Alpha Shape Analysis (ASA) Framework for Post- Clustering Property Determination in Atom Probe Tomographic Data

Background: COVID-19 emerged in late 2019 and became a pandemic disease with severe mortality and morbidity. No specific remedy exists at present, but some drugs, such as Dexamethasone, have shown clinical benefits against the causative agent, the SARS-CoV-2 virus. Objective: To analyze the binding affinity between drugs and an SARS-CoV-2 protein through geometrical methods and to study the theoretical effectiveness of Dexamethasone as a potential treatment for COVID-19. Method: The binding affinity of Dexamethasone to the target SARS-CoV-2 protein was compared with those of different inhibitors. Drug molecules were docked to the SARS-CoV-2 main protease, and the system was simulated by molecular dynamics, allowing alpha shape analysis to extract geometrical features, such as the matching rates of atoms, solid angles, and the distances between atoms at interfaces. Binding affinities between drugs and the main protease were assessed by these geometrical data and the free energy of binding. Results: The behaviour of Dexamethasone was similar to other inhibitors. The efficacy of Dexamethasone as a treatment may be due to it being a glucocorticoid and its properties as a potent inhibitor. Conclusion: This study revealed the mechanism of action of Dexamethasone and provided a geometrical method to distinguish among potential drugs for the treatment of COVID-19.

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Best-fit ellipsoids of atom-probe tomographic data to study coalescence of γ′ (L12) precipitates in Ni–Al–Cr

Scripta Materialia ◽

10.1016/j.scriptamat.2007.04.020 ◽

2007 ◽

Vol 57 (4) ◽

pp. 353-356 ◽

Cited By ~ 28

Author(s):

Richard A. Karnesky ◽

Chantal K. Sudbrack ◽

David N. Seidman

Keyword(s):

Atom Probe ◽

Tomographic Data ◽

Best Fit

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Preferential Sputtering of Ni3Al Single Crystals Studied Using Atom-Probe Field-Ion Microscopy and XPS

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096813 ◽

1981 ◽

Vol 39 ◽

pp. 16-17

Author(s):

M.P. Thomas ◽

A.R. Waugh ◽

M.J. Southon ◽

Brian Ralph

Keyword(s):

Single Crystals ◽

Photoelectron Spectroscopy ◽

Surface Composition ◽

Depth Profiling ◽

Analytical Techniques ◽

Atom Probe ◽

Probe Field ◽

Preferential Sputtering ◽

Argon Ion Bombardment ◽

Argon Ion

It is well known that ion-induced sputtering from numerous multicomponent targets results in marked changes in surface composition (1). Preferential removal of one component results in surface enrichment in the less easily removed species. In this investigation, a time-of-flight atom-probe field-ion microscope A.P. together with X-ray photoelectron spectroscopy XPS have been used to monitor alterations in surface composition of Ni3Al single crystals under argon ion bombardment. The A.P. has been chosen for this investigation because of its ability using field evaporation to depth profile through a sputtered surface without the need for further ion sputtering. Incident ion energy and ion dose have been selected to reflect conditions widely used in surface analytical techniques for cleaning and depth-profiling of samples, typically 3keV and 1018 - 1020 ion m-2.

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High-resolution x-ray imaging of small copper-rich precipitates in steels

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100104704 ◽

1988 ◽

Vol 46 ◽

pp. 528-529

Author(s):

J. R. Michael ◽

K. A. Taylor

Keyword(s):

Electron Microscopy ◽

Thermomechanical Processing ◽

Atom Probe ◽

Ferrite Matrix ◽

Scanning Transmission Electron Microscope ◽

Probe Field ◽

X Ray ◽

Subsequent Transformation ◽

Transmission Electron ◽

Scanning Transmission

Although copper is considered an incidental or trace element in many commercial steels, some grades contain up to 1-2 wt.% Cu for precipitation strengthening. Previous electron microscopy and atom-probe/field-ion microscopy (AP/FIM) studies indicate that the precipitation of copper from ferrite proceeds with the formation of Cu-rich bcc zones and the subsequent transformation of these zones to fcc copper particles. However, the similarity between the atomic scattering amplitudes for iron and copper and the small misfit between between Cu-rich particles and the ferrite matrix preclude the detection of small (<5 nm) Cu-rich particles by conventional transmission electron microscopy; such particles have been imaged directly only by FIM. Here results are presented whereby the Cu Kα x-ray signal was used in a dedicated scanning transmission electron microscope (STEM) to image small Cu-rich particles in a steel. The capability to detect these small particles is expected to be helpful in understanding the behavior of copper in steels during thermomechanical processing and heat treatment.

