronomical Observations ◽  
Optical Instruments ◽  
Fundamental Polyhedron

Considering the future development and general solution of the problem under consideration and also the high precision attainable by astronomical observations, the following procedure may be the most rational approach:1. On the main tectonic plates of the Earth’s crust, powerful movable radio telescopes should be mounted at the same points where standard optical instruments are installed. There should be two stations separated by a distance of about 6 to 8000 kilometers on each plate. Thus, we obtain a fundamental polyhedron embracing the whole Earth with about 10 to 12 apexes, and with its sides represented by VLBI.

Using crystallographic symmetry in diffraction and contrast analysis

1989 ◽  
Vol 47 ◽  
pp. 504-505
Author(s):  
U. Dahmen ◽  
K.H. Westmacott
Keyword(s):  
Electron Microscopy ◽  
High Symmetry ◽  
Two Phase ◽  
Tem Analysis ◽  
Crystallographic Symmetry ◽  
The Matrix ◽  
Contrast Analysis ◽  
Practical Tool ◽  
Convergent Beam ◽  
Beam Diffraction

Despite the increased use of convergent beam diffraction, symmetry concepts in their more general form are not commonly applied as a practical tool in electron microscopy. Crystal symmetry provides an abundance of information that can be used to facilitate and improve the TEM analysis of crystalline solids. This paper draws attention to some aspects of symmetry that can be put to practical use in the analysis of structures and morphologies of two-phase materials.It has been shown that the symmetry of the matrix that relates different variants of a precipitate can be used to determine the axis of needle- or lath-shaped precipitates or the habit plane of plate-shaped precipitates. By tilting to a special high symmetry orientation of the matrix and by measuring angles between symmetry-related variants of the precipitate it is possible to find their habit from a single micrograph.

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