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Peter Moeck

Portland State University, Physics, Faculty Member

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Universitat de València

American University in Cairo

Kansas State University

Armando Marques-Guedes

UNL - New University of Lisbon

Field Museum

National Institute of Technology, Calicut

Oxford Brookes University

Visvesvaraya Technological University

University of Illinois at Urbana-Champaign

Richard Crawford

The University of Texas at Austin

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Papers by Peter Moeck

Determining Projected Symmetries for Structural Fingerprinting of Nanocrystals

Microscopy and Microanalysis, Jul 1, 2009

Because nanocrystals cannot be fingerprinted structurally from laboratory-based powder X-ray diff... more Because nanocrystals cannot be fingerprinted structurally from laboratory-based powder X-ray diffraction patterns, novel transmission electron microscopy (TEM) based structural fingerprinting strategies have been proposed [1]. These strategies utilize information on the projected reciprocal lattice geometry, 2D symmetry, and structure factors. While high resolution transmission electron microscopy images (HRTEM-Is) allow for the extraction of both structure factor amplitudes and phase angles of nanocrystals that are less than 5 to 10 nm thin, precession electron diffraction spot patterns (PED-SPs) allow for the extraction of structure factor amplitudes only [2]. For PED, the nanocrystals can be up to about five times thicker and the TEM's resolution is not limiting the structural fingerprinting [3]. A HRTEM-I and a PED-SP from the same crystal in the same orientation do, however, possess different 2D symmetries.

Crystallographic Processing of Scanning Tunneling Microscopy Images of Cobalt Phthalocyanines on Silver and Graphite

Microscopy and Microanalysis, Jul 1, 2011

Monolayers of cobalt phthalocyanine (CoPc) on silver (111) and highly (0001) oriented pyrolytic g... more Monolayers of cobalt phthalocyanine (CoPc) on silver (111) and highly (0001) oriented pyrolytic graphite (HOPG) were imaged with a scanning tunneling microscope (STM) at cryogenic temperatures (around 30 K) at Chemnitz University of Technology, Figs. 1a and 2a. Domains of regular arrays with periodicity in two dimensions (2D) and a variety of plane symmetries [1] were observed.

Crystallography Open Database: History, Development, and Perspectives

Freely Accessible Internet Resources for Nanoscience and Nanotechnology Education and Research at Portland State University's Research Servers

MRS Proceedings, 2006

ABSTRACTBecause a great deal of nanoscience and nanotechnology relies on crystalline nanometer si... more ABSTRACTBecause a great deal of nanoscience and nanotechnology relies on crystalline nanometer sized or nanometer structured materials, crystallographers have to provide their specific contributions to the National Nanotechnology Initiative. Here we review two open access internet-based crystallographic databases, the Crystallography Open Database (COD) and the Nano-Crystallography Database (NCD), that store information in the Crystallographic Information File (CIF) format. Having more than ten thousand crystallographic data sets available on the internet in a standardized format allows for many kinds of internet-based crystallographic calculations and visualizations. Examples for this that are dealt with in this paper are interactive crystal structure visualizations in three dimensions (3D) and calculations of theoretical lattice-fringe fingerprint plots for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

$Research paper thumbnail of Crystallite Thickness Estimates from Precession Electron Diffraction Patterns for Structural Fingerprinting in the Quasi-kinematic Limit$

Crystallite Thickness Estimates from Precession Electron Diffraction Patterns for Structural Fingerprinting in the Quasi-kinematic Limit

Microscopy and Microanalysis, Jul 1, 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, ... more

Nanocrystal Phase Identification by Lattice Fringe Fingerprinting from High Resolution Transmission Electron Microscope Images

Bulletin of the American Physical Society, May 20, 2006

Crystallographic Image Processing Software for Scanning Probe Microscopists

Bulletin of the American Physical Society, Mar 17, 2010

microscopy (SPM) images can be processed "crystallographically" [1,2]. An estimate of the point s... more microscopy (SPM) images can be processed "crystallographically" [1,2]. An estimate of the point spread function of the SPM can be obtained and subsequently its influence removed from the images. Also a difference Fourier synthesis can be calculated in order to enhance the visibility of structural defects. We are currently in the process of developing dedicated PC-based software for the wider SPM community.

Progress in Crystallographic Image Processing for Scanning Probe Microscopy

Microscopy and Microanalysis, Aug 1, 2015

Crystallographic Image Processing (CIP) originated with the electron crystallography community. N... more Crystallographic Image Processing (CIP) originated with the electron crystallography community. Nobel Laureate Sir Aaron Klug (OM, FRS) and coworkers pioneered the technique for the analysis of long-range ordered biological materials in parallel illumination Transmission Electron Microscopes (TEMs). Corrections for the effects of the TEM's phase contrast transfer function and for less than optimal imaging conditions are part of this kind of CIP. There are also "electron microscope independent" 2D crystallography foundations to this kind of image processing.