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Atom-probe analysis of the solid-liquid interface

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100139755 ◽

1995 ◽

Vol 53 ◽

pp. 676-677

Author(s):

J.A. Panitz

Keyword(s):

Molecular Level ◽

Selective Adsorption ◽

Electronic Devices ◽

Atom Probe ◽

Chemical Agent ◽

Hostile Environment ◽

Solid Interface ◽

Solid Liquid Interface ◽

Solid Liquid ◽

Chemically Selective

The first few atomic layers of a solid can form a barrier between its interior and an often hostile environment. Although adsorption at the vacuum-solid interface has been studied in great detail, little is known about adsorption at the liquid-solid interface. Adsorption at a liquid-solid interface is of intrinsic interest, and is of technological importance because it provides a way to coat a surface with monolayer or multilayer structures. A pinhole free monolayer (with a reasonable dielectric constant) could lead to the development of nanoscale capacitors with unique characteristics and lithographic resists that surpass the resolution of their conventional counterparts. Chemically selective adsorption is of particular interest because it can be used to passivate a surface from external modification or change the wear and the lubrication properties of a surface to reflect new and useful properties. Immunochemical adsorption could be used to fabricate novel molecular electronic devices or to construct small, “smart”, unobtrusive sensors with the potential to detect a wide variety of preselected species at the molecular level. These might include a particular carcinogen in the environment, a specific type of explosive, a chemical agent, a virus, or even a tumor in the human body.

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A Comparison of Tem and Apfim to the Interpretation of Modulated Microstructures

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010011742x ◽

1985 ◽

Vol 43 ◽

pp. 70-71

Author(s):

M.G. Burke ◽

M.K. Miller

Keyword(s):

Low Temperature ◽

Microstructural Characterization ◽

Superlattice Reflection ◽

High Volume ◽

Atom Probe ◽

Dark Field ◽

Miscibility Gap ◽

Second Phase ◽

Two Phase ◽

Probe Field

Interpretation of fine-scale microstructures containing high volume fractions of second phase is complex. In particular, microstructures developed through decomposition within low temperature miscibility gaps may be extremely fine. This paper compares the morphological interpretations of such complex microstructures by the high-resolution techniques of TEM and atom probe field-ion microscopy (APFIM).The Fe-25 at% Be alloy selected for this study was aged within the low temperature miscibility gap to form a <100> aligned two-phase microstructure. This triaxially modulated microstructure is composed of an Fe-rich ferrite phase and a B2-ordered Be-enriched phase. The microstructural characterization through conventional bright-field TEM is inadequate because of the many contributions to image contrast. The ordering reaction which accompanies spinodal decomposition in this alloy permits simplification of the image by the use of the centered dark field technique to image just one phase. A CDF image formed with a B2 superlattice reflection is shown in fig. 1. In this CDF micrograph, the the B2-ordered Be-enriched phase appears as bright regions in the darkly-imaging ferrite. By examining the specimen in a [001] orientation, the <100> nature of the modulations is evident.

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An Improved Method for the Preparation and TEM Examination of Sharp Pointed Tips used in APFIM and STM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100134107 ◽

1990 ◽

Vol 48 (2) ◽

pp. 102-103

Author(s):

E.A. Fischione ◽

P.E. Fischione ◽

J.J. Haugh ◽

M.G. Burke

Keyword(s):

Atom Probe ◽

Preparation Process ◽

Improved Method ◽

Ion Milling ◽

Polishing Process ◽

Probe Field ◽

Scanning Tunnelling ◽

Stm Tips ◽

Tunnelling Microscopy ◽

Ion Microscopy

A common requirement for both Atom Probe Field-Ion Microscopy (APFIM) and Scanning Tunnelling Microscopy (STM) is a sharp pointed tip for use as either the specimen (APFIM) or the probe (STM). Traditionally, tips have been prepared by either chemical or electropolishing techniques. Recently, ion-milling has been successfully employed in the production of APFIM tips [1]. Conventional electropolishing techniques are applicable to a wide variety of metals, but generally require careful manual adjustments during the polishing process and may also be time-consuming. In order to reduce the time and effort involved in the preparation process, a compact, self-contained polishing unit has been developed. This system is based upon the conventional two-stage electropolishing technique in which the specimen/tip blank is first locally thinned or “necked”, and subsequently electropolished until separation occurs.[2,3] The result of this process is the production of two APFIM or STM tips. A mechanized polishing unit that provides these functions while automatically maintaining alignment has been designed and developed.

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Atomic Spectroscopy in the FIM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100145157 ◽

1986 ◽

Vol 44 ◽

pp. 758-761

Author(s):

J. J. Hren ◽

S. D. Walck

Keyword(s):

Electron Microscope ◽

Electric Fields ◽

Atom Probe ◽

Atomic Spectroscopy ◽

Single Atom ◽

Statistical Sampling ◽

Commercial Instrument ◽

Available Technology ◽

High Electric Fields ◽

Field Ion Microscope

The field ion microscope (FIM) has had the ability to routinely image the surface atoms of metals since Mueller perfected it in 1956. Since 1967, the TOF Atom Probe has had single atom sensitivity in conjunction with the FIM. “Why then hasn't the FIM enjoyed the success of the electron microscope?” The answer is closely related to the evolution of FIM/Atom Probe techniques and the available technology. This paper will review this evolution from Mueller's early discoveries, to the development of a viable commercial instrument. It will touch upon some important contributions of individuals and groups, but will not attempt to be all inclusive. Variations in instrumentation that define the class of problems for which the FIM/AP is uniquely suited and those for which it is not will be described. The influence of high electric fields inherent to the technique on the specimens studied will also be discussed. The specimen geometry as it relates to preparation, statistical sampling and compatibility with the TEM will be examined.

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