Literature DB >> 12944610

The maximum-entropy method in superspace.

Sander van Smaalen1, Lukás Palatinus, Martin Schneider.   

Abstract

One of the applications of the maximum-entropy method (MEM) in crystallography is the reconstruction of the electron density from phased structure factors. Here the application of the MEM to incommensurately modulated crystals and incommensurate composite crystals is considered. The MEM is computed directly in superspace, where the electron density in the (3+d)-dimensional unit cell (d > 0) is determined from the scattering data of aperiodic crystals. Periodic crystals (d = 0) are treated as a special case of the general formalism. The use of symmetry in the MEM is discussed and an efficient algorithm is proposed for handling crystal symmetry. The method has been implemented into a computer program BayMEM and applications are presented to the electron density of the periodic crystal NaV(2)O(5) and the electron density of the incommensurate composite crystal (LaS)(1.14)NbS(2). The MEM in superspace is shown to provide a model-independent estimate of the shapes of the modulation functions of incommensurate crystals. The discrete character of the electron density is found to be the major source of error, limiting the accuracy of the reconstructed modulation functions to approximately 10% of the sizes of the pixels. MaxEnt optimization using the Cambridge and Sakata-Sato algorithms are compared. The Cambridge algorithm is found to perform better than the Sakata-Sato algorithm, being faster, always reaching convergence, and leading to more reliable density maps. Nevertheless, the Sakata-Sato algorithm leads to similar density maps, even in cases where it does not reach complete convergence.

Entities:  

Year:  2003        PMID: 12944610     DOI: 10.1107/S010876730301434X

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN: 0108-7673            Impact factor:   2.290


  14 in total

1.  Isotope engineering of van der Waals interactions in hexagonal boron nitride.

Authors:  T Q P Vuong; S Liu; A Van der Lee; R Cuscó; L Artús; T Michel; P Valvin; J H Edgar; G Cassabois; B Gil
Journal:  Nat Mater       Date:  2017-12-11       Impact factor: 43.841

2.  Modulated anharmonic ADPs are intrinsic to aperiodic crystals: a case study on incommensurate Rb2ZnCl4.

Authors:  Liang Li; Alexander Wölfel; Andreas Schönleber; Swastik Mondal; Antoine M M Schreurs; Loes M J Kroon-Batenburg; Sander van Smaalen
Journal:  Acta Crystallogr B       Date:  2011-05-14

3.  Topological Properties of Chemical Bonds from Static and Dynamic Electron Densities.

Authors:  Siriyara Jagannatha Prathapa; Jeanette Held; Sander van Smaalen
Journal:  Z Anorg Allg Chem       Date:  2013-07-23       Impact factor: 1.492

4.  Carrier concentration dependence of structural disorder in thermoelectric Sn1-x Te.

Authors:  Mattia Sist; Ellen Marie Jensen Hedegaard; Sebastian Christensen; Niels Bindzus; Karl Frederik Færch Fischer; Hidetaka Kasai; Kunihisa Sugimoto; Bo Brummerstedt Iversen
Journal:  IUCrJ       Date:  2016-08-22       Impact factor: 4.769

5.  Soft-mode driven polarity reversal in ferroelectrics mapped by ultrafast x-ray diffraction.

Authors:  Christoph Hauf; Antonio-Andres Hernandez Salvador; Marcel Holtz; Michael Woerner; Thomas Elsaesser
Journal:  Struct Dyn       Date:  2018-04-06       Impact factor: 2.920

6.  Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM).

Authors:  Jeanette Netzel; Sander van Smaalen
Journal:  Acta Crystallogr B       Date:  2009-08-28

7.  Refinement of organic crystal structures with multipolar electron scattering factors.

Authors:  Barbara Gruza; Michał Leszek Chodkiewicz; Joanna Krzeszczakowska; Paulina Maria Dominiak
Journal:  Acta Crystallogr A Found Adv       Date:  2020-01-01       Impact factor: 2.290

8.  The active site of hen egg-white lysozyme: flexibility and chemical bonding.

Authors:  Jeanette Held; Sander van Smaalen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-03-21

9.  Location of Cu(2+) in CHA zeolite investigated by X-ray diffraction using the Rietveld/maximum entropy method.

Authors:  Casper Welzel Andersen; Martin Bremholm; Peter Nicolai Ravnborg Vennestrøm; Anders Bank Blichfeld; Lars Fahl Lundegaard; Bo Brummerstedt Iversen
Journal:  IUCrJ       Date:  2014-09-23       Impact factor: 4.769

10.  The electrostatic potential of dynamic charge densities.

Authors:  Christian B Hübschle; Sander van Smaalen
Journal:  J Appl Crystallogr       Date:  2017-10-20       Impact factor: 3.304

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