Crystallographic Image Processing for Scanning Probe Microscopes

Microscopy and Microanalysis, Jul 1, 2012

Scanning probe microscopy (SPM) images of regularly arranged spatially periodic objects can be pr... more Scanning probe microscopy (SPM) images of regularly arranged spatially periodic objects can be processed crystallographically. The resulting information may be used to remove from the SPM image distortions that are due to a "less than perfect" imaging process. The combined effects of these distortions result in a point spread function that gives a quantitative measure of the microscope's performance for a certain set of experimental conditions. On the basis of highly symmetric "calibration samples", the point spread function of the microscope may be extracted and utilized for the correction of SPM images of unknowns that were recorded under essentially the same experimental conditions. We concentrate in this paper on more theoretical aspects of our method. A "blunt" scanning tunnelling microscopy (STM) tip that consists of multiple "mini-tips" with electron orbital dimensions may be "symmetrized" on the basis of prior knowledge on the plane symmetry of a two-dimensional periodic array. This is illustrated with the crystallographic processing of a STM image of a regular array of fluorinated cobalt phthalocyanine molecules on graphite and backed up conceptually by simple simulations. Keywords scanning probe microscopy; scanning tunnelling microscopy; 2D periodic symmetry; point spread function 1 "Traditional" refers here to SPMs that have just one "kind" of a probe-sample interactions signal attached to each 2D scanning increment. Nontraditional SPMs are defined by having two or more such kinds of signals attached to each 2D scanning increment. Examples of non-traditional SPMs are spin-polarized STMs and critical dimension SPMs. Utilizing "black-white" and "colour symmetries" (e.g. Shubnikov AV, Below NV. et al.,

Information-Theory Based Symmetry Classifications of Sets of S/TEM Zone-Axis Images in Support of Nanocrystallography and Discrete Electron Tomography

Microscopy and Microanalysis

$Research paper thumbnail of Information-theoretic point symmetry classifications/quantifications of an electron diffraction spot pattern from a crystal with strong translational pseudosymmetry$

Information-theoretic point symmetry classifications/quantifications of an electron diffraction spot pattern from a crystal with strong translational pseudosymmetry

The recently developed information-theoretic approach to crystallographic symmetry classification... more The recently developed information-theoretic approach to crystallographic symmetry classifications and quantifications in two dimensions (2D) from digital transmission electron and scanning probe microscope images is adapted for the analysis of an experimental [001] transmission electron diffraction spot pattern from Ba3Nb16O23. The extracted lattice parameters of this crystal are within experimental error bars consistent with a metric tensor that suggests the presence of hexagonal translation symmetry. The point symmetry of the combined low, medium, and high resolution spots is, however, no higher than 2mm. The likelihood of this electron diffraction pattern belonging to a rectangular-centered crystal rather than a hexagonal crystal is quantified on the basis of its information-theoretic point group symmetry classifications. Presumably due to a slight misorientation away from the exact [001] zone axis combined with the curvature of the Ewald sphere, the group of highest resolution ...

Crystallographic symmetry classifications of noisy 2D periodic images in the presence of pseudo-symmetries of the Fedorov type

Microscopy and Microanalysis, 2019

3D printing of representation surfaces from tensor data of KH2PO4 and low-quartz utilizing the WinTensor software

Zeitschrift für Kristallographie - Crystalline Materials, 2015

Tensorial properties such as thermal expansion, optical rotation, the electro-optic effect, elast... more Tensorial properties such as thermal expansion, optical rotation, the electro-optic effect, elastic constants, and many more are prepared with a Windows executable, WinTensor, for rendering a graphical representation that can be viewed on a monitor or printed out for a tangible 3D model. Examples of 3D printed representation surfaces in KH

Semiconductor Quantum Dots

Dekker Encyclopedia of Nanoscience and Nanotechnology, Second Edition - Six Volume Set (Print Version), 2008

Preparing 3D Print Files for Nano-Tech/Science Education from Entries of Large Open-Access Crystallographic Databases at Dedicated Websites

2018 IEEE 13th Nanotechnology Materials and Devices Conference (NMDC), 2018

A straightforward route from crystallographic information framework files (CIFs) files at the Ope... more A straightforward route from crystallographic information framework files (CIFs) files at the Open-Access Crystallography project (nanocrystallography.research.pdx.edu) websites to 3D print files for atomic-level crystal and molecule structure models for nano-tech/science education is described. An alternative to this route utilizing a similar set of websites that were created by Professor Bob Hanson is also mentioned. Only the exported 3D print files are downloaded from these kinds of websites as no local installation of any supporting program or applet is necessary.

$Research paper thumbnail of Precession Electron Diffraction for Electron Crystallography$

Precession Electron Diffraction for Electron Crystallography

Microscopy and Microanalysis

A brief history of the precession electron diffraction technique is provided. The commercial Digi... more A brief history of the precession electron diffraction technique is provided. The commercial DigiSTAR [1] implementation that can be added to any modern transmission electron microscope (TEM) in order to provide precessing primary beam capabilities is briefly mentioned. The advantages that precession electron diffraction combined with energy filtering, Fig. 1, and energy filtering alone, Fig. 2, bring to electron crystallography are discussed and demonstrated on experimental [001] and [111] diffraction spot patterns from the mineral mayenite.

Geometry of Crystals, Polycrystals, and Phase Transformations

Geometry of Crystals, Polycrystals, and Phase Transformations, 2017

Crystallography Open Database – an open-access collection of crystal structures

Journal of Applied Crystallography, 2009

The Crystallography Open Database (COD), which is a project that aims to gather all available ino... more The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

$Research paper thumbnail of A Computer Program for Objective Point Symmetry Classifications of Electron Diffraction Spot Patterns with Apparent Hexagonal or Rectangular-Centered Lattice Metric$

A Computer Program for Objective Point Symmetry Classifications of Electron Diffraction Spot Patterns with Apparent Hexagonal or Rectangular-Centered Lattice Metric

Microscopy and Microanalysis

Distinguishing Between Quaternary Symmetries and Pseudo-symmetries in a Prokaryotic Potassium Channel in Both the Open and Closed Conformation

Microscopy and Microanalysis

Information theory based methods for objective classifications of digital images and electron dif... more Information theory based methods for objective classifications of digital images and electron diffraction spot patterns into two dimensional (2D) Bravais lattice types [1], projected Laue classes and plane symmetry groups [2,3], as well as 2D point symmetry groups [4] have recently been developed. The objectivity of these crystallographic symmetry classifications is ensured by the selections of the best geometric models for complementing aspects of the 2D periodic signal in the image and/or diffraction data on the basis of geometric Akaike Information Criteria [5]. As recently reviewed [6], these particular crystallographic image classification techniques are the only ones that can be considered to be objective, i.e. researcher and arbitrary thresholds independent.

Determining Projected Symmetries for Structural Fingerprinting of Nanocrystals

Microscopy and Microanalysis, Jul 1, 2009

Because nanocrystals cannot be fingerprinted structurally from laboratory-based powder X-ray diff... more Because nanocrystals cannot be fingerprinted structurally from laboratory-based powder X-ray diffraction patterns, novel transmission electron microscopy (TEM) based structural fingerprinting strategies have been proposed [1]. These strategies utilize information on the projected reciprocal lattice geometry, 2D symmetry, and structure factors. While high resolution transmission electron microscopy images (HRTEM-Is) allow for the extraction of both structure factor amplitudes and phase angles of nanocrystals that are less than 5 to 10 nm thin, precession electron diffraction spot patterns (PED-SPs) allow for the extraction of structure factor amplitudes only [2]. For PED, the nanocrystals can be up to about five times thicker and the TEM's resolution is not limiting the structural fingerprinting [3]. A HRTEM-I and a PED-SP from the same crystal in the same orientation do, however, possess different 2D symmetries.

Crystallographic Processing of Scanning Tunneling Microscopy Images of Cobalt Phthalocyanines on Silver and Graphite

Microscopy and Microanalysis, Jul 1, 2011

Monolayers of cobalt phthalocyanine (CoPc) on silver (111) and highly (0001) oriented pyrolytic g... more Monolayers of cobalt phthalocyanine (CoPc) on silver (111) and highly (0001) oriented pyrolytic graphite (HOPG) were imaged with a scanning tunneling microscope (STM) at cryogenic temperatures (around 30 K) at Chemnitz University of Technology, Figs. 1a and 2a. Domains of regular arrays with periodicity in two dimensions (2D) and a variety of plane symmetries [1] were observed.

Crystallography Open Database: History, Development, and Perspectives

Freely Accessible Internet Resources for Nanoscience and Nanotechnology Education and Research at Portland State University's Research Servers

MRS Proceedings, 2006

ABSTRACTBecause a great deal of nanoscience and nanotechnology relies on crystalline nanometer si... more ABSTRACTBecause a great deal of nanoscience and nanotechnology relies on crystalline nanometer sized or nanometer structured materials, crystallographers have to provide their specific contributions to the National Nanotechnology Initiative. Here we review two open access internet-based crystallographic databases, the Crystallography Open Database (COD) and the Nano-Crystallography Database (NCD), that store information in the Crystallographic Information File (CIF) format. Having more than ten thousand crystallographic data sets available on the internet in a standardized format allows for many kinds of internet-based crystallographic calculations and visualizations. Examples for this that are dealt with in this paper are interactive crystal structure visualizations in three dimensions (3D) and calculations of theoretical lattice-fringe fingerprint plots for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

$Research paper thumbnail of Crystallite Thickness Estimates from Precession Electron Diffraction Patterns for Structural Fingerprinting in the Quasi-kinematic Limit$

Crystallite Thickness Estimates from Precession Electron Diffraction Patterns for Structural Fingerprinting in the Quasi-kinematic Limit

Microscopy and Microanalysis, Jul 1, 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, ... more

Nanocrystal Phase Identification by Lattice Fringe Fingerprinting from High Resolution Transmission Electron Microscope Images

Bulletin of the American Physical Society, May 20, 2006

Crystallographic Image Processing Software for Scanning Probe Microscopists

Bulletin of the American Physical Society, Mar 17, 2010

microscopy (SPM) images can be processed "crystallographically" [1,2]. An estimate of the point s... more microscopy (SPM) images can be processed "crystallographically" [1,2]. An estimate of the point spread function of the SPM can be obtained and subsequently its influence removed from the images. Also a difference Fourier synthesis can be calculated in order to enhance the visibility of structural defects. We are currently in the process of developing dedicated PC-based software for the wider SPM community.

Progress in Crystallographic Image Processing for Scanning Probe Microscopy

Microscopy and Microanalysis, Aug 1, 2015

Crystallographic Image Processing (CIP) originated with the electron crystallography community. N... more Crystallographic Image Processing (CIP) originated with the electron crystallography community. Nobel Laureate Sir Aaron Klug (OM, FRS) and coworkers pioneered the technique for the analysis of long-range ordered biological materials in parallel illumination Transmission Electron Microscopes (TEMs). Corrections for the effects of the TEM's phase contrast transfer function and for less than optimal imaging conditions are part of this kind of CIP. There are also "electron microscope independent" 2D crystallography foundations to this kind of image processing.

Crystallographic Image Processing for Scanning Probe Microscopes

Microscopy and Microanalysis, Jul 1, 2012

Scanning probe microscopy (SPM) images of regularly arranged spatially periodic objects can be pr... more Scanning probe microscopy (SPM) images of regularly arranged spatially periodic objects can be processed crystallographically. The resulting information may be used to remove from the SPM image distortions that are due to a "less than perfect" imaging process. The combined effects of these distortions result in a point spread function that gives a quantitative measure of the microscope's performance for a certain set of experimental conditions. On the basis of highly symmetric "calibration samples", the point spread function of the microscope may be extracted and utilized for the correction of SPM images of unknowns that were recorded under essentially the same experimental conditions. We concentrate in this paper on more theoretical aspects of our method. A "blunt" scanning tunnelling microscopy (STM) tip that consists of multiple "mini-tips" with electron orbital dimensions may be "symmetrized" on the basis of prior knowledge on the plane symmetry of a two-dimensional periodic array. This is illustrated with the crystallographic processing of a STM image of a regular array of fluorinated cobalt phthalocyanine molecules on graphite and backed up conceptually by simple simulations. Keywords scanning probe microscopy; scanning tunnelling microscopy; 2D periodic symmetry; point spread function 1 "Traditional" refers here to SPMs that have just one "kind" of a probe-sample interactions signal attached to each 2D scanning increment. Nontraditional SPMs are defined by having two or more such kinds of signals attached to each 2D scanning increment. Examples of non-traditional SPMs are spin-polarized STMs and critical dimension SPMs. Utilizing "black-white" and "colour symmetries" (e.g. Shubnikov AV, Below NV. et al.,

Information-Theory Based Symmetry Classifications of Sets of S/TEM Zone-Axis Images in Support of Nanocrystallography and Discrete Electron Tomography

Microscopy and Microanalysis

$Research paper thumbnail of Information-theoretic point symmetry classifications/quantifications of an electron diffraction spot pattern from a crystal with strong translational pseudosymmetry$

Information-theoretic point symmetry classifications/quantifications of an electron diffraction spot pattern from a crystal with strong translational pseudosymmetry

The recently developed information-theoretic approach to crystallographic symmetry classification... more The recently developed information-theoretic approach to crystallographic symmetry classifications and quantifications in two dimensions (2D) from digital transmission electron and scanning probe microscope images is adapted for the analysis of an experimental [001] transmission electron diffraction spot pattern from Ba3Nb16O23. The extracted lattice parameters of this crystal are within experimental error bars consistent with a metric tensor that suggests the presence of hexagonal translation symmetry. The point symmetry of the combined low, medium, and high resolution spots is, however, no higher than 2mm. The likelihood of this electron diffraction pattern belonging to a rectangular-centered crystal rather than a hexagonal crystal is quantified on the basis of its information-theoretic point group symmetry classifications. Presumably due to a slight misorientation away from the exact [001] zone axis combined with the curvature of the Ewald sphere, the group of highest resolution ...

Crystallographic symmetry classifications of noisy 2D periodic images in the presence of pseudo-symmetries of the Fedorov type

Microscopy and Microanalysis, 2019

3D printing of representation surfaces from tensor data of KH2PO4 and low-quartz utilizing the WinTensor software

Zeitschrift für Kristallographie - Crystalline Materials, 2015

Tensorial properties such as thermal expansion, optical rotation, the electro-optic effect, elast... more Tensorial properties such as thermal expansion, optical rotation, the electro-optic effect, elastic constants, and many more are prepared with a Windows executable, WinTensor, for rendering a graphical representation that can be viewed on a monitor or printed out for a tangible 3D model. Examples of 3D printed representation surfaces in KH

Semiconductor Quantum Dots

Dekker Encyclopedia of Nanoscience and Nanotechnology, Second Edition - Six Volume Set (Print Version), 2008

Preparing 3D Print Files for Nano-Tech/Science Education from Entries of Large Open-Access Crystallographic Databases at Dedicated Websites

2018 IEEE 13th Nanotechnology Materials and Devices Conference (NMDC), 2018

A straightforward route from crystallographic information framework files (CIFs) files at the Ope... more A straightforward route from crystallographic information framework files (CIFs) files at the Open-Access Crystallography project (nanocrystallography.research.pdx.edu) websites to 3D print files for atomic-level crystal and molecule structure models for nano-tech/science education is described. An alternative to this route utilizing a similar set of websites that were created by Professor Bob Hanson is also mentioned. Only the exported 3D print files are downloaded from these kinds of websites as no local installation of any supporting program or applet is necessary.

$Research paper thumbnail of Precession Electron Diffraction for Electron Crystallography$

Precession Electron Diffraction for Electron Crystallography

Microscopy and Microanalysis

A brief history of the precession electron diffraction technique is provided. The commercial Digi... more A brief history of the precession electron diffraction technique is provided. The commercial DigiSTAR [1] implementation that can be added to any modern transmission electron microscope (TEM) in order to provide precessing primary beam capabilities is briefly mentioned. The advantages that precession electron diffraction combined with energy filtering, Fig. 1, and energy filtering alone, Fig. 2, bring to electron crystallography are discussed and demonstrated on experimental [001] and [111] diffraction spot patterns from the mineral mayenite.

Geometry of Crystals, Polycrystals, and Phase Transformations

Geometry of Crystals, Polycrystals, and Phase Transformations, 2017

Crystallography Open Database – an open-access collection of crystal structures

Journal of Applied Crystallography, 2009

The Crystallography Open Database (COD), which is a project that aims to gather all available ino... more The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

$Research paper thumbnail of A Computer Program for Objective Point Symmetry Classifications of Electron Diffraction Spot Patterns with Apparent Hexagonal or Rectangular-Centered Lattice Metric$

A Computer Program for Objective Point Symmetry Classifications of Electron Diffraction Spot Patterns with Apparent Hexagonal or Rectangular-Centered Lattice Metric

Microscopy and Microanalysis

Distinguishing Between Quaternary Symmetries and Pseudo-symmetries in a Prokaryotic Potassium Channel in Both the Open and Closed Conformation

Microscopy and Microanalysis

Information theory based methods for objective classifications of digital images and electron dif... more Information theory based methods for objective classifications of digital images and electron diffraction spot patterns into two dimensional (2D) Bravais lattice types [1], projected Laue classes and plane symmetry groups [2,3], as well as 2D point symmetry groups [4] have recently been developed. The objectivity of these crystallographic symmetry classifications is ensured by the selections of the best geometric models for complementing aspects of the 2D periodic signal in the image and/or diffraction data on the basis of geometric Akaike Information Criteria [5]. As recently reviewed [6], these particular crystallographic image classification techniques are the only ones that can be considered to be objective, i.e. researcher and arbitrary thresholds independent